def make_overhead_snapshot(group_name, **kwargs):
"""Make a snapshot of the overhead view."""
sns_this = kwargs.pop('sns')
snaps_drop_dn = kwargs.pop('snapshot_drop')
if kwargs: raise Exception('unprocessed kwargs: %s' % kwargs)
tempdir = get_snapshots_folder(snaps_drop_dn, overwrite_snaps=True)
for sn_this in sns_this:
slice_path = calc_contacts['extras'][sn_this]['slice_path']
if not hasattr(work, 'source'): work.parse_sources()
gro, xtc = [
os.path.join(work.postdir, '%s.%s' % (slice_path, i))
for i in ['gro', 'xtc']
]
tpr = work.source.get_last(sn_this, subtype='tpr')
kwargs_vmdmake = {
'CGBONDSPATH': '/home/share/libs/cg_bonds.tcl',
'GMXDUMP': '/usr/local/gromacs/bin/gmx'
}
frame = 500
view = vmdmake.VMDWrap(site=tempdir,
gro=gro,
xtc=xtc,
tpr=tpr,
frames='',
res=(2000, 2000),
**kwargs_vmdmake)
view.do('load_dynamic', 'standard', 'bonder')
view['snapshot_filename'] = snapshot_namer(sn=sn_this,
frame=frame,
group=group_name)
view.set_color_cursor('black')
view.select(
**{
'protein': 'noh and protein',
'style': 'cartoon',
'structure_color': False,
'goodsell': do_goodsell,
'smooth': False,
'xy': True,
'color_specific': True
})
for resname in lipid_colors.keys():
view.set_color_cursor(lipid_colors[resname])
view.select(
**{
'residue_lipid_%s' % resname: 'noh and resname %s' %
resname,
'goodsell': do_goodsell,
'smooth': False,
'style': licorice_thick,
'color_specific': True,
'xy': True
})
view.command("animate goto %d" % frame)
view.do('reset', 'zview')
view.command('scale by 0.8')
view.do('snapshot')
view.show(quit=True)
def snapshots():
"""Make many snapshots."""
# ongoing
snapshot_batches = {
'v1': {
'sns': sns_contacts,
'snapshot_drop': 'snapshots_overhead'
},
}
# render snapshots and summaries
if 0:
for key, val in snapshot_batches.items():
make_overhead_snapshot(group_name=key, **val)
# combine overhead snapshots
if 0:
replicate_mapping = [
('pip2_20_no_chol', ['mdia2bilayer_nochl2',
'mdia2bilayer_nochl3']),
('pip2_10', ['mdia2bilayer10', 'mdia2bilayer10_2']),
('pip2_20', ['mdia2bilayerphys', 'mdia2bilayerphys2']),
('pip2_30', ['mdia2bilayer30', 'mdia2bilayer30_2'])
]
#! hardcoded
sns = sns_contacts
ncols = 1
group_name = 'v1'
#! frame is fixed
frame = 500
snaps_drop_dn = 'snapshots_overhead'
# plot panels together
figsize = (6, 12)
nrows, ncols = 4, 2
axes, fig = panelplot(layout={
'out': {
'hspace': 0.5,
'wspace': 0.5,
'grid': [1, ncols]
},
'ins': [{
'hspace': 0.0,
'wspace': 0.0,
'grid': [nrows, 1]
} for i in range(len(sns))]
},
figsize=figsize)
for rnum, (name, sns_those) in enumerate(replicate_mapping):
for snum, sn in enumerate(sns_those):
ax = axes[snum][rnum]
tempdir = get_snapshots_folder(snaps_drop_dn,
overwrite_snaps=True)
fn = os.path.join(
work.plotdir, tempdir,
snapshot_namer(sn=sn, group=group_name, frame=frame) +
'.png')
image = scipy.ndimage.imread(fn)
ax.imshow(image)
ax.axis('off')
ax.set_title(work.meta[sn]['label'])
picturesave('fig.snapshots_overhead.%s' % group_name,
directory=work.plotdir,
meta={})
# nice side view of one simulation
if 1:
# one target for the nice rendering
sn_this = 'mdia2bilayerphys'
snaps_drop_dn = 'snapshots_side'
tempdir = get_snapshots_folder(snaps_drop_dn, overwrite_snaps=True)
licorice_thick = 'Licorice 0.5 12.0 12.0'
lipid_colors_full = dict(POPC='gray', **lipid_colors)
alt_views = 'transparent brushedmetal diffuse ghost glass1 glass2 glass3 glossy hardplastic metallicpastel steel translucent edgy edgyshiny edgyglass aoshiny aochalky aoedgy blownglass glassbubble rtchrome'.split(
)
# after doing the survey it looks best with edgy on the outside and maybe
standard_view = ['goodsell', 'aochalky'][-1]
alt_views = ['aochalky']
xres, yres = 2000, 1400
frame = 300
zoom = 2.0
slice_path = calc_contacts['extras'][sn_this]['slice_path']
if not hasattr(work, 'source'): work.parse_sources()
gro, xtc = [
os.path.join(work.postdir, '%s.%s' % (slice_path, i))
for i in ['gro', 'xtc']
]
tpr = work.source.get_last(sn_this, subtype='tpr')
kwargs_vmdmake = {
'CGBONDSPATH': '/home/share/libs/cg_bonds.tcl',
'GMXDUMP': '/usr/local/gromacs/bin/gmx'
}
# loop over alternative view on the sides for comparison representations
for aa, alt_view in enumerate(alt_views):
view = vmdmake.VMDWrap(site=tempdir,
gro=gro,
xtc=xtc,
tpr=tpr,
frames='',
res=(xres, yres),
**kwargs_vmdmake)
view.do('load_dynamic', 'standard', 'bonder')
extra_tag = '.rep_side_%s' % alt_views if len(
alt_views) > 1 else ''
view['snapshot_filename'] = 'snap.side.v1.%s.frame_%d%s' % (
sn_this, frame, extra_tag)
view.set_color_cursor('black')
#! note that we do not plot the proteins in the images so be careful to zoom all the way
view.select(
**{
'protein': 'noh and protein',
'style': licorice_thick,
'structure_color': False,
'smooth': False,
'ystrip': False,
'goodsell': True
})
view.set_color_cursor('black')
view.select(
**{
'protein_cartoon': 'noh and protein',
'style': 'cartoon',
'structure_color': False,
'smooth': False,
'ystrip': False,
'color_specific': True,
'goodsell': True
})
for resname in lipid_colors_full.keys():
view.set_color_cursor(lipid_colors_full[resname])
view.select(
**{
'residue_lipid_%s' % resname: 'noh and resname %s' %
resname,
'smooth': False,
'style': licorice_thick,
standard_view: True,
'color_specific': True
})
view.select(
**{
'residue_lipid_%s_glass' % resname:
'noh and resname %s' % resname,
'style': licorice_thick,
'smooth': False,
alt_view: True,
'color_specific': True,
'ystrip': True
})
view.command("animate goto %d" % frame)
view.command('package require pbctools')
view.command('pbc box -color black')
view.do('reset', 'xview')
view.command('scale by %.2f' % zoom)
view.do('snapshot')
view.show(quit=True)
print('done %d/%d' % (aa, len(alt_views)))
}
#---loop over video styles
for cut_name,cut_spec in film_cuts.items():
#---loop over simulations
for sn in sns_ordered:
#---settings
ptdins_cutoff = 10.0
non_ptdins_atom_names = 'name P or name P3'
ptdins_resname = work.meta[sn]['ptdins_resname']
#---make a video of the nearby PIP2
slice_path = calc['extras'][sn]['slice_path']
gro,xtc = [os.path.join(work.postdir,'%s.%s'%(slice_path,j)) for j in ['gro','xtc']]
tpr = work.raw.get_last(sn,subtype='tpr')
view = vmdmake.VMDWrap(site=tempdir,gro=gro,xtc=xtc,tpr=tpr,
frames='',xres=4000,yres=4000,**kwargs_vmdmake)
view.do('load_dynamic','standard','bonder')
view.select(protein='protein',style='cartoon',structure_color=True,smooth=do_smooth,goodsell=True)
if cut_spec.get('protein_residue_highlight',None):
view.select(lys='protein and (%s)'%' or '.join(['resname %s'%i for i in
cut_spec['protein_residue_highlight']]),
style='licorice',smooth=do_smooth,goodsell=True,resname_color=True)
if cut_spec.get('show_near_ptdins',True):
select_ptdins = ('not hydrogen and (resname %s and '
'same residue as (resname %s and within %.1f of protein))'%(
ptdins_resname,ptdins_resname,ptdins_cutoff))
view.select(near_pip2=select_ptdins,smooth=do_smooth,goodsell=True,style='licorice',update=True)
#---loop over lipids
for lipid_name,lipid_color in lipid_colors.items():
view.set_color_cursor(lipid_color)
if cut_spec['lipid_style']=='phosphate_beads':
def render_lipid_pair(**kwargs):
"""
Abstracted the vmdmake routine for looping.
"""
global special_ion_color
#---default settings
hbond_style = ['dashed','cylinder'][-1]
licorice_thick = 0.4
hbond_cylinder_radius = 0.15
goodsell_ions = False
goodsell_lipids = True
#---unpack the kwargs
sn = kwargs.pop('sn')
frame = kwargs.pop('frame')
tempdir = kwargs.pop('tempdir')
hydrogen_bonds = kwargs.pop('hydrogen_bonds',{})
pair = kwargs.pop('pair',{})
snapshot_fn = kwargs.pop('fn')
associates = kwargs.pop('associates',None)
lipid_color_specific = kwargs.pop('lipid_color_specific',None)
if not pair: raise Exception('render_lipid_pair requires a pair')
gro,xtc,tpr = [kwargs.pop(i) for i in 'gro xtc tpr'.split()]
lipid_atoms = kwargs.pop('lipid_atoms',None)
lipid_style = kwargs.pop('lipid_style',{})
show_water = kwargs.pop('show_water',False)
lipid_colors = kwargs.pop('lipid_colors',False)
if kwargs: raise Exception('unprocessed arguments: %s'%kwargs)
#---run VMD to make the snapshots via vmdmake
view = vmdmake.VMDWrap(site=tempdir,gro=gro,xtc=xtc,tpr=tpr,
frames='',res=(4000,4000),**kwargs_vmdmake)
view.do('load_dynamic','standard','bonder')
view.command("animate goto %d"%(frame))
selections = []
#---change water oxygen color for show_water (starting with v15)
view.command('color Name O pink')
#---show both lipids
sel1 = "(resname %s and resid %s) and not hydrogen"%(pair['resname_1'],pair['resid_1'])
sel2 = "(resname %s and resid %s) and not hydrogen"%(pair['resname_2'],pair['resid_2'])
if lipid_atoms is not None:
sel1 = '(%s) and (%s)'%(sel1,' or '.join(['name %s'%i for i in lipid_atoms]))
sel2 = '(%s) and (%s)'%(sel2,' or '.join(['name %s'%i for i in lipid_atoms]))
selections.append(sel1)
#---disallow the two lipid coloring schemes to work at the same time
if lipid_color_specific and lipid_colors:
raise Exception('incompatible arguments: lipid_color_specific and lipid_colors')
if lipid_color_specific: view.set_color_cursor(lipid_color_specific)
if lipid_colors: view.set_color_cursor(lipid_colors[pair['resname_1']])
view.select(**dictsum({'partner_1':selections[-1],
'style':'Licorice %.3f 12.000000 12.000000'%licorice_thick,'goodsell':goodsell_lipids},lipid_style,
{'color_specific':True} if lipid_color_specific or lipid_colors else {}))
selections.append(sel2)
if lipid_colors: view.set_color_cursor(lipid_colors[pair['resname_2']])
view.select(**dictsum({'partner_2':selections[-1],
'style':'Licorice %.3f 12.000000 12.000000'%licorice_thick,'goodsell':goodsell_lipids},lipid_style,
{'color_specific':True} if lipid_color_specific or lipid_colors else {}))
#---show associates
if associates:
for assoc_num,assoc in enumerate(associates):
if lipid_colors: view.set_color_cursor(lipid_colors[assoc['resname']])
selections.append("(resname %s and resid %s) and not hydrogen"%(assoc['resname'],assoc['resid']))
view.select(**dictsum({'assoc_%d'%assoc_num:selections[-1],'style':
'Licorice %.3f 12.000000 12.000000'%licorice_thick,'goodsell':goodsell_lipids},
{'color_specific':True} if lipid_color_specific or lipid_colors else {}))
#---for each hydrogen bond, show the lipids with the hydrogen (both are plotted to include the bond)
if lipid_color_specific:
view.set_color_cursor(lipid_color_specific)
this_style = dictsum({'style':'Licorice %.3f 12.000000 12.000000'%licorice_thick,
'goodsell':goodsell_lipids},lipid_style,{'color_specific':True} if lipid_color_specific else {})
for hnum,hbond in enumerate(hydrogen_bonds):
#---the first residue in the pair is the donor and we draw it here
selstring = "(resname %s and resid %s)"%(hbond['resname_1'],hbond['resid_1'])
if lipid_atoms is not None:
selstring = '(%s) and (%s)'%(selstring,' or '.join(['name %s'%i for i in lipid_atoms]))
selections.append('(%s and not hydrogen) or (%s and name %s)'%(selstring,selstring,hbond['name_h']))
select_args = dict(**{'partner_1_hbond_%d'%hnum:selections[-1]})
select_args.update(**this_style)
view.select(**select_args)
#---also set the endpoints for the bond itself
#---! currently set for heavy-heavy dashed line below
#view.select(**{'partner_1_hbond_%d_ref'%hnum:'(%s and name %s)'%(selstring,hbond['name_h'])})
view.command('set partner_1_hbond_%d_ref [atomselect top "%s"]'%(
hnum,'(%s and name %s)'%(selstring,hbond['name_1'])))
#---draw the other lipid
selstring = "(resname %s and resid %s)"%(hbond['resname_2'],hbond['resid_2'])
if lipid_atoms is not None:
selstring = '(%s) and (%s)'%(selstring,' or '.join(['name %s'%i for i in lipid_atoms]))
selections.append('(%s and not hydrogen)'%selstring)
select_args = dict(**{'partner_2_hbond_%d'%hnum:selections[-1]})
select_args.update(**this_style)
view.select(**select_args)
view.command('set partner_2_hbond_%d_ref [atomselect top "%s"]'%(
hnum,'(%s and name %s)'%(selstring,hbond['name_2'])))
#---set the selections
#---! debugging this now
view.command('set me [atomselect top "%s"]'%' or '.join(['(%s)'%i for i in selections[:2]]))
#---removed the VMD HBonds call because it is too permissive (allows too many atom types)
#---set selections for the vmd_render_good_side_bond method over a bond (or at least two points)
#---we could use representative points like "C14" or "P" but the conformations are too dynamic
for resid_ind in [1,2]:
view.command("set %s [atomselect top \"(resname %s and resid %s and name %s)\"]"%(
'partner_%d_bead'%resid_ind,pair['resname_%d'%resid_ind],
pair['resid_%d'%resid_ind],pair['name_%d'%resid_ind]))
#---show the good side
view.command(vmd_render_good_side_bond)
#---see vmdmake.py for vmd colors
cation = work.meta[sn].get('cation_relevant',work.meta[sn]['cation'])
#---trying to fix color
#---previously used the special_ion_color when show_water but reverting to original colors for v15
if lipid_colors or (show_water and False): view.set_color_cursor(special_ion_color)
elif show_water: view.set_color_cursor({'MG':'red','Cal':'blue'}.get(cation,'purple'))
else: view.set_color_cursor({'MG':'pink','Cal':'blue','NA':'green','K':'tan'}.get(cation,'purple'))
#---show ions near both residues
for resid_ind in [1,2]:
view.select(**{'near_ions_%d'%resid_ind:
"name %s and within 4.6 of (resname %s and resid %s)"%(
cation,work.meta[sn]['ptdins_resname'],pair['resid_%d'%resid_ind]),
'smooth':False,'style':'VDW 0.4 12.0','goodsell':goodsell_ions,'color_specific':True})
#---option to show waters near the ions
if show_water:
if show_water.get('distance_color',False):
for resid_ind in [1,2]:
view.command('set pivots [atomselect top "[$near_ions_%d text]"]'%resid_ind)
view.command(custom_water_coloring)
#---deprecated method which passed the show water dictionary through to the view select
elif show_water.get('deprecated_method',False):
#---! this representation HAS MAJOR PROBLEMS. cg_bonds.tcl can be used to fix the extralong bonds
#---! ...in PIP2 but it erases the bonds with water. we always just use the VDW representation
#---! ...with large spheres. enormous amount of wasted time trying to fix this annoying bug.
#---! ...need to get some kind of way of loading the TPR natively in VMD
for resid_ind in [1,2]:
view.select(**dictsum({'near_water_near_ions_%d'%resid_ind:
"same residue as (water and within 3.0 of "+
"(name %s and within 4.6 of (resname %s and resid %s)))"%(
cation,work.meta[sn]['ptdins_resname'],pair['resid_%d'%resid_ind]),
'smooth':False,'style':'licorice','goodsell':True},show_water))
#---note that version 8 used normal water coloring but the other colors were not quite right
#---...while version 14 colored waters by distance but probably went out too far
#---deprecated method
elif show_water.get('hydration_shell',False):
for resid_ind in [1,2]:
view.select(**{'near_water_near_ions_%d'%resid_ind:
"same residue as (water and within 3.05 of "+
"(name %s and within 4.6 of (resname %s and resid %s)))"%(
cation,work.meta[sn]['ptdins_resname'],pair['resid_%d'%resid_ind]),
'smooth':False,'style':'licorice','goodsell':True})
else: raise Exception('no valid show_water methods')
#---emphasize the hydrogen bonds
for hnum,hbond in enumerate(hydrogen_bonds):
if hbond_style=='cylinder':
if not show_water: view.command('draw color black')
#---changed cylinder from silver to cyan for v15
else: view.command('draw color iceblue')
view.command(("draw cylinder [expr [$partner_1_hbond_%d_ref get {x y z}]] "+
"[expr [$partner_2_hbond_%d_ref get {x y z}]] radius %.3f")%(
hnum,hnum,hbond_cylinder_radius))
elif hbond_style=='dashed':
view.command(("draw line [expr [$partner_1_hbond_%d_ref get {x y z}]] "+
"[expr [$partner_2_hbond_%d_ref get {x y z}]] style dashed")%(hnum,hnum))
else: raise Exception('unclear hydrogen bond style %s'%hbond_style)
#---render to disk
view['snapshot_filename'] = snapshot_fn
view.do('snapshot')
view.show(quit=True)
gro,xtc = [os.path.join(work.postdir,'%s.%s'%(calc['extras'][sn]['slice_path'],suf))
for suf in ['gro','xtc']]
#---get the tpr from the raw data
tpr = work.raw.get_last(sn,subtype='tpr')
#---precompute snapshot filenames and plot if any are missing
snapshot_fns = [snapshot_namer(sn=work.raw.prefixer(sn_this),tag=tag,pos=pos)
for (sn_this,pos),val in reps.items() if sn_this==sn]
if any([not os.path.isfile(os.path.join(tempdir,i+'.png')) for i in snapshot_fns]):
#---each render needs to start from the beginning because we move things around for the good side
#---loop over desired lipid/frame pairs for rendering
for key in [r for r in reps if r[0]==sn]:
#---run VMD to make the snapshots via vmdmake
view = vmdmake.VMDWrap(site=tempdir,gro=gro,xtc=xtc,tpr=tpr,
frames='',res=(2000,2000),**kwargs_vmdmake)
view.do('load_dynamic','standard','bonder')
val = reps[key]
frame,resid_rel,angle = [val[i] for i in ['frame','resid_rel','theta']]
sn,pos = key
view['snapshot_filename'] = snapshot_namer(sn=work.raw.prefixer(sn),pos=pos,tag=tag)
view.command("set lipids_select [atomselect top \"resname %s\"]"%
work.meta[sn]['ptdins_resname'])
view.command("set my_index [lindex [lsort -unique [$lipids_select get resid]] %d]"%
resid_rel)
headsel = '(%s)'%' or '.join(['name %s'%i for i in work.vars['head_atoms'].split()])
view.select(**{'me':"resname %s and resid $my_index and not hydrogen and %s"%(
work.meta[sn]['ptdins_resname'],headsel),
'smooth':False,'style':'licorice','goodsell':True})
view.command("animate goto %d"%frame)
}
for key in ['ptdins', 'P35P', 'PIPP', 'PIPU', 'SAPI', 'PI2P']:
lipid_colors[key] = 'magenta'
cation_color = 'green'
anion_color = 'gray'
gro, xtc = [
os.path.join(work.postdir,
'%s.%s' % (calc['extras'][sn]['slice_path'], suf))
for suf in ['gro', 'xtc']
]
#---get the tpr from the raw data
tpr = work.raw.get_last(sn, subtype='tpr')
view = vmdmake.VMDWrap(site=work.paths['post_plot_spot'],
gro=gro,
xtc=xtc,
tpr=tpr,
frames='',
res=(4000, 4000))
view['snapshot_filename'] = vmd_fn
view.do('load_dynamic', 'standard', 'bonder')
view.command("animate goto %d" % (frame))
resname = work.meta[sn]['ptdins_resname']
select = {'ptdins': 'resname %s and not hydrogen' % resname}
if do_ptdins_color:
view.set_color_cursor(lipid_colors[resname])
view.select(**dictsum(select, lipid_style, {'color_specific': True}))
else:
view.select(**dictsum(select, lipid_style))
#---show other lipids in their respective colors
for resname in [
i for i in lipid_colors