def download_pdb(pdb_id, output_dir):
filename = pdb_id.upper() + '.pdb'
path = os.path.join(output_dir, filename)
if os.path.exists(path):
comment('%s: using existing file %s\n' % (pdb_id, filename))
else:
comment('Downloading %s from RCSB... ' % pdb_id)
url = ('http://www.rcsb.org/pdb/download/downloadFile.do'
'?fileFormat=pdb&compression=NO&structureId=' + pdb_id.upper())
try:
u = urlopen(url)
except HTTPError as e:
put_error(str(e))
sys.exit(1)
content = u.read()
try:
if not os.path.isdir(output_dir):
os.makedirs(output_dir)
with open(path, 'wb') as f:
f.write(content)
comment('done.\n')
except IOError as e:
put_error('Failed to save downloaded file on disk', comment=str(e))
sys.exit(1)
return path
def parse_workflow_commands():
prog = __package__ or os.path.basename(sys.argv[0])
args = sys.argv[1:]
if not args or args[0] not in ('info', 'repeat'):
return False
if len(args) == 1:
sys.stderr.write("Specify output_dir.\n")
return True
# it's handy to use "/my/path/05-cad.log" as "/my/path" "5"
ext = os.path.splitext(args[1])[1]
if os.path.isfile(args[1]) and ext in ('.log', '.err'):
dirname, basename = os.path.split(args[1])
args[1:2] = [dirname, basename.split('-')[0]]
wf = open_pickled_workflow(args[1])
steps = args[2:]
if not steps:
show_workflow_info(wf, dict(prog=prog, output_dir=args[1]))
return True
for job in parse_steps(steps, wf):
if args[0] == 'info':
show_job_info(job)
elif args[0] == 'repeat':
try:
job.data = {} # reset data from parsing
job.run()
utils.comment("\n")
except JobError as e:
utils.put_error(e.msg, comment=e.note)
sys.exit(1)
return True
def check_ccp4_envvars():
for necessary_var in ("CCP4", "CCP4_SCR"):
if necessary_var not in os.environ:
put_error('$%s not found, giving up' % necessary_var)
sys.exit(1)
if not os.path.isdir(os.environ["CCP4_SCR"]):
put_error('No such directory: $CCP4_SCR, refmac shall not work!')
def download_pdb(pdb_id, output_dir):
filename = pdb_id.upper()+'.pdb'
path = os.path.join(output_dir, filename)
if os.path.exists(path):
comment('%s: using existing file %s\n' % (pdb_id, filename))
else:
comment('Downloading %s from RCSB... ' % pdb_id)
url = 'http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=' + pdb_id.upper()
try:
u = urllib2.urlopen(url)
except urllib2.HTTPError as e:
put_error(str(e))
sys.exit(1)
content = u.read()
try:
if not os.path.isdir(output_dir):
os.makedirs(output_dir)
with open(path, 'wb') as f:
f.write(content)
comment('done.\n')
except IOError as e:
put_error('Failed to save downloaded file on disk',
comment=str(e))
sys.exit(1)
return path
def __init__(self, output_dir, from_job=0):
self.output_dir = os.path.abspath(output_dir)
self.jobs = []
self.file_info = {}
self.temporary_files = set()
self.from_job = from_job # skip jobs before from_job (for testing)
if from_job >= 1:
try:
_pkl = self.load_pickle()
self.repl_jobs = _pkl.jobs
self.file_info = _pkl.file_info
except:
self.repl_jobs = None
self.dry_run = False
self.enable_logs = True
self.argv = sys.argv
if not os.path.isdir(self.output_dir):
try:
os.makedirs(self.output_dir)
except OSError as e:
utils.put_error(e)
sys.exit(1)
# this can seriously affect Refmac compiled with GFortran
bad_var = os.getenv('GFORTRAN_UNBUFFERED_ALL')
if bad_var and bad_var[0] not in ('0', 'n', 'N'):
utils.put_error(
'$GFORTRAN_UNBUFFERED_ALL may terribly slow down Refmac',
comment='It is unset internally in dimple.')
del os.environ['GFORTRAN_UNBUFFERED_ALL']
# avoid html-like crap in the output of CCP4 program
os.environ['CCP_SUPPRESS_HTML'] = '1'
def __init__(self, output_dir, from_job=0):
self.output_dir = os.path.abspath(output_dir)
self.jobs = []
self.file_info = {}
self.temporary_files = set()
self.from_job = from_job # skip jobs before from_job (for testing)
if from_job >= 1:
try:
_pkl = self.load_pickle()
self.repl_jobs = _pkl.jobs
self.file_info = _pkl.file_info
except:
self.repl_jobs = None
self.dry_run = False
self.enable_logs = True
self.argv = sys.argv
if not os.path.isdir(self.output_dir):
try:
os.makedirs(self.output_dir)
except OSError as e:
utils.put_error(e)
sys.exit(1)
# this can seriously affect Refmac compiled with GFortran
bad_var = os.getenv('GFORTRAN_UNBUFFERED_ALL')
if bad_var and bad_var[0] not in ('0', 'n', 'N'):
utils.put_error(
'$GFORTRAN_UNBUFFERED_ALL may terribly slow down Refmac',
comment='It is unset internally in dimple.')
del os.environ['GFORTRAN_UNBUFFERED_ALL']
# avoid html-like crap in the output of CCP4 program
os.environ['CCP_SUPPRESS_HTML'] = '1'
def check_ccp4_envvars():
for necessary_var in ('CCP4', 'CCP4_SCR'):
if necessary_var not in os.environ:
put_error('$%s not found, giving up' % necessary_var)
sys.exit(1)
if not os.path.isdir(os.environ['CCP4_SCR']):
put_error('No such directory: $CCP4_SCR, refmac shall not work!')
def parse_workflow_commands():
prog = __package__ or os.path.basename(sys.argv[0])
args = sys.argv[1:]
if not args or args[0] not in ('info', 'repeat'):
return False
if len(args) == 1:
sys.stderr.write("Specify output_dir.\n")
return True
# it's handy to use "/my/path/05-cad.log" as "/my/path" "5"
ext = os.path.splitext(args[1])[1]
if os.path.isfile(args[1]) and ext in ('.log', '.err'):
dirname, basename = os.path.split(args[1])
args[1:2] = [dirname, basename.split('-')[0]]
wf = open_pickled_workflow(args[1])
steps = args[2:]
if not steps:
show_workflow_info(wf, dict(prog=prog, output_dir=args[1]))
return True
for job in parse_steps(steps, wf):
if args[0] == 'info':
show_job_info(job)
elif args[0] == 'repeat':
try:
job.data = {} # reset data from parsing
job.run()
utils.comment("\n")
except JobError as e:
utils.put_error(e.msg, comment=e.note)
sys.exit(1)
return True
def main(args):
if workflow.parse_workflow_commands():
return
options = parse_dimple_commands(args)
check_ccp4_envvars()
wf = workflow.Workflow(options.output_dir, from_job=options.from_step)
utils.start_log(os.path.join(options.output_dir, "dimple.log"),
output_dir=options.output_dir)
utils.log_value("version", __version__)
utils.start_log_screen(os.path.join(options.output_dir, "screen.log"))
try:
dimple(wf=wf, opt=options)
check_contaminants_if_bad(wf, mtz=options.mtz)
exit_status = 0
except workflow.JobError as e:
put_error(e.msg, comment=e.note)
try:
utils.report_disk_space([wf.output_dir, os.getenv("CCP4_SCR")])
except KeyboardInterrupt:
comment("\nok, exiting...")
exit_status = 1
except RuntimeError as e:
put_error(e)
exit_status = 1
finally:
comment("\n")
if options.cleanup:
wf.delete_files(wf.temporary_files)
wf.options = options
wf.dump_pickle()
return exit_status
def delete_files(self, filenames):
for f in filenames:
path = self.path(f)
if os.path.exists(path):
try:
os.remove(path)
except OSError, e:
utils.put_error(e)
def delete_files(self, filenames):
for f in filenames:
path = self.path(f)
if os.path.exists(path):
try:
os.remove(path)
except OSError, e:
utils.put_error(e)
def _write_script(path, content, executable=False):
try:
with open(path, 'w') as f:
f.write(content)
if executable: # chmod +x
mode = os.stat(path).st_mode
os.chmod(path, mode | ((mode & 0444) >> 2))
except (IOError, OSError) as e:
put_error(e)
def find_path():
if os.name == 'nt':
default_path = "C:/WinCoot/runwincoot.bat"
if os.path.exists(default_path):
return default_path
else:
utils.put_error("WinCoot not found.")
else:
return utils.syspath("coot")
def _write_script(path, content, executable=False):
try:
with open(path, 'w') as f:
f.write(content)
if executable: # chmod +x
mode = os.stat(path).st_mode
os.chmod(path, mode | ((mode & 0o444) >> 2))
except (IOError, OSError) as e:
put_error(e)
def check_col_type(self, label, expected_type):
if label not in self.columns:
put_error("Column '%s' not found in %s" % (label, self.filename))
sys.exit(1)
col_type = self.columns[label]
if col_type != expected_type:
put_error("Column '%s' in %s has type '%s' (expected '%s')" %
(label, self.filename, col_type, expected_type))
return False
return True
def check_col_type(self, label, expected_type):
if label not in self.columns:
put_error("Column '%s' not found in %s" % (label, self.filename))
sys.exit(1)
col_type = self.columns[label]
if col_type != expected_type:
put_error("Column '%s' in %s has type '%s' (expected '%s')" %
(label, self.filename, col_type, expected_type))
return False
return True
def check_freerflags_column(free_mtz, expected_symmetry):
names = ['FreeR_flag', 'FREE']
rfree_meta = read_metadata(free_mtz)
if not match_symmetry(rfree_meta, expected_symmetry):
comment("\nWARNING: R-free flag reference file is %s not %s." %
(rfree_meta.symmetry, expected_symmetry.symmetry))
for name in names:
if name in rfree_meta.columns:
rfree_meta.check_col_type(name, 'I')
return name
put_error("free-R column not found in %s" % free_mtz)
sys.exit(1)
def special_mtz_mode(args):
print('Usage: %s' % USAGE_SHORT)
check_ccp4_envvars()
wf = workflow.Workflow('')
wf.enable_logs = False
try:
mtz_meta = wf.read_mtz_metadata(args[0])
print('Basic MTZ file info:')
print(mtz_meta.info())
contam_info = contaminants.get_info(mtz_meta)
if contam_info:
print(contam_info)
except (IOError, RuntimeError) as e:
put_error(e)
def special_mtz_mode(args):
print 'Usage: %s' % USAGE_SHORT
check_ccp4_envvars()
wf = workflow.Workflow('')
wf.enable_logs = False
try:
mtz_meta = wf.read_mtz_metadata(args[0])
print 'Basic MTZ file info:'
print mtz_meta.info()
contam_info = contaminants.get_info(mtz_meta)
if contam_info:
print contam_info
except (IOError, RuntimeError) as e:
put_error(e)
def check_freerflags_column(free_mtz, expected_symmetry, column):
rfree_meta = read_metadata(free_mtz)
if expected_symmetry and not match_symmetry(rfree_meta, expected_symmetry):
comment("\nWARNING: R-free flag reference file is %s not %s." %
(rfree_meta.symmetry, expected_symmetry.symmetry))
if column is not None:
if not rfree_meta.check_col_type(column, 'I'):
sys.exit(1)
return column
for name in DEFAULT_FREE_COLS:
if name in rfree_meta.columns:
rfree_meta.check_col_type(name, 'I')
return name
put_error("free-R column not found in %s" % free_mtz)
sys.exit(1)
def check_freerflags_column(free_mtz, expected_symmetry, column):
rfree_meta = read_metadata(free_mtz)
if not match_symmetry(rfree_meta, expected_symmetry):
comment("\nWARNING: R-free flag reference file is %s not %s." %
(rfree_meta.symmetry, expected_symmetry.symmetry))
if column is not None:
if not rfree_meta.check_col_type(column, 'I'):
sys.exit(1)
return column
for name in DEFAULT_FREE_COLS:
if name in rfree_meta.columns:
rfree_meta.check_col_type(name, 'I')
return name
put_error("free-R column not found in %s" % free_mtz)
sys.exit(1)
def special_pdb_mode(args):
print 'Proper usage: %s' % USAGE_SHORT
check_ccp4_envvars()
print '...actually we can run rwcontents for you'
wf = workflow.Workflow('')
wf.enable_logs = False
for p in args:
try:
wf.read_pdb_metadata(p, print_errors=True)
_comment_summary_line(os.path.basename(p), wf.file_info[p])
wf.rwcontents(xyzin=p).run()
except (IOError, RuntimeError) as e:
put_error(e)
except workflow.JobError as e:
put_error(e.msg, comment=e.note)
print '\n\n...but this is NOT how dimple is supposed to be run.'
def open_pickled_workflow(file_or_dir):
if os.path.isdir(file_or_dir):
pkl = os.path.join(file_or_dir, PICKLE_FILENAME)
else:
pkl = file_or_dir
if not os.path.exists(pkl):
utils.put_error("workflow data file not found",
"No such file or directory: %s" % pkl)
sys.exit(1)
f = open(pkl, "rb")
try:
return pickle.load(f)
except pickle.UnpicklingError:
utils.put_error('"Unpickling" failed',
'Maybe this is not a pickle file: %s' % pkl)
sys.exit(1)
def special_pdb_mode(args):
print('Proper usage: %s' % USAGE_SHORT)
check_ccp4_envvars()
print('...actually we can run rwcontents for you')
wf = workflow.Workflow('')
wf.enable_logs = False
for p in args:
try:
wf.read_pdb_metadata(p, print_errors=True)
_comment_summary_line(os.path.basename(p), wf.file_info[p])
wf.rwcontents(xyzin=p).run()
except (IOError, RuntimeError) as e:
put_error(e)
except workflow.JobError as e:
put_error(e.msg, comment=e.note)
print('\n\n...but this is NOT how dimple is supposed to be run.')
def open_pickled_workflow(file_or_dir):
if os.path.isdir(file_or_dir):
pkl = os.path.join(file_or_dir, PICKLE_FILENAME)
else:
pkl = file_or_dir
if not os.path.exists(pkl):
utils.put_error("workflow data file not found",
"No such file or directory: %s" % pkl)
sys.exit(1)
f = open(pkl, "rb")
try:
return pickle.load(f)
except pickle.UnpicklingError:
utils.put_error('"Unpickling" failed',
'Maybe this is not a pickle file: %s' % pkl)
sys.exit(1)
def read_metadata(pdb, print_errors):
if pdb.endswith('.gz'):
f = gzip.open(pdb, 'rb')
else:
f = open(pdb)
meta = None
for line in f:
if line.startswith('CRYST1'):
meta = PdbMeta(line)
break
if meta is None and print_errors:
if f.tell() == 0:
put_error('empty file: %s' % pdb)
else:
put_error('CRYST1 line not found in %s' % pdb)
f.close()
return meta
def read_metadata(pdb, print_errors):
if pdb.endswith('.gz'):
f = gzip.open(pdb, 'rb')
else:
f = open(pdb)
meta = None
for line in f:
if line.startswith("CRYST1"):
meta = PdbMeta(line)
break
if meta is None and print_errors:
if f.tell() == 0:
put_error("empty file: %s" % pdb)
else:
put_error("CRYST1 line not found in %s" % pdb)
f.close()
return meta
def _find_i_sigi_columns(mtz_meta, opt):
if opt.icolumn:
icolumn = opt.icolumn
mtz_meta.check_col_type(icolumn, 'J')
else:
j_columns = [k for k, v in mtz_meta.columns.items() if v == 'J']
if len(j_columns) == 1:
icolumn = j_columns[0]
elif 'IMEAN' in j_columns:
icolumn = 'IMEAN'
elif len(j_columns) > 1:
put_error('Multiple intensity columns: %s. '
'Pick one with --icolumn' % j_columns)
else:
put_error('No intensity (IMEAN) column in the MTZ file')
# the default value of sigicolumn ('SIG<ICOL>') needs substitution
sigicolumn = opt.sigicolumn.replace('<ICOL>', icolumn)
mtz_meta.check_col_type(sigicolumn, 'Q')
return (icolumn, sigicolumn)
def _check_picture_tools():
ok = True
coot_path, coot_ver = coots.find_path_and_version()
if coot_path:
if coot_ver is None:
put_error("coot not working(?), no pictures")
ok = False
else:
if "with python" not in coot_ver:
put_error("coot with Python support is needed")
ok = False
if "\n0.6." in coot_ver:
put_error("coot 0.7+ is needed (0.6 would crash)")
ok = False
else:
put_error("No coot, no pictures")
ok = False
if not utils.syspath("render"):
put_error("No Raster3d, no pictures")
ok = False
return ok
def main(args):
if workflow.parse_workflow_commands():
return
options = parse_dimple_commands(args)
for necessary_var in ("CCP4", "CCP4_SCR"):
if necessary_var not in os.environ:
put_error('$%s not found, giving up' % necessary_var)
sys.exit(1)
if not os.path.isdir(os.environ["CCP4_SCR"]):
put_error('No such directory: $CCP4_SCR, refmac shall not work!')
wf = workflow.Workflow(options.output_dir, from_job=options.from_step)
utils.start_log(os.path.join(options.output_dir, "dimple.log"),
output_dir=options.output_dir)
utils.log_value("version", __version__)
utils.start_log_screen(os.path.join(options.output_dir, "screen.log"))
try:
dimple(wf=wf, opt=options)
exit_status = 0
except workflow.JobError as e:
put_error(e.msg, comment=e.note)
try:
utils.report_disk_space([wf.output_dir, os.getenv("CCP4_SCR")])
except KeyboardInterrupt:
comment("\nok, exiting...")
exit_status = 1
except RuntimeError as e:
put_error(e)
exit_status = 1
finally:
comment("\n")
if options.cleanup:
wf.delete_files(wf.temporary_files)
wf.options = options
wf.dump_pickle()
return exit_status
def main(args):
if workflow.parse_workflow_commands():
return
options = parse_dimple_commands(args)
check_ccp4_envvars()
try:
wf = workflow.Workflow(options.output_dir, from_job=options.from_step)
utils.start_log(os.path.join(options.output_dir, 'dimple.log'),
output_dir=options.output_dir)
utils.log_value('version', __version__)
utils.start_log_screen(os.path.join(options.output_dir, 'screen.log'))
dimple(wf=wf, opt=options)
check_contaminants_if_bad(wf, mtz=options.mtz)
exit_status = 0
except workflow.JobError as e:
put_error(e.msg, comment=e.note)
try:
utils.report_disk_space([wf.output_dir, os.getenv('CCP4_SCR')])
except KeyboardInterrupt:
comment('\nok, exiting...')
exit_status = 1
except (RuntimeError, IOError, OSError) as e:
put_error(e)
exit_status = 1
finally:
comment('\n')
if options.cleanup:
wf.delete_files(wf.temporary_files)
wf.options = options
try:
wf.dump_pickle()
except IOError as e:
put_error(e)
exit_status = 1
return exit_status
def _generate_scripts_and_pictures(wf, opt, data):
blobs = data["blobs"] if data else []
coot_path = coots.find_path()
if not blobs:
comment("\nUnmodelled blobs not found.")
elif opt.img_format:
if coot_path:
coot_ver = coots.find_version(coot_path)
if coot_ver is None:
put_error("coot not working(?), no pictures")
opt.img_format = None
elif "with python" not in coot_ver:
put_error("coot with Python support is needed")
opt.img_format = None
else:
put_error("No coot, no pictures")
opt.img_format = None
if not utils.syspath("render"):
put_error("No Raster3d, no pictures")
opt.img_format = None
if opt.img_format:
if len(blobs) == 1:
comment("\nRendering density blob at (%.1f, %.1f, %.1f)" %
blobs[0])
else:
comment("\nRendering 2 largest blobs: at (%.1f, %.1f, %.1f) "
"and at (%.1f, %.1f, %.1f)" % (blobs[0]+blobs[1]))
com = data and data["center"]
# run-coot.py centers on the biggest blob. It uses relative paths -
# it can be run only from the output directory, but is not affected
# by moving that directory to different location.
# There are blobN-coot.py scripts generated below with absolute paths.
# write coot script (apart from pictures) that centers on the biggest blob
script_path = os.path.join(wf.output_dir, "run-coot.py")
script = coots.basic_script(pdb=opt.xyzout, mtz=opt.hklout,
center=(blobs and blobs[0]), toward=com,
white_bg=opt.white_bg)
_write_script(script_path, script, executable=True)
# blob images, for now for not more than two blobs
d = os.path.abspath(wf.output_dir)
for n, b in enumerate(blobs[:2]):
py_path = os.path.join(wf.output_dir, "blob%d-coot.py" % (n+1))
content = coots.basic_script(pdb=os.path.join(d, opt.xyzout),
mtz=os.path.join(d, opt.hklout),
center=blobs[n], toward=com,
white_bg=opt.white_bg)
_write_script(py_path, content)
# coot.sh - one-line script for convenience
if blobs:
coot_sh_text = '{coot} --no-guano {out}/blob1-coot.py\n'
else:
coot_sh_text = '{coot} --no-guano {out}/final.mtz {out}/final.pdb\n'
coot_sh_path = os.path.join(wf.output_dir, "coot.sh")
_write_script(coot_sh_path, coot_sh_text.format(coot=coot_path or 'coot',
out=wf.output_dir),
executable=True)
if opt.img_format and blobs:
script = ''
basenames = []
# as a workaround for buggy coot the maps are reloaded for each blob
for n, b in enumerate(blobs[:2]):
script += coots.basic_script(pdb=opt.xyzout, mtz=opt.hklout,
center=b, toward=com,
white_bg=opt.white_bg)
rs, names = coots.r3d_script(center=b, toward=com,
blobname="blob%s" % (n+1))
script += rs
basenames += names
coot_job = wf.coot_py(script)
try:
coot_job.run()
except workflow.JobError:
# check for a possible cause to hint the user
# (possible workaround: change $HOME to non-existing directory)
if utils.silently_run(coot_job.args, cwd=wf.output_dir)[0] != 0:
put_error("coot fails with options: --no-graphics --python",
comment="It happens when scripts in .coot or "
".coot-preferences are not compatible\n"
"with the --no-graphics mode.")
raise
for n, basename in enumerate(basenames):
job = wf.render_r3d(basename, img_format=opt.img_format)
if n % 3 == 0:
job.run()
else: # minimal output
job.run(show_progress=False, new_line=False)
wf.delete_files([name+".r3d" for name in basenames])
return coot_sh_path
def dimple(wf, opt):
comment(" ### Dimple v%s. Problems and suggestions:"
" ccp4.github.io/dimple ###" % __version__)
mtz_meta = wf.read_mtz_metadata(opt.mtz)
_comment_summary_line("MTZ (%.1fA)" % mtz_meta.dmax, mtz_meta)
if opt.dls_naming:
opt.pdbs = dls_name_filter(opt.pdbs)
opt.pdbs = utils.filter_out_duplicate_files(opt.pdbs, relto=opt.output_dir)
if not opt.pdbs:
comment("\nNo non-empty pdb files given. Nothing to do.")
return
for p in opt.pdbs:
wf.read_pdb_metadata(p, print_errors=(len(opt.pdbs) > 1))
if len(opt.pdbs) > 1:
comment("\nPDBs in order of similarity (using the first one):")
opt.pdbs.sort(key=lambda x: calculate_difference(wf.file_info[x],
mtz_meta))
utils.log_value("data_file", opt.mtz)
utils.log_value("pdb_files", opt.pdbs)
for p in opt.pdbs:
_comment_summary_line(os.path.basename(p), wf.file_info[p])
ini_pdb = "ini.pdb"
wf.copy_uncompressed(opt.pdbs[0], ini_pdb)
pdb_meta = wf.file_info[opt.pdbs[0]]
if pdb_meta is None:
put_error("PDB file missing CRYST1 record, starting from MR")
if opt.no_hetatm or check_hetatm_x(wf.path(ini_pdb), pdb_meta):
if not opt.no_hetatm:
comment("\nHETATM marked as element X would choke many programs.")
rb_xyzin = "prepared.pdb"
wf.temporary_files.add(rb_xyzin)
n_het = wf.remove_hetatm(xyzin=ini_pdb, xyzout=rb_xyzin,
remove_all=opt.no_hetatm)
comment("\nRemoved %d HETATM atoms" % n_het)
else:
rb_xyzin = ini_pdb
# run rwcontents even without CRYST1 - it will show mol. weight only
wf.rwcontents(xyzin=rb_xyzin).run()
rw_data = wf.jobs[-1].data
if pdb_meta is None:
pass # we already had a warning message
elif rw_data.get('solvent_percent') is None:
put_error("rwcontents could not interpret %s" % rb_xyzin)
elif rw_data['solvent_percent'] > HIGH_SOLVENT_PCT:
comment("\nHmm... %.1f%% of solvent or incomplete model" %
rw_data['solvent_percent'])
if abs(wf.jobs[-1].data.get('volume', 0) - pdb_meta.get_volume()) > 10:
comment("\ndebug: problem when calculating volume?")
####### pointless - reindexing #######
if match_symmetry(mtz_meta, pdb_meta) and opt.mr_when_r > 0 and (
0.7 < mtz_meta.get_volume() / pdb_meta.get_volume() < 1.4):
reindexed_mtz = "pointless.mtz"
wf.temporary_files.add(reindexed_mtz)
wf.pointless(hklin=opt.mtz, xyzin=rb_xyzin, hklout=reindexed_mtz,
keys="TOLERANCE 5").run(may_fail=True)
alt_reindex = wf.jobs[-1].data.get('alt_reindex')
if wf.jobs[-1].exit_status == 0 and alt_reindex:
for ar in alt_reindex:
comment("\n %-10s CC: %-8.3f cell diff: %.1fA" % (
ar['op'], ar['cc'], ar['cell_deviat']))
else:
# until recently (2015) pointless didn't print CC for non-ambiguous
# spacegroups (e.g. C2), but now it always prints
comment("\n no good indexing")
reindexed_mtz = opt.mtz
else:
reindexed_mtz = opt.mtz
reindexed_mtz_meta = wf.read_mtz_metadata(reindexed_mtz)
if reindexed_mtz_meta.symmetry != mtz_meta.symmetry:
_comment_summary_line('reindexed MTZ', reindexed_mtz_meta)
####### (c)truncate - calculate amplitudes if needed #######
if not opt.fcolumn:
opt.fcolumn = 'F' if 'F' in mtz_meta.columns else 'FP'
elif opt.icolumn or opt.ItoF_prog:
put_error('Ignoring options --fcolumn/--sigfcolumn')
opt.sigfcolumn = opt.sigfcolumn.replace('<FCOL>', opt.fcolumn)
if (opt.ItoF_prog or opt.icolumn or opt.fcolumn not in mtz_meta.columns
or opt.sigfcolumn not in mtz_meta.columns):
f_mtz = "amplit.mtz"
wf.temporary_files.add(f_mtz)
i_sigi_cols = _find_i_sigi_columns(mtz_meta, opt)
if opt.ItoF_prog == 'ctruncate' or (opt.ItoF_prog is None and opt.slow):
wf.ctruncate(hklin=reindexed_mtz, hklout=f_mtz,
colin="/*/*/[%s,%s]" % i_sigi_cols).run()
else:
wf.truncate(hklin=reindexed_mtz, hklout=f_mtz,
labin="IMEAN=%s SIGIMEAN=%s" % i_sigi_cols,
labout="F=F SIGF=SIGF").run()
opt.fcolumn = 'F'
opt.sigfcolumn = 'SIGF'
else:
f_mtz = reindexed_mtz
####### rigid body - check if model is good for refinement? #######
refmac_labin_nofree = "FP=%s SIGFP=%s" % (opt.fcolumn, opt.sigfcolumn)
refmac_xyzin = None
cell_diff = calculate_difference(pdb_meta, reindexed_mtz_meta)
if pdb_meta is None:
pass # the error message was already printed
elif opt.mr_when_r <= 0:
comment("\nMR requested unconditionally.")
elif cell_diff > 0.1 and opt.mr_when_r < 1:
comment("\nDifferent unit cells.")
elif pdb_meta.symmetry != reindexed_mtz_meta.symmetry:
comment("\nDifferent space groups.")
else:
comment("\nRigid-body refinement with resolution 3.5 A, 10 cycles.")
if 'aa_count' in rw_data and 'water_count' in rw_data:
if rw_data['aa_count'] != 0:
comment(" %.1f waters/aa." % (rw_data['water_count'] /
rw_data['aa_count']))
else:
comment(' %d/0 waters/aa.' % rw_data['water_count'])
wf.temporary_files |= {"refmacRB.pdb", "refmacRB.mtz"}
# it may fail because of "Disagreement between mtz and pdb"
wf.refmac5(hklin=f_mtz, xyzin=rb_xyzin,
hklout="refmacRB.mtz", xyzout="refmacRB.pdb",
labin=refmac_labin_nofree,
libin=None,
keys="""refinement type rigidbody resolution 15 3.5
rigidbody ncycle 10""").run(may_fail=True)
# if the error is caused by mtz/pdb disagreement, continue with MR
if wf.jobs[-1].exit_status != 0:
comment("\nTry MR.")
elif not wf.jobs[-1].data.get("overall_r"):
comment("\nWARNING: unknown R factor, something went wrong.\n")
refmac_xyzin = "refmacRB.pdb"
elif wf.jobs[-1].data["overall_r"] > opt.mr_when_r:
comment("\nRun MR for R > %g." % opt.mr_when_r)
else:
comment("\nNo MR for R < %g." % opt.mr_when_r)
refmac_xyzin = "refmacRB.pdb"
####### phaser/molrep - molecular replacement #######
if refmac_xyzin is None:
vol_ratio = None
if pdb_meta:
# num_mol accounts for strict NCS (MTRIX without iGiven)
vol_ratio = (mtz_meta.asu_volume() /
pdb_meta.asu_volume(rw_data['num_mol']))
comment(" Volume of asu: %.1f%% of model asu." % (100 * vol_ratio))
if opt.mr_when_r >= 1:
comment("\nWould try MR, but it is disabled.")
return
if opt.mr_num:
mr_num = opt.mr_num
else:
mr_num = guess_number_of_molecules(mtz_meta, rw_data, vol_ratio)
mw = rw_data.get('weight')
if isinstance(mr_num, float):
wf.ensembler(pdbin=rb_xyzin, root='ens').run()
n_models = len(wf.jobs[-1].data['models'])
mw = None
rb_xyzin = "ens_merged.pdb"
mr_num = max(int(round(mr_num * n_models)), 1)
# phaser is used by default if number of searched molecules is known
if opt.mr_prog == 'molrep':
wf.temporary_files |= {"molrep.pdb", "molrep_dimer.pdb",
"molrep.crd"}
wf.molrep(f=f_mtz, m=rb_xyzin).run()
refmac_xyzin = "molrep.pdb"
else:
wf.temporary_files |= {"phaser.1.pdb", "phaser.1.mtz"}
wf.phaser_auto(hklin=f_mtz,
labin="F=%s SIGF=%s" % (opt.fcolumn, opt.sigfcolumn),
model=dict(pdb=rb_xyzin, identity=100, num=mr_num,
mw=mw),
sg_alt="ALL", opt=opt,
root='phaser').run(may_fail=True)
if not _after_phaser_comments(wf.jobs[-1],
sg_in=reindexed_mtz_meta.symmetry):
return
refmac_xyzin = "phaser.1.pdb"
f_mtz = "phaser.1.mtz"
if False:
wf.findwaters(pdbin=refmac_xyzin, hklin=f_mtz,
f="FC", phi="PHIC", pdbout="prepared_wat.pdb", sigma=2)
refmac_xyzin = "prepared_wat.pdb"
####### adding free-R flags #######
f_mtz_meta = wf.read_mtz_metadata(f_mtz)
cad_reso = opt.reso or (f_mtz_meta.dmax - MtzMeta.d_eps)
if opt.free_r_flags:
free_mtz = opt.free_r_flags
free_col = check_freerflags_column(wf.path(free_mtz),
expected_symmetry=pdb_meta,
column=opt.freecolumn)
comment("\nFree-R flags from the %s file, column %s." %
(("reference" if free_mtz != opt.mtz else 'input'), free_col))
else:
free_col = DEFAULT_FREE_COLS[0]
if free_col in f_mtz_meta.columns:
comment("\nReplace free-R flags")
else:
comment("\nGenerate free-R flags")
free_mtz = "free.mtz"
wf.temporary_files |= {"unique.mtz", free_mtz}
if opt.seed_freerflag or cell_diff > 1e3: # i.e. different SG
wf.unique(hklout="unique.mtz", ref=f_mtz_meta,
resolution=cad_reso).run()
else:
comment(" (repeatably)")
# Here we'd like to have always the same set of free-r flags
# for given PDB file. That's why we don't use information
# from the data file (mtz).
wf.unique(hklout="unique.mtz", ref=pdb_meta, resolution=1.0).run()
# CCP4 freerflag uses always the same pseudo-random sequence by default
wf.freerflag(hklin="unique.mtz", hklout=free_mtz,
keys=("SEED" if opt.seed_freerflag else "")).run()
if free_mtz == opt.mtz and opt.reso is None:
prepared_mtz = f_mtz
else:
prepared_mtz = "prepared.mtz"
wf.temporary_files.add(prepared_mtz)
wf.cad(data_in=[(f_mtz,
[c for c in f_mtz_meta.columns if c != free_col]),
(free_mtz, [free_col])],
hklout=prepared_mtz,
keys=["sysab_keep", # does it matter?
"reso overall 1000.0 %g" % cad_reso]).run()
freerflag_missing = wf.count_mtz_missing(prepared_mtz, free_col)
if freerflag_missing:
wf.freerflag(hklin=prepared_mtz, hklout="prepared2.mtz",
keys="COMPLETE FREE="+free_col,
parser=" (again, for %d refl. more)" % freerflag_missing
).run()
prepared_mtz = "prepared2.mtz"
wf.temporary_files.add(prepared_mtz)
####### refinement #######
if opt.weight:
refmac_weight = "matrix %f" % opt.weight
else:
refmac_weight = "auto"
restr_ref_keys = """\
make newligand continue
refinement type restrained
weight %s
""" % refmac_weight
if opt.freecolumn_val:
restr_ref_keys += "free %s\n" % opt.freecolumn_val
refmac_labin = "%s FREE=%s" % (refmac_labin_nofree, free_col)
comment("\nRestrained refinement, %d+%d cycles." % (opt.jelly,
opt.restr_cycles))
if opt.jelly:
wf.temporary_files |= {"jelly.pdb", "jelly.mtz"}
wf.refmac5(hklin=prepared_mtz, xyzin=refmac_xyzin,
hklout="jelly.mtz", xyzout="jelly.pdb",
labin=refmac_labin, libin=opt.libin,
keys=restr_ref_keys+"ridge distance sigma 0.01\n"
"make hydrogen no\n"
"ncycle %d" % opt.jelly
+opt.extra_ref_keys).run()
comment(_refmac_rms_line(wf.jobs[-1].data))
refmac_xyzin = "jelly.pdb"
restr_job = wf.refmac5(hklin=prepared_mtz, xyzin=refmac_xyzin,
hklout=opt.hklout, xyzout=opt.xyzout,
labin=refmac_labin, libin=opt.libin,
keys=restr_ref_keys+("ncycle %d" % opt.restr_cycles)
+opt.extra_ref_keys).run()
comment(_refmac_rms_line(restr_job.data))
# if that run is repeated with --from-step it's useful to compare Rfree
if wf.from_job > 0 and wf.from_job <= len(wf.jobs): # from_job is 1-based
prev = [j for j in wf.repl_jobs if j.name == restr_job.name]
if prev and prev[0].data and "free_r" in prev[0].data:
comment("\nPreviously: R/Rfree %.4f/%.4f Rfree change: %+.4f" % (
prev[0].data["overall_r"], prev[0].data["free_r"],
restr_job.data["free_r"] - prev[0].data["free_r"]))
####### check blobs and finish #######
if restr_job.data["free_r"] <= BAD_FINAL_RFREE:
fb_job = wf.find_blobs(opt.hklout, opt.xyzout, sigma=0.8).run()
coot_script = _generate_scripts_and_pictures(wf, opt, fb_job.data)
if coot_script:
comment("\nTo see it in Coot run %s" % coot_script)
else:
comment("\nGiving up (Rfree > %g). No blob search." % BAD_FINAL_RFREE)
_generate_scripts_and_pictures(wf, opt, None)
def parse_dimple_commands(args):
dstr = ' (default: %(default)s)'
parser = argparse.ArgumentParser(
usage=USAGE_SHORT, epilog=workflow.commands_help, prog=PROG,
formatter_class=argparse.RawDescriptionHelpFormatter)
# positional args can be separated by options, but not after the 3rd one
# see http://bugs.python.org/issue15112 , http://bugs.python.org/issue14191
parser.add_argument('pos_arg1')
parser.add_argument('pos_arg2')
parser.add_argument('pos_arg3')
parser.add_argument('more_args', nargs='*')
group1 = parser.add_argument_group('most commonly used options')
group1.add_argument('-s', '--slow', action='count',
help='more refinement, etc. (can be used 2x)')
group1.add_argument('-M', '--mr-when-r', type=float, default=0.4,
metavar='NUM',
help='threshold for Molecular Replacement'+dstr)
group2 = parser.add_argument_group('options contolling input/output')
group2.add_argument('-I', '--icolumn', metavar='ICOL',
help='I column label (default: IMEAN)')
group2.add_argument('--sigicolumn', metavar='SIGICOL', default='SIG<ICOL>',
help='SIGI column label'+dstr)
group2.add_argument('--fcolumn', metavar='FCOL',
help='F column label (default: F)')
group2.add_argument('--sigfcolumn', metavar='SIGFCOL', default='SIG<FCOL>',
help='SIGF column label'+dstr)
group2.add_argument('--libin', metavar='CIF',
help='ligand descriptions for refmac (LIBIN)')
group2.add_argument('-R', '--free-r-flags', metavar='MTZ_FILE',
help='file with freeR flags '
'("-" = use flags from data mtz)')
group2.add_argument('--freecolumn', metavar='COL[=N]',
help='Rfree column with optional value (default: 0)')
group2.add_argument('--hklout', metavar='out.mtz', default='final.mtz',
help='output mtz file'+dstr)
group2.add_argument('--xyzout', metavar='out.pdb', default='final.pdb',
help='output pdb file'+dstr)
group2.add_argument('-f', choices=['png', 'jpeg', 'tiff', 'none'],
dest='img_format',
help='format of generated images'+dstr)
group2.add_argument('--no-cleanup', dest='cleanup', action='store_false',
help='leave intermediate files')
group2.add_argument('--cleanup', action='store_true',
help=argparse.SUPPRESS) # obsolete
group3 = parser.add_argument_group('options customizing the run')
group3.add_argument('--no-hetatm', action='store_true',
help='remove HETATM atoms from the given model')
group3.add_argument('--jelly', metavar='N_ITER', type=int,
help='run refmac jelly-body before the final refinement')
group3.add_argument('--reso', type=float, help='limit the resolution [A]')
group3.add_argument('--restr-cycles', metavar='N', type=int,
help='cycles of refmac final refinement (default: 8)')
group3.add_argument('--weight', metavar='VALUE', type=float,
help='refmac matrix weight (default: auto-weight)')
group3.add_argument('--mr-prog', choices=['phaser', 'molrep'],
default='phaser',
help='Molecular Replacement program' + dstr)
group3.add_argument('--mr-num', type=int,
help='number of molecules for MR (default: auto)')
group3.add_argument('--mr-reso', type=float, default=3.25,
help='high resolution for MR '
'(if >10 interpreted as eLLG)' + dstr)
group3.add_argument('--ItoF-prog', choices=['truncate', 'ctruncate'],
help='program to calculate amplitudes')
group3.add_argument('--seed-freerflag', action='store_true',
help=argparse.SUPPRESS)
group3.add_argument('--dls-naming', action='store_true',
help=argparse.SUPPRESS)
group3.add_argument('--from-step', metavar='N', type=int, default=0,
help=argparse.SUPPRESS)
parser.add_argument('--version', action='version',
version='%(prog)s '+__version__)
# customize usage message: get rid of 'positional arguments',
# rename default 'optional arguments' and shift it to the end.
# pylint: disable=protected-access
default_group = parser._action_groups[1]
default_group.title = 'other options'
parser._action_groups = parser._action_groups[2:] + [default_group]
# special mode for compatibility with ccp4i
legacy_args = {"HKLIN": "", "XYZIN": "",
"HKLOUT": "--hklout", "XYZOUT": "--xyzout"}
if len(args) == 8 and args[0] in legacy_args:
args = [legacy_args.get(a) or a
for a in args if legacy_args.get(a) != ""]
output_dir = os.path.join(os.environ.get("CCP4_SCR", ''), "dimple_out")
args.append(output_dir)
# special mode for checking pdb file[s]
if len(args) >= 1 and all(arg.endswith('.pdb') for arg in args):
special_pdb_mode(args)
sys.exit(0)
# special mode for checking mtz file
if len(args) == 1 and args[0].endswith('.mtz'):
special_mtz_mode(args)
sys.exit(1)
opt = parser.parse_args(args)
all_args = [opt.pos_arg1, opt.pos_arg2, opt.pos_arg3] + opt.more_args
# all_args should be one mtz, one or more pdbs and output_dir
opt.output_dir = all_args.pop()
if opt.img_format == 'none': # this option is kept for compatibility only
opt.img_format = None
if (opt.output_dir.endswith('.mtz') or opt.output_dir.endswith('.pdb')
or opt.output_dir.endswith('.gz')):
put_error('The last argument should be output directory')
sys.exit(1)
# special mode for re-running jobs
if all_args[0] == 'rerun':
if os.path.isdir(all_args[1]):
logfile = os.path.join(all_args[1], 'dimple.log')
else:
logfile = all_args[1]
old_wf = utils.read_section_from_log(logfile, 'workflow')
try:
old_dir = os.path.join(old_wf['cwd'], old_wf['output_dir'])
old_pdb = os.path.join(old_dir, 'ini.pdb')
if not os.path.exists(old_pdb):
if not old_wf.get('pdb_files'):
put_error('No pdb files in the original run?')
sys.exit(1)
old_pdb = os.path.join(old_dir, old_wf['pdb_files'][0])
if 'data_file' not in old_wf: # temporary, to be removed soon
old_mtz_arg = [a for a in old_wf['args'].split()
if a.endswith('.mtz')][0]
old_wf['data_file'] = os.path.join(old_wf['cwd'], old_mtz_arg)
old_mtz = os.path.join(old_dir, old_wf['data_file'])
except (TypeError, KeyError):
put_error('Reading logfile failed', comment='is it dimple.log?')
sys.exit(1)
all_args[0:2] = [old_pdb, old_mtz]
mtz_args = [a for a in all_args if a.lower().endswith('.mtz')]
if len(mtz_args) != 1:
put_error("One mtz file should be given")
sys.exit(1)
opt.mtz = mtz_args[0]
all_args.remove(opt.mtz)
opt.pdbs = all_args
for n, a in enumerate(opt.pdbs):
if is_pdb_id(a):
opt.pdbs[n] = download_pdb(a, opt.output_dir)
elif not (a.lower().endswith('.pdb') or a.lower().endswith('.pdb.gz')):
put_error("unexpected arg (neither mtz nor pdb): %s" % a)
sys.exit(1)
if len(opt.pdbs) == 0:
put_error("At least one pdb file should be given")
sys.exit(1)
if opt.seed_freerflag and opt.free_r_flags:
put_error("Option --seed-freerflag and --free-r-flags"
" don't make sense together")
sys.exit(1)
if opt.free_r_flags == '-':
opt.free_r_flags = opt.mtz
opt.freecolumn_val = None
if opt.freecolumn and '=' in opt.freecolumn:
opt.freecolumn, opt.freecolumn_val = opt.freecolumn.rsplit('=', 1)
if opt.freecolumn and not opt.free_r_flags:
if opt.freecolumn == DEFAULT_FREE_COLS[0] and opt.freecolumn_val:
pass # this may be useful for excluding different set
else:
put_error("--freecolumn suggests that you want to use existing free"
" flags.\nFor this you need also option --free-r-flags")
sys.exit(1)
# extra checks
for filename in opt.pdbs + [opt.mtz, opt.free_r_flags, opt.libin]:
if filename and not os.path.isfile(filename):
put_error("File not found: " + filename)
sys.exit(1)
if os.path.exists(opt.output_dir) and not os.path.isdir(opt.output_dir):
put_error("Not a directory: " + opt.output_dir)
sys.exit(1)
# Since we'll execute programs from opt.output_dir, adjust paths.
opt.mtz = utils.adjust_path(opt.mtz, opt.output_dir)
opt.pdbs = [utils.adjust_path(a, opt.output_dir) for a in opt.pdbs]
if opt.free_r_flags:
opt.free_r_flags = utils.adjust_path(opt.free_r_flags, opt.output_dir)
if opt.libin:
opt.libin = utils.adjust_path(opt.libin, opt.output_dir)
# the default value of sigicolumn ('SIG<ICOL>') needs substitution
opt.sigicolumn = opt.sigicolumn.replace('<ICOL>', opt.icolumn or 'IMEAN')
# set defaults that depend on the 'slow' level
if opt.slow is None:
opt.slow = 0
elif opt.slow > 2:
opt.slow = 2
if opt.restr_cycles is None:
opt.restr_cycles = [8, 10, 12][opt.slow]
if opt.jelly is None:
opt.jelly = [4, 10, 100][opt.slow]
return opt
def parse_dimple_commands(args):
dstr = ' (default: %(default)s)'
parser = argparse.ArgumentParser( # noqa: E126 visual indent
usage=USAGE_SHORT,
epilog=workflow.commands_help,
prog=PROG,
formatter_class=argparse.RawDescriptionHelpFormatter)
# positional args can be separated by options, but not after the 3rd one
# see http://bugs.python.org/issue15112 , http://bugs.python.org/issue14191
parser.add_argument('pos_arg1')
parser.add_argument('pos_arg2')
parser.add_argument('pos_arg3')
parser.add_argument('more_args', nargs='*')
group1 = parser.add_argument_group('most commonly used options')
group1.add_argument('-s',
'--slow',
action='count',
help='more refinement, etc. (can be used 2x)')
group1.add_argument('-M',
'--mr-when-r',
type=float,
default=0.4,
metavar='NUM',
help='threshold for Molecular Replacement' + dstr)
group2 = parser.add_argument_group('options contolling input/output')
group2.add_argument('-I',
'--icolumn',
metavar='ICOL',
help='I column label (default: IMEAN)')
group2.add_argument('--sigicolumn',
metavar='SIGICOL',
default='SIG<ICOL>',
help='SIGI column label' + dstr)
group2.add_argument('--fcolumn',
metavar='FCOL',
help='F column label (default: F)')
group2.add_argument('--sigfcolumn',
metavar='SIGFCOL',
default='SIG<FCOL>',
help='SIGF column label' + dstr)
group2.add_argument('--libin',
metavar='CIF',
help='ligand descriptions for refmac (LIBIN)')
group2.add_argument('--refmac-key',
metavar='LINE',
action='append',
help='extra Refmac keywords to be used in refinement')
group2.add_argument('-R',
'--free-r-flags',
metavar='MTZ_FILE',
help='file with freeR flags '
'("-" = use flags from data mtz)')
group2.add_argument('--freecolumn',
metavar='COL[=N]',
help='Rfree column with optional value (default: 0)')
group2.add_argument('--hklout',
metavar='out.mtz',
default='final.mtz',
help='output mtz file' + dstr)
group2.add_argument('--xyzout',
metavar='out.pdb',
default='final.pdb',
help='output pdb file' + dstr)
group2.add_argument('-f',
choices=['png', 'jpeg', 'none'],
dest='img_format',
help='format of generated images' + dstr)
group2.add_argument('--white-bg',
dest='white_bg',
action='store_true',
help='white background in Coot and in images')
group2.add_argument('--no-cleanup',
dest='cleanup',
action='store_false',
help='leave intermediate files')
group2.add_argument('--cleanup',
action='store_true',
help=argparse.SUPPRESS) # obsolete
group_w = parser.add_argument_group('what is calculated')
group_w.add_argument('--no-blob-search',
dest='blob_search',
action='store_false',
help='do not search for unmodelled blobs')
group_w.add_argument('--anode',
action='store_true',
help='use SHELX/AnoDe to find peaks in anomalous map')
group3 = parser.add_argument_group('options customizing the run')
group3.add_argument('--no-hetatm',
action='store_true',
help='remove HETATM atoms from the given model')
group3.add_argument('--rigid-cycles',
metavar='N',
type=int,
help='cycles of rigid-body refinement (default: 10)')
group3.add_argument('--jelly',
metavar='N',
type=int,
help='cycles of jelly-body refinement (default: 4)')
group3.add_argument('--restr-cycles',
metavar='N',
type=int,
help='cycles of refmac final refinement (default: 8)')
group3.add_argument('--reso', type=float, help='limit the resolution [A]')
group3.add_argument('--weight',
metavar='VALUE',
type=float,
help='refmac matrix weight (default: auto-weight)')
group3.add_argument('--mr-prog',
choices=['phaser', 'molrep'],
default='phaser',
help='Molecular Replacement program' + dstr)
group3.add_argument('--mr-num',
type=int,
help='number of molecules for MR (default: auto)')
group3.add_argument('--mr-reso',
type=float,
default=3.25,
help='high resolution for MR '
'(if >10 interpreted as eLLG)' + dstr)
group3.add_argument('--ItoF-prog',
choices=['truncate', 'ctruncate'],
help='program to calculate amplitudes')
group3.add_argument('--seed-freerflag',
action='store_true',
help=argparse.SUPPRESS)
group3.add_argument('--dls-naming',
action='store_true',
help=argparse.SUPPRESS)
group3.add_argument('--from-step',
metavar='N',
type=int,
default=0,
help=argparse.SUPPRESS)
parser.add_argument('--version',
action='version',
version='%(prog)s ' + __version__)
# customize usage message: get rid of 'positional arguments',
# rename default 'optional arguments' and shift it to the end.
# pylint: disable=protected-access
default_group = parser._action_groups[1]
default_group.title = 'other options'
parser._action_groups = parser._action_groups[2:] + [default_group]
# special mode for compatibility with ccp4i
legacy_args = {
'HKLIN': '',
'XYZIN': '',
'HKLOUT': '--hklout',
'XYZOUT': '--xyzout'
}
if len(args) == 8 and args[0] in legacy_args:
args = [
legacy_args.get(a) or a for a in args if legacy_args.get(a) != ''
]
output_dir = os.path.join(os.environ.get('CCP4_SCR', ''), 'dimple_out')
args.append(output_dir)
# special mode for checking pdb file[s]
if len(args) >= 1 and all(arg.endswith('.pdb') for arg in args):
special_pdb_mode(args)
sys.exit(0)
# special mode for checking mtz file
if len(args) == 1 and args[0].endswith('.mtz'):
special_mtz_mode(args)
sys.exit(1)
opt = parser.parse_args(args)
all_args = [opt.pos_arg1, opt.pos_arg2, opt.pos_arg3] + opt.more_args
# all_args should be one mtz, one or more pdbs and output_dir
opt.output_dir = all_args.pop()
if opt.img_format == 'none': # this option is kept for compatibility only
opt.img_format = None
if (opt.output_dir.endswith('.mtz') or opt.output_dir.endswith('.pdb')
or opt.output_dir.endswith('.gz')):
put_error('The last argument should be output directory')
sys.exit(1)
# special mode for re-running jobs
if all_args[0] == 'rerun':
if os.path.isdir(all_args[1]):
logfile = os.path.join(all_args[1], 'dimple.log')
else:
logfile = all_args[1]
old_wf = utils.read_section_from_log(logfile, 'workflow')
try:
old_dir = os.path.join(old_wf['cwd'], old_wf['output_dir'])
old_pdb = os.path.join(old_dir, 'ini.pdb')
if not os.path.exists(old_pdb):
if not old_wf.get('pdb_files'):
put_error('No pdb files in the original run?')
sys.exit(1)
old_pdb = os.path.join(old_dir, old_wf['pdb_files'][0])
if 'data_file' not in old_wf: # temporary, to be removed soon
old_mtz_arg = [
a for a in old_wf['args'].split() if a.endswith('.mtz')
][0]
old_wf['data_file'] = os.path.join(old_wf['cwd'], old_mtz_arg)
old_mtz = os.path.join(old_dir, old_wf['data_file'])
except (TypeError, KeyError):
put_error('Reading logfile failed', comment='is it dimple.log?')
sys.exit(1)
all_args[0:2] = [old_pdb, old_mtz]
mtz_args = [a for a in all_args if a.lower().endswith('.mtz')]
if len(mtz_args) != 1:
put_error('One mtz file should be given')
sys.exit(1)
opt.mtz = mtz_args[0]
all_args.remove(opt.mtz)
opt.pdbs = all_args
for n, a in enumerate(opt.pdbs):
if is_pdb_id(a):
opt.pdbs[n] = download_pdb(a, opt.output_dir)
elif not any(a.lower().endswith(ext)
for ext in ['.pdb', '.pdb.gz', '.ent', '.ent.gz']):
put_error('unexpected arg (neither mtz nor pdb): %s' % a)
sys.exit(1)
if len(opt.pdbs) == 0:
put_error('At least one pdb file should be given')
sys.exit(1)
if opt.seed_freerflag and opt.free_r_flags:
put_error('Option --seed-freerflag and --free-r-flags'
' do not make sense together')
sys.exit(1)
if opt.free_r_flags == '-':
opt.free_r_flags = opt.mtz
opt.freecolumn_val = None
if opt.freecolumn and '=' in opt.freecolumn:
opt.freecolumn, opt.freecolumn_val = opt.freecolumn.rsplit('=', 1)
if opt.freecolumn and not opt.free_r_flags:
if opt.freecolumn == DEFAULT_FREE_COLS[0] and opt.freecolumn_val:
pass # this may be useful for excluding different set
else:
put_error(
'--freecolumn suggests that you want to use existing free'
' flags.\nFor this you need also option --free-r-flags')
sys.exit(1)
opt.extra_ref_keys = ''.join('\n' + key for key in opt.refmac_key or [])
# extra checks
for filename in opt.pdbs + [opt.mtz, opt.free_r_flags, opt.libin]:
if filename and not os.path.isfile(filename):
put_error('File not found: ' + filename)
sys.exit(1)
if os.path.exists(opt.output_dir) and not os.path.isdir(opt.output_dir):
put_error('Not a directory: ' + opt.output_dir)
sys.exit(1)
# Since we'll execute programs from opt.output_dir, adjust paths.
opt.mtz = utils.adjust_path(opt.mtz, opt.output_dir)
opt.pdbs = [utils.adjust_path(a, opt.output_dir) for a in opt.pdbs]
if opt.free_r_flags:
opt.free_r_flags = utils.adjust_path(opt.free_r_flags, opt.output_dir)
if opt.libin:
opt.libin = utils.adjust_path(opt.libin, opt.output_dir)
# set defaults that depend on the 'slow' level
if opt.slow is None:
opt.slow = 0
elif opt.slow > 2:
opt.slow = 2
if opt.rigid_cycles is None:
opt.rigid_cycles = 10
if opt.restr_cycles is None:
opt.restr_cycles = [8, 10, 12][opt.slow]
if opt.jelly is None:
opt.jelly = [4, 10, 100][opt.slow]
return opt
def _generate_scripts_and_pictures(wf, opt, data, pha=None):
blobs = data['blobs'] if data else []
coot_path = coots.find_path()
if not blobs:
comment('\nUnmodelled blobs not found.')
elif opt.img_format:
if coot_path:
coot_ver = coots.find_version(coot_path)
if coot_ver is None:
put_error('coot not working(?), no pictures')
opt.img_format = None
elif 'with python' not in coot_ver:
put_error('coot with Python support is needed')
opt.img_format = None
else:
put_error('No coot, no pictures')
opt.img_format = None
if not utils.syspath('render'):
put_error('No Raster3d, no pictures')
opt.img_format = None
if opt.img_format:
if len(blobs) == 1:
comment('\nRendering density blob at (%.1f, %.1f, %.1f)' %
blobs[0])
else:
comment('\nRendering 2 largest blobs: at (%.1f, %.1f, %.1f) '
'and at (%.1f, %.1f, %.1f)' % (blobs[0] + blobs[1]))
com = data and data.get('center')
if pha:
normal_map = False
refl = pha
prefix = 'anom-'
else:
normal_map = True
refl = opt.hklout
prefix = ''
# run-coot.py centers on the biggest blob. It uses relative paths -
# it can be run only from the output directory, but is not affected
# by moving that directory to different location.
# There are blobN-coot.py scripts generated below with absolute paths.
# write coot script (apart from pictures) that centers on the biggest blob
script_path = os.path.join(wf.output_dir, prefix + 'run-coot.py')
script = coots.basic_script(pdb=opt.xyzout,
refl=refl,
normal_map=normal_map,
center=(blobs and blobs[0]),
toward=com,
white_bg=opt.white_bg)
_write_script(script_path, script, executable=True)
# blob images, for now for not more than two blobs
d = os.path.abspath(wf.output_dir)
for n, b in enumerate(blobs[:2]):
py_path = os.path.join(wf.output_dir,
'%sblob%d-coot.py' % (prefix, n + 1))
content = coots.basic_script(pdb=os.path.join(d, opt.xyzout),
refl=os.path.join(d, refl),
normal_map=normal_map,
center=blobs[n],
toward=com,
white_bg=opt.white_bg)
_write_script(py_path, content)
# coot.sh - one-line script for convenience
if blobs:
coot_sh_text = '{coot} --no-guano {out}/%sblob1-coot.py\n' % prefix
else:
coot_sh_text = '{coot} --no-guano {out}/final.mtz {out}/final.pdb\n'
coot_sh_path = os.path.join(wf.output_dir, prefix + 'coot.sh')
_write_script(coot_sh_path,
coot_sh_text.format(coot=coot_path or 'coot',
out=wf.output_dir),
executable=True)
if opt.img_format and blobs:
script = ''
basenames = []
# as a workaround for buggy coot the maps are reloaded for each blob
for n, b in enumerate(blobs[:2]):
script += coots.basic_script(pdb=opt.xyzout,
refl=refl,
normal_map=normal_map,
center=b,
toward=com,
white_bg=opt.white_bg)
rs, names = coots.r3d_script(center=b,
toward=com,
blobname='%sblob%s' % (prefix, n + 1))
script += rs
basenames += names
coot_job = wf.coot_py(script)
try:
coot_job.run()
except workflow.JobError:
# check for a possible cause to hint the user
# (possible workaround: change $HOME to non-existing directory)
if utils.silently_run(coot_job.args, cwd=wf.output_dir)[0] != 0:
put_error('coot fails with options: --no-graphics --python',
comment='It happens when scripts in .coot or '
'.coot-preferences are not compatible\n'
'with the --no-graphics mode.')
raise
for n, basename in enumerate(basenames):
try:
job = wf.render_r3d(basename, img_format=opt.img_format)
if n % 3 == 0:
job.run()
else: # minimal output
job.run(show_progress=False, new_line=False)
wf.delete_files([basename + '.r3d'])
except workflow.JobError as e:
# Raster3D may fail saying "increase MAXDET and recompile".
# This is not critical, so Dimple doesn't stop.
put_error('Rendering failed, no picture', comment=' ' + e.note)
return coot_sh_path
def dimple(wf, opt):
comment(' ### Dimple v%s. Problems and suggestions:'
' ccp4.github.io/dimple ###' % __version__)
mtz_meta = wf.read_mtz_metadata(opt.mtz)
_comment_summary_line('MTZ (%.1fA)' % mtz_meta.dmax, mtz_meta)
if opt.dls_naming:
opt.pdbs = dls_name_filter(opt.pdbs)
opt.pdbs = utils.filter_out_duplicate_files(opt.pdbs, relto=opt.output_dir)
if not opt.pdbs:
comment('\nNo non-empty pdb files given. Nothing to do.')
return
for p in opt.pdbs:
wf.read_pdb_metadata(p, print_errors=(len(opt.pdbs) > 1))
if len(opt.pdbs) > 1:
comment('\nPDBs in order of similarity (using the first one):')
opt.pdbs.sort(
key=lambda x: calculate_difference(wf.file_info[x], mtz_meta))
utils.log_value('data_file', opt.mtz)
utils.log_value('pdb_files', opt.pdbs)
for p in opt.pdbs:
_comment_summary_line(os.path.basename(p), wf.file_info[p])
ini_pdb = 'ini.pdb'
wf.copy_uncompressed(opt.pdbs[0], ini_pdb)
pdb_meta = wf.file_info[opt.pdbs[0]]
if pdb_meta is None:
put_error('PDB file missing CRYST1 record, starting from MR')
if opt.no_hetatm or check_hetatm_x(wf.path(ini_pdb), pdb_meta):
if not opt.no_hetatm:
comment('\nHETATM marked as element X would choke many programs.')
rb_xyzin = 'prepared.pdb'
wf.temporary_files.add(rb_xyzin)
n_het = wf.remove_hetatm(xyzin=ini_pdb,
xyzout=rb_xyzin,
remove_all=opt.no_hetatm)
comment('\nRemoved %d HETATM atoms' % n_het)
else:
rb_xyzin = ini_pdb
# run rwcontents even without CRYST1 - it will show mol. weight only
wf.rwcontents(xyzin=rb_xyzin).run()
rw_data = wf.jobs[-1].data
if pdb_meta is None:
pass # we already had a warning message
elif rw_data.get('solvent_percent') is None:
put_error('rwcontents could not interpret %s' % rb_xyzin)
elif rw_data['solvent_percent'] > HIGH_SOLVENT_PCT:
comment('\nHmm... %.1f%% of solvent or incomplete model' %
rw_data['solvent_percent'])
if abs(wf.jobs[-1].data.get('volume', 0) - pdb_meta.get_volume()) > 10:
comment('\ndebug: problem when calculating volume?')
####### pointless - reindexing #######
if match_symmetry(mtz_meta, pdb_meta) and opt.mr_when_r > 0 and (
0.7 < mtz_meta.get_volume() / pdb_meta.get_volume() < 1.4):
reindexed_mtz = 'pointless.mtz'
wf.temporary_files.add(reindexed_mtz)
wf.pointless(hklin=opt.mtz,
xyzin=rb_xyzin,
hklout=reindexed_mtz,
keys='TOLERANCE 5').run(may_fail=True)
alt_reindex = wf.jobs[-1].data.get('alt_reindex')
if wf.jobs[-1].exit_status == 0 and alt_reindex:
for ar in alt_reindex:
comment('\n %-10s CC: %-8.3f cell diff: %.1fA' %
(ar['op'], ar['cc'], ar['cell_deviat']))
else:
# until recently (2015) pointless didn't print CC for non-ambiguous
# spacegroups (e.g. C2), but now it always prints
comment('\n no good indexing')
reindexed_mtz = opt.mtz
else:
reindexed_mtz = opt.mtz
reindexed_mtz_meta = wf.read_mtz_metadata(reindexed_mtz)
if reindexed_mtz_meta.symmetry != mtz_meta.symmetry:
_comment_summary_line('reindexed MTZ', reindexed_mtz_meta)
####### (c)truncate - calculate amplitudes if needed #######
if not opt.fcolumn:
opt.fcolumn = 'F' if 'F' in mtz_meta.columns else 'FP'
elif opt.icolumn or opt.ItoF_prog:
put_error('Ignoring options --fcolumn/--sigfcolumn')
opt.sigfcolumn = opt.sigfcolumn.replace('<FCOL>', opt.fcolumn)
if (opt.ItoF_prog or opt.icolumn or opt.fcolumn not in mtz_meta.columns
or opt.sigfcolumn not in mtz_meta.columns):
f_mtz = 'amplit.mtz'
wf.temporary_files.add(f_mtz)
i_sigi_cols = _find_i_sigi_columns(mtz_meta, opt)
if opt.ItoF_prog == 'ctruncate' or (opt.ItoF_prog is None
and opt.slow):
colano = None
if opt.anode and all(
col in mtz_meta.columns
for col in ['I(+)', 'SIGI(+)', 'I(-)', 'SIGI(-)']):
colano = '/*/*/[I(+),SIGI(+),I(-),SIGI(-)]'
wf.ctruncate(hklin=reindexed_mtz,
hklout=f_mtz,
colin='/*/*/[%s,%s]' % i_sigi_cols,
colano=colano).run()
else:
wf.truncate(hklin=reindexed_mtz,
hklout=f_mtz,
labin='IMEAN=%s SIGIMEAN=%s' % i_sigi_cols,
labout='F=F SIGF=SIGF').run()
opt.fcolumn = 'F'
opt.sigfcolumn = 'SIGF'
else:
f_mtz = reindexed_mtz
####### rigid body - check if model is good for refinement? #######
refmac_labin_nofree = 'FP=%s SIGFP=%s' % (opt.fcolumn, opt.sigfcolumn)
refmac_xyzin = None
cell_diff = calculate_difference(pdb_meta, reindexed_mtz_meta)
if pdb_meta is None:
pass # the error message was already printed
elif opt.mr_when_r <= 0:
comment('\nMR requested unconditionally.')
elif cell_diff > 0.1 and opt.mr_when_r < 1:
comment('\nDifferent unit cells.')
elif pdb_meta.symmetry != reindexed_mtz_meta.symmetry:
comment('\nDifferent space groups.')
else:
comment('\nRigid-body refinement with resolution 3.5 A, %d cycles.' %
opt.rigid_cycles)
if 'aa_count' in rw_data and 'water_count' in rw_data:
if rw_data['aa_count'] != 0:
comment(' %.1f waters/aa.' %
(rw_data['water_count'] / rw_data['aa_count']))
else:
comment(' %d/0 waters/aa.' % rw_data['water_count'])
wf.temporary_files |= {'refmacRB.pdb', 'refmacRB.mtz'}
# it may fail because of "Disagreement between mtz and pdb"
wf.refmac5(hklin=f_mtz,
xyzin=rb_xyzin,
hklout='refmacRB.mtz',
xyzout='refmacRB.pdb',
labin=refmac_labin_nofree,
libin=None,
keys="""refinement type rigidbody resolution 15 3.5
rigidbody ncycle %d""" %
opt.rigid_cycles).run(may_fail=True)
# if the error is caused by mtz/pdb disagreement, continue with MR
if wf.jobs[-1].exit_status != 0:
comment('\nTry MR.')
elif not wf.jobs[-1].data.get('overall_r'):
comment('\nWARNING: unknown R factor, something went wrong.\n')
refmac_xyzin = 'refmacRB.pdb'
elif wf.jobs[-1].data['overall_r'] > opt.mr_when_r:
comment('\nRun MR for R > %g.' % opt.mr_when_r)
else:
comment('\nNo MR for R < %g.' % opt.mr_when_r)
refmac_xyzin = 'refmacRB.pdb'
####### phaser/molrep - molecular replacement #######
if refmac_xyzin is None:
vol_ratio = None
if pdb_meta:
# num_mol accounts for strict NCS (MTRIX without iGiven)
vol_ratio = (mtz_meta.asu_volume() /
pdb_meta.asu_volume(rw_data['num_mol']))
comment(' Volume of asu: %.1f%% of model asu.' % (100 * vol_ratio))
if opt.mr_when_r >= 1:
comment('\nWould try MR, but it is disabled.')
return
if opt.mr_num:
mr_num = opt.mr_num
else:
mr_num = guess_number_of_molecules(mtz_meta, rw_data, vol_ratio)
mw = rw_data.get('weight')
if isinstance(mr_num, float):
wf.ensembler(pdbin=rb_xyzin, root='ens').run()
n_models = len(wf.jobs[-1].data['models'])
mw = None
rb_xyzin = 'ens_merged.pdb'
mr_num = max(int(round(mr_num * n_models)), 1)
# phaser is used by default if number of searched molecules is known
if opt.mr_prog == 'molrep':
wf.temporary_files |= {
'molrep.pdb', 'molrep_dimer.pdb', 'molrep.crd'
}
wf.molrep(f=f_mtz, m=rb_xyzin).run()
refmac_xyzin = 'molrep.pdb'
else:
wf.temporary_files |= {'phaser.1.pdb', 'phaser.1.mtz'}
wf.phaser_auto(hklin=f_mtz,
labin='F=%s SIGF=%s' %
(opt.fcolumn, opt.sigfcolumn),
model=dict(pdb=rb_xyzin,
identity=100,
num=mr_num,
mw=mw),
sg_alt='ALL',
opt=opt,
root='phaser').run(may_fail=True)
if not _after_phaser_comments(wf.jobs[-1],
sg_in=reindexed_mtz_meta.symmetry):
raise RuntimeError('No phaser solution.')
refmac_xyzin = 'phaser.1.pdb'
f_mtz = 'phaser.1.mtz'
if False:
wf.findwaters(pdbin=refmac_xyzin,
hklin=f_mtz,
f='FC',
phi='PHIC',
pdbout='prepared_wat.pdb',
sigma=2)
refmac_xyzin = 'prepared_wat.pdb'
####### adding free-R flags #######
f_mtz_meta = wf.read_mtz_metadata(f_mtz)
cad_reso = opt.reso or (f_mtz_meta.dmax - MtzMeta.d_eps)
if opt.free_r_flags:
free_mtz = opt.free_r_flags
free_col = check_freerflags_column(wf.path(free_mtz),
expected_symmetry=pdb_meta,
column=opt.freecolumn)
comment('\nFree-R flags from the %s file, column %s.' %
(('reference' if free_mtz != opt.mtz else 'input'), free_col))
else:
free_col = DEFAULT_FREE_COLS[0]
if free_col in f_mtz_meta.columns:
comment('\nReplace free-R flags')
else:
comment('\nGenerate free-R flags')
free_mtz = 'free.mtz'
wf.temporary_files |= {'unique.mtz', free_mtz}
if opt.seed_freerflag or cell_diff > 1e3: # i.e. different SG
wf.unique(hklout='unique.mtz', ref=f_mtz_meta,
resolution=cad_reso).run()
else:
comment(' (repeatably)')
# Here we'd like to have always the same set of free-r flags
# for given PDB file. That's why we don't use information
# from the data file (mtz).
wf.unique(hklout='unique.mtz', ref=pdb_meta, resolution=1.0).run()
# CCP4 freerflag uses always the same pseudo-random sequence by default
wf.freerflag(hklin='unique.mtz',
hklout=free_mtz,
keys=('SEED' if opt.seed_freerflag else '')).run()
if free_mtz == opt.mtz and opt.reso is None:
prepared_mtz = f_mtz
else:
prepared_mtz = 'prepared.mtz'
wf.temporary_files.add(prepared_mtz)
wf.cad(
data_in=[(f_mtz, [c for c in f_mtz_meta.columns if c != free_col]),
(free_mtz, [free_col])],
hklout=prepared_mtz,
keys=[
'sysab_keep', # does it matter?
'reso overall 1000.0 %g' % cad_reso
]).run()
freerflag_missing = wf.count_mtz_missing(prepared_mtz, free_col)
if freerflag_missing:
wf.freerflag(hklin=prepared_mtz,
hklout='prepared2.mtz',
keys='COMPLETE FREE=' + free_col,
parser=' (again, for %d refl. more)' %
freerflag_missing).run()
prepared_mtz = 'prepared2.mtz'
wf.temporary_files.add(prepared_mtz)
####### refinement #######
if opt.weight:
refmac_weight = 'matrix %f' % opt.weight
else:
refmac_weight = 'auto'
restr_ref_keys = """\
make newligand continue
refinement type restrained
weight %s
""" % refmac_weight
if opt.freecolumn_val:
restr_ref_keys += 'free %s\n' % opt.freecolumn_val
refmac_labin = '%s FREE=%s' % (refmac_labin_nofree, free_col)
comment('\nRestrained refinement, %d+%d cycles.' %
(opt.jelly, opt.restr_cycles))
if opt.jelly:
wf.temporary_files |= {'jelly.pdb', 'jelly.mtz'}
wf.refmac5(hklin=prepared_mtz,
xyzin=refmac_xyzin,
hklout='jelly.mtz',
xyzout='jelly.pdb',
labin=refmac_labin,
libin=opt.libin,
keys=restr_ref_keys + 'ridge distance sigma 0.01\n'
'make hydrogen no\n'
'ncycle %d' % opt.jelly + opt.extra_ref_keys).run()
comment(_refmac_rms_line(wf.jobs[-1].data))
refmac_xyzin = 'jelly.pdb'
restr_job = wf.refmac5(
hklin=prepared_mtz,
xyzin=refmac_xyzin,
hklout=opt.hklout,
xyzout=opt.xyzout,
labin=refmac_labin,
libin=opt.libin,
keys=(restr_ref_keys + 'ncycle %d' % opt.restr_cycles +
opt.extra_ref_keys)).run()
comment(_refmac_rms_line(restr_job.data))
# if that run is repeated with --from-step it's useful to compare Rfree
if wf.from_job > 0 and wf.from_job <= len(wf.jobs): # from_job is 1-based
prev = [j for j in wf.repl_jobs if j.name == restr_job.name]
if prev and prev[0].data and 'free_r' in prev[0].data:
comment('\nPreviously: R/Rfree %.4f/%.4f Rfree change: %+.4f' %
(prev[0].data['overall_r'], prev[0].data['free_r'],
restr_job.data['free_r'] - prev[0].data['free_r']))
####### check blobs #######
if opt.blob_search:
if restr_job.data['free_r'] <= BAD_FINAL_RFREE:
fb_job = wf.find_blobs(opt.hklout, opt.xyzout, sigma=0.8).run()
coot_script = _generate_scripts_and_pictures(wf, opt, fb_job.data)
if coot_script:
comment('\nTo see it in Coot run %s' % coot_script)
else:
comment('\nNo blob search for Rfree > %g.' % BAD_FINAL_RFREE)
_generate_scripts_and_pictures(wf, opt, None)
if opt.anode:
# check if mtz contains I+/- and SIGI+/-
column_types = list(reindexed_mtz_meta.columns.values())
if column_types.count('K') != 2 and column_types.count('M') != 2:
comment('\nColumns I+/- and SIG+/- not found. Skipping AnoDe.')
return
anode_name = 'anode'
# convert to sca for input to shelxc
scaout = anode_name + '.sca'
wf.mtz2sca(prepared_mtz, scaout).run()
wf.shelxc(scaout, reindexed_mtz_meta.cell,
reindexed_mtz_meta.symmetry).run()
wf.copy_uncompressed(opt.xyzout, anode_name + '.pdb')
anode_job = wf.anode(anode_name).run()
wf.temporary_files |= {
scaout, anode_name + '.pdb', anode_name + '.hkl',
anode_name + '.pha', anode_name + '_sad.cif',
anode_name + '_fa.hkl'
}
cell = Cell(reindexed_mtz_meta.cell, reindexed_mtz_meta.symmetry)
# need orthogonal not fractional coordinates to generate coot script
anode_job.data['blobs'] = cell.orthogonalize(anode_job.data['xyz'])
comment(_anode_anom_peak_lines(anode_job.data))
coot_script = _generate_scripts_and_pictures(wf,
opt,
anode_job.data,
pha=anode_name + '.pha')
def dimple(wf, opt):
comment(" ### Dimple v%s. Problems and suggestions:"
" ccp4.github.io/dimple ###" % __version__)
mtz_meta = wf.read_mtz_metadata(opt.mtz)
_comment_summary_line("MTZ (%.1fA)" % mtz_meta.dmax, mtz_meta)
if opt.dls_naming:
opt.pdbs = dls_name_filter(opt.pdbs)
opt.pdbs = utils.filter_out_duplicate_files(opt.pdbs, relto=opt.output_dir)
if not opt.pdbs:
comment("\nNo non-empty pdb files given. Nothing to do.")
return
for p in opt.pdbs:
wf.read_pdb_metadata(p, print_errors=(len(opt.pdbs) > 1))
if len(opt.pdbs) > 1:
comment("\nPDBs in order of similarity (using the first one):")
opt.pdbs.sort(key=lambda x: calculate_difference(wf.file_info[x],
mtz_meta))
utils.log_value("data_file", opt.mtz)
utils.log_value("pdb_files", opt.pdbs)
for p in opt.pdbs:
_comment_summary_line(os.path.basename(p), wf.file_info[p])
ini_pdb = "ini.pdb"
wf.copy_uncompressed(opt.pdbs[0], ini_pdb)
pdb_meta = wf.file_info[opt.pdbs[0]]
if pdb_meta is None:
put_error("PDB file missing CRYST1 record, starting from MR")
if opt.no_hetatm or check_hetatm_x(wf.path(ini_pdb), pdb_meta):
if not opt.no_hetatm:
comment("\nHETATM marked as element X would choke many programs.")
rb_xyzin = "prepared.pdb"
wf.temporary_files.add(rb_xyzin)
n_het = wf.remove_hetatm(xyzin=ini_pdb, xyzout=rb_xyzin,
remove_all=opt.no_hetatm)
comment("\nRemoved %d HETATM atoms" % n_het)
else:
rb_xyzin = ini_pdb
# run rwcontents even without CRYST1 - it will show mol. weight only
wf.rwcontents(xyzin=rb_xyzin).run()
rw_data = wf.jobs[-1].data
if pdb_meta is None:
pass # we already had a warning message
elif rw_data.get('solvent_percent') is None:
put_error("rwcontents could not interpret %s" % rb_xyzin)
elif rw_data['solvent_percent'] > HIGH_SOLVENT_PCT:
comment("\nHmm... %.1f%% of solvent or incomplete model" %
rw_data['solvent_percent'])
if abs(wf.jobs[-1].data.get('volume', 0) - pdb_meta.get_volume()) > 10:
comment("\ndebug: problem when calculating volume?")
####### pointless - reindexing #######
if match_symmetry(mtz_meta, pdb_meta) and opt.mr_when_r > 0 and (
0.7 < mtz_meta.get_volume() / pdb_meta.get_volume() < 1.4):
reindexed_mtz = "pointless.mtz"
wf.temporary_files.add(reindexed_mtz)
wf.pointless(hklin=opt.mtz, xyzin=rb_xyzin, hklout=reindexed_mtz,
keys="TOLERANCE 5").run(may_fail=True)
alt_reindex = wf.jobs[-1].data.get('alt_reindex')
if wf.jobs[-1].exit_status == 0 and alt_reindex:
for ar in alt_reindex:
comment("\n %-10s CC: %-8.3f cell diff: %.1fA" % (
ar['op'], ar['cc'], ar['cell_deviat']))
else:
# until recently (2015) pointless didn't print CC for non-ambiguous
# spacegroups (e.g. C2), but now it always prints
comment("\n no good indexing")
reindexed_mtz = opt.mtz
else:
reindexed_mtz = opt.mtz
reindexed_mtz_meta = wf.read_mtz_metadata(reindexed_mtz)
if reindexed_mtz_meta.symmetry != mtz_meta.symmetry:
_comment_summary_line('reindexed MTZ', reindexed_mtz_meta)
####### (c)truncate - calculate amplitudes if needed #######
if not opt.fcolumn:
opt.fcolumn = 'F' if 'F' in mtz_meta.columns else 'FP'
elif opt.icolumn or opt.ItoF_prog:
put_error('Ignoring options --fcolumn/--sigfcolumn')
opt.sigfcolumn = opt.sigfcolumn.replace('<FCOL>', opt.fcolumn)
if (opt.ItoF_prog or opt.icolumn or opt.fcolumn not in mtz_meta.columns
or opt.sigfcolumn not in mtz_meta.columns):
mtz_meta.check_col_type(opt.icolumn or 'IMEAN', 'J')
mtz_meta.check_col_type(opt.sigicolumn, 'Q')
f_mtz = "amplit.mtz"
wf.temporary_files.add(f_mtz)
i_sigi_cols = (opt.icolumn or 'IMEAN', opt.sigicolumn)
if opt.ItoF_prog == 'ctruncate' or (opt.ItoF_prog is None and opt.slow):
wf.ctruncate(hklin=reindexed_mtz, hklout=f_mtz,
colin="/*/*/[%s,%s]" % i_sigi_cols).run()
else:
wf.truncate(hklin=reindexed_mtz, hklout=f_mtz,
labin="IMEAN=%s SIGIMEAN=%s" % i_sigi_cols,
labout="F=F SIGF=SIGF").run()
opt.fcolumn = 'F'
opt.sigfcolumn = 'SIGF'
else:
f_mtz = reindexed_mtz
####### rigid body - check if model is good for refinement? #######
refmac_labin_nofree = "FP=%s SIGFP=%s" % (opt.fcolumn, opt.sigfcolumn)
refmac_xyzin = None
cell_diff = calculate_difference(pdb_meta, reindexed_mtz_meta)
if pdb_meta is None:
pass # the error message was already printed
elif opt.mr_when_r <= 0:
comment("\nMR requested unconditionally.")
elif cell_diff > 0.1 and opt.mr_when_r < 1:
comment("\nDifferent unit cells.")
elif pdb_meta.symmetry != reindexed_mtz_meta.symmetry:
comment("\nDifferent space groups.")
else:
comment("\nRigid-body refinement with resolution 3.5 A, 10 cycles.")
if 'aa_count' in rw_data and 'water_count' in rw_data:
comment(" %.1f waters/aa." % (rw_data['water_count'] /
rw_data['aa_count']))
wf.temporary_files |= {"refmacRB.pdb", "refmacRB.mtz"}
# it may fail because of "Disagreement between mtz and pdb"
wf.refmac5(hklin=f_mtz, xyzin=rb_xyzin,
hklout="refmacRB.mtz", xyzout="refmacRB.pdb",
labin=refmac_labin_nofree,
libin=None,
keys="""refinement type rigidbody resolution 15 3.5
rigidbody ncycle 10""").run(may_fail=True)
# if the error is caused by mtz/pdb disagreement, continue with MR
if wf.jobs[-1].exit_status != 0:
comment("\nTry MR.")
elif not wf.jobs[-1].data.get("overall_r"):
comment("\nWARNING: unknown R factor, something went wrong.\n")
refmac_xyzin = "refmacRB.pdb"
elif wf.jobs[-1].data["overall_r"] > opt.mr_when_r:
comment("\nRun MR for R > %g." % opt.mr_when_r)
else:
comment("\nNo MR for R < %g." % opt.mr_when_r)
refmac_xyzin = "refmacRB.pdb"
####### phaser/molrep - molecular replacement #######
if refmac_xyzin is None:
vol_ratio = None
if pdb_meta:
# num_mol accounts for strict NCS (MTRIX without iGiven)
vol_ratio = (mtz_meta.asu_volume() /
pdb_meta.asu_volume(rw_data['num_mol']))
comment(" Volume of asu: %.1f%% of model asu." % (100 * vol_ratio))
if opt.mr_when_r >= 1:
comment("\nWould try MR, but it is disabled.")
return
if opt.mr_num:
mr_num = opt.mr_num
else:
mr_num = guess_number_of_molecules(mtz_meta, rw_data, vol_ratio)
mw = rw_data.get('weight')
if isinstance(mr_num, float):
wf.ensembler(pdbin=rb_xyzin, root='ens').run()
n_models = len(wf.jobs[-1].data['models'])
mw = None
rb_xyzin = "ens_merged.pdb"
mr_num = max(int(round(mr_num * n_models)), 1)
# phaser is used by default if number of searched molecules is known
if opt.mr_prog == 'molrep':
wf.temporary_files |= {"molrep.pdb", "molrep_dimer.pdb",
"molrep.crd"}
wf.molrep(f=f_mtz, m=rb_xyzin).run()
refmac_xyzin = "molrep.pdb"
else:
wf.temporary_files |= {"phaser.1.pdb", "phaser.1.mtz"}
wf.phaser_auto(hklin=f_mtz,
labin="F=%s SIGF=%s" % (opt.fcolumn, opt.sigfcolumn),
model=dict(pdb=rb_xyzin, identity=100, num=mr_num,
mw=mw),
sg_alt="ALL", opt=opt,
root='phaser').run(may_fail=True)
if not _after_phaser_comments(wf.jobs[-1],
sg_in=reindexed_mtz_meta.symmetry):
return
refmac_xyzin = "phaser.1.pdb"
f_mtz = "phaser.1.mtz"
if False:
wf.findwaters(pdbin=refmac_xyzin, hklin=f_mtz,
f="FC", phi="PHIC", pdbout="prepared_wat.pdb", sigma=2)
refmac_xyzin = "prepared_wat.pdb"
####### adding free-R flags #######
f_mtz_meta = wf.read_mtz_metadata(f_mtz)
cad_reso = opt.reso or (f_mtz_meta.dmax - MtzMeta.d_eps)
if opt.free_r_flags:
free_mtz = opt.free_r_flags
free_col = check_freerflags_column(wf.path(free_mtz),
expected_symmetry=pdb_meta,
column=opt.freecolumn)
comment("\nFree-R flags from the %s file, column %s." %
(("reference" if free_mtz != opt.mtz else 'input'), free_col))
else:
free_col = DEFAULT_FREE_COLS[0]
if free_col in f_mtz_meta.columns:
comment("\nReplace free-R flags")
else:
comment("\nGenerate free-R flags")
free_mtz = "free.mtz"
wf.temporary_files |= {"unique.mtz", free_mtz}
if opt.seed_freerflag or cell_diff > 1e3: # i.e. different SG
wf.unique(hklout="unique.mtz", ref=f_mtz_meta,
resolution=cad_reso).run()
else:
comment(" (repeatably)")
# Here we'd like to have always the same set of free-r flags
# for given PDB file. That's why we don't use information
# from the data file (mtz).
wf.unique(hklout="unique.mtz", ref=pdb_meta, resolution=1.0).run()
# CCP4 freerflag uses always the same pseudo-random sequence by default
wf.freerflag(hklin="unique.mtz", hklout=free_mtz,
keys=("SEED" if opt.seed_freerflag else "")).run()
if free_mtz == opt.mtz and opt.reso is None:
prepared_mtz = f_mtz
else:
prepared_mtz = "prepared.mtz"
wf.temporary_files.add(prepared_mtz)
wf.cad(data_in=[(f_mtz,
[c for c in f_mtz_meta.columns if c != free_col]),
(free_mtz, [free_col])],
hklout=prepared_mtz,
keys=["sysab_keep", # does it matter?
"reso overall 1000.0 %g" % cad_reso]).run()
freerflag_missing = wf.count_mtz_missing(prepared_mtz, free_col)
if freerflag_missing:
wf.freerflag(hklin=prepared_mtz, hklout="prepared2.mtz",
keys="COMPLETE FREE="+free_col,
parser=" (again, for %d refl. more)" % freerflag_missing
).run()
prepared_mtz = "prepared2.mtz"
wf.temporary_files.add(prepared_mtz)
####### refinement #######
if opt.weight:
refmac_weight = "matrix %f" % opt.weight
else:
refmac_weight = "auto"
restr_ref_keys = """\
make newligand continue
refinement type restrained
weight %s
""" % refmac_weight
if opt.freecolumn_val:
restr_ref_keys += "free %s\n" % opt.freecolumn_val
refmac_labin = "%s FREE=%s" % (refmac_labin_nofree, free_col)
comment("\nRestrained refinement, %d+%d cycles." % (opt.jelly,
opt.restr_cycles))
if opt.jelly:
wf.temporary_files |= {"jelly.pdb", "jelly.mtz"}
wf.refmac5(hklin=prepared_mtz, xyzin=refmac_xyzin,
hklout="jelly.mtz", xyzout="jelly.pdb",
labin=refmac_labin, libin=opt.libin,
keys=restr_ref_keys+"ridge distance sigma 0.01\n"
"make hydrogen no\n"
"ncycle %d" % opt.jelly).run()
comment(_refmac_rms_line(wf.jobs[-1].data))
refmac_xyzin = "jelly.pdb"
restr_job = wf.refmac5(hklin=prepared_mtz, xyzin=refmac_xyzin,
hklout=opt.hklout, xyzout=opt.xyzout,
labin=refmac_labin, libin=opt.libin,
keys=restr_ref_keys+("ncycle %d" % opt.restr_cycles)).run()
comment(_refmac_rms_line(restr_job.data))
# if that run is repeated with --from-step it's useful to compare Rfree
if wf.from_job > 0 and wf.from_job <= len(wf.jobs): # from_job is 1-based
prev = [j for j in wf.repl_jobs if j.name == restr_job.name]
if prev and prev[0].data and "free_r" in prev[0].data:
comment("\nPreviously: R/Rfree %.4f/%.4f Rfree change: %+.4f" % (
prev[0].data["overall_r"], prev[0].data["free_r"],
restr_job.data["free_r"] - prev[0].data["free_r"]))
####### check blobs and finish #######
if restr_job.data["free_r"] <= BAD_FINAL_RFREE:
fb_job = wf.find_blobs(opt.hklout, opt.xyzout, sigma=0.8).run()
coot_script = _generate_scripts_and_pictures(wf, opt, fb_job.data)
if coot_script:
comment("\nTo see it in Coot run %s" % coot_script)
else:
comment("\nGiving up (Rfree > %g). No blob search." % BAD_FINAL_RFREE)
_generate_scripts_and_pictures(wf, opt, None)
def _generate_scripts_and_pictures(wf, opt, data):
blobs = data["blobs"] if data else []
if not blobs:
comment("\nUnmodelled blobs not found.")
elif opt.img_format and _check_picture_tools():
if len(blobs) == 1:
comment("\nRendering density blob at (%.1f, %.1f, %.1f)" %
blobs[0])
else:
comment("\nRendering 2 largest blobs: at (%.1f, %.1f, %.1f) "
"and at (%.1f, %.1f, %.1f)" % (blobs[0]+blobs[1]))
com = data and data["center"]
# run-coot.py centers on the biggest blob. It uses relative paths -
# it can be run only from the output directory, but is not affected
# by moving that directory to different location.
# There are blobN-coot.py scripts generated below with absolute paths.
# write coot script (apart from pictures) that centers on the biggest blob
script_path = os.path.join(wf.output_dir, "run-coot.py")
script = coots.basic_script(pdb=opt.xyzout, mtz=opt.hklout,
center=(blobs and blobs[0]), toward=com)
_write_script(script_path, script, executable=True)
# blob images, for now for not more than two blobs
d = os.path.abspath(wf.output_dir)
for n, b in enumerate(blobs[:2]):
py_path = os.path.join(wf.output_dir, "blob%d-coot.py" % (n+1))
content = coots.basic_script(pdb=os.path.join(d, opt.xyzout),
mtz=os.path.join(d, opt.hklout),
center=blobs[n], toward=com)
_write_script(py_path, content)
# coot.sh - one-line script for convenience
if blobs:
coot_sh_text = '{coot} --no-guano {out}/blob1-coot.py\n'
else:
coot_sh_text = '{coot} --no-guano {out}/final.mtz {out}/final.pdb\n'
coot_sh_path = os.path.join(wf.output_dir, "coot.sh")
_write_script(coot_sh_path, coot_sh_text.format(coot=coots.find_path(),
out=wf.output_dir),
executable=True)
if opt.img_format and blobs:
script = ''
basenames = []
# as a workaround for buggy coot the maps are reloaded for each blob
for n, b in enumerate(blobs[:2]):
script += coots.basic_script(pdb=opt.xyzout, mtz=opt.hklout,
center=b, toward=com)
rs, names = coots.r3d_script(b, com, blobname="blob%s"%(n+1))
script += rs
basenames += names
coot_job = wf.coot_py(script)
try:
coot_job.run()
except workflow.JobError:
# check for a possible cause to hint the user
# (possible workaround: change $HOME to non-existing directory)
if utils.silently_run(coot_job.args, cwd=wf.output_dir)[0] != 0:
put_error("coot fails with options: --no-graphics --python",
comment="It happens when scripts in .coot or "
".coot-preferences are not compatible\n"
"with the --no-graphics mode.")
raise
for n, basename in enumerate(basenames):
job = wf.render_r3d(basename, img_format=opt.img_format)
if n % 3 == 0:
job.run()
else: # minimal output
job.run(show_progress=False, new_line=False)
wf.delete_files([name+".r3d" for name in basenames])
return coot_sh_path
