Re: [PyMOL] morphing
Hi Hasan,
if your structures are identical in sequence (same number of atoms), the
direct way for morphing would be to load them into the same object in
two states and then call rigimol.morph, like this:
from epymol import rigimol
cmd.extend('morph', rigimol.morph)
load conf1.pdb, inobj, 1
load conf2.pdb, inobj, 2
morph inobj, outobj, refinement=5
If the sequence is different or one of the structures have missing
atoms, you need to match them before creating the two-state object. I
have a script that does this, see attachment. It provides a morpheasy
command.
import morpheasy
load conf1.pdb
load conf2.pdb
morpheasy conf1, conf2
Hope that helps.
Cheers,
Thomas
Hasan Demirci wrote, On 01/25/12 22:37:
Hi,
In the past I was using rigimol to morph my structures.
I used to follow the path
pymol -qc prepare.pml
pymol -qc rigimol.pml
pymol domains.pml
pymol -qc refine.py
pymol view.pml
I lost my old pml files and in the current pymolv1.5 as far as I can see
rigimol (or any of the pml files) doesn't exist anymore.
I have two structures and they are dramatically different from one
another due to a mutation.
I would be grateful if you can help me with the morphing and refinement
scripts in pymolv1.5 (both windows 64 and/or linux 64 version is fine).
With my very best regards.
Hasan-
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
'''
Simplified morphing workflow
(c) 2011 Thomas Holder
License: BSD-2-Clause
'''
from pymol import cmd
def morpheasy(source, target, source_state=0, target_state=0, name=None,
refinement=5, quiet=1):
'''
DESCRIPTION
Morph source to target, based on sequence alignment
'''
try:
from epymol import rigimol
except ImportError:
print 'No epymol available, please use a Incentive PyMOL build'
return
# arguments
source_state = int(source_state)
target_state = int(target_state)
source_state = int(source_state if source_state 0 else cmd.get('state', source))
target_state = int(target_state if target_state 0 else cmd.get('state', target))
refinement = int(refinement)
quiet = int(quiet)
# temporary objects
# IMPORTANT: cmd.get_raw_alignment does not work with underscore object names!
alnobj = cmd.get_unused_name('_aln')
so_obj = cmd.get_unused_name('source') # see above
ta_obj = cmd.get_unused_name('target') # see above
so_sel = cmd.get_unused_name('_source_sel')
ta_sel = cmd.get_unused_name('_target_sel')
cmd.create(so_obj, source, source_state, 1)
cmd.create(ta_obj, target, target_state, 1)
# align sequence
cmd.align(ta_obj, so_obj, object=alnobj, cycles=0, transform=0,
mobile_state=1, target_state=1)
cmd.select(so_sel, '%s and %s' % (so_obj, alnobj))
cmd.select(ta_sel, '%s and %s' % (ta_obj, alnobj))
alnmap = dict(cmd.get_raw_alignment(alnobj))
alnmap.update(dict((v,k) for (k,v) in alnmap.iteritems()))
# copy source atom identifiers to temporary target
idmap = dict()
cmd.iterate(so_sel, 'idmap[model,index] = (segi,chain,resi,resn,name)',
space={'idmap': idmap})
cmd.alter(ta_sel, '(segi,chain,resi,resn,name) = idmap[alnmap[model,index]]',
space={'idmap': idmap, 'alnmap': alnmap})
# remove unaligned
cmd.remove('%s and not %s' % (so_obj, so_sel))
cmd.remove('%s and not %s' % (ta_obj, ta_sel))
assert cmd.count_atoms(so_obj) == cmd.count_atoms(ta_obj)
cmd.sort(so_obj)
cmd.sort(ta_obj)
# append target to source as 2-state morph-in object
cmd.create(so_obj, ta_obj, 1, 2)
# morph
if name is None:
name = cmd.get_unused_name('morph')
rigimol.morph(so_obj, name, refinement=refinement, async=0)
# clean up
for obj in [alnobj, so_obj, so_sel, ta_obj, ta_sel]:
cmd.delete(obj)
return name
cmd.extend('morpheasy', morpheasy)
--
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[PyMOL] Set values for dihedral angles
Dear PyMol users! I'm looking for the possible way to change some backbone didedral values in my peptide and dont perturbe the secondary structure of the rest of the peptide. E.g I have alpha-helix with sequence x-S-T-G-xI want to make turn motif in the STG tripeptide only by changing dihedral of this amino acids. When I've tried make it by means of DYNOPLOT plugin the rest of the alpha helix was distorded. Is there any possible ways to make this conversion ? James -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Set values for dihedral angles
Hi James, the modeling capabilities of PyMOL are rather limited, there are probably more powerful tools for such tasks. Without guaranty that the result will be reasonable, try this: # lock all but the STG tripeptide protect not pepseq STG # activate sculpting sculpt_activate all set sculpting # switch to edit mode edit_mode Now drag atoms with the mouse or pick bonds and use commands like torsion. Hope that helps. Cheers, Thomas James Starlight wrote, On 01/26/12 13:45: Dear PyMol users! I'm looking for the possible way to change some backbone didedral values in my peptide and dont perturbe the secondary structure of the rest of the peptide. E.g I have alpha-helix with sequence x-S-T-G-xI want to make turn motif in the STG tripeptide only by changing dihedral of this amino acids. When I've tried make it by means of DYNOPLOT plugin the rest of the alpha helix was distorded. Is there any possible ways to make this conversion ? James -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Access to pymolwiki
I am not able to reach the site? Is it down? Troels Emtekær Linnet -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Access to pymolwiki
Hi Troels, I can get to it. Still having problems? Cheers, -- Jason 2012/1/26 Troels Emtekær Linnet tlin...@gmail.com: I am not able to reach the site? Is it down? Troels Emtekær Linnet -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Set values for dihedral angles
James- I think you need to seriously consider using software that's actually designed to compute and refine protein models, such as Modeller. There are forcefield and structural constraints that PyMol is just not designed to do, and your results may not have the scientific validity you require. Jed Thomas Holder wrote: Hi James, the modeling capabilities of PyMOL are rather limited, there are probably more powerful tools for such tasks. Without guaranty that the result will be reasonable, try this: # lock all but the STG tripeptide protect not pepseq STG # activate sculpting sculpt_activate all set sculpting # switch to edit mode edit_mode Now drag atoms with the mouse or pick bonds and use commands like torsion. Hope that helps. Cheers, Thomas James Starlight wrote, On 01/26/12 13:45: Dear PyMol users! I'm looking for the possible way to change some backbone didedral values in my peptide and dont perturbe the secondary structure of the rest of the peptide. E.g I have alpha-helix with sequence x-S-T-G-xI want to make turn motif in the STG tripeptide only by changing dihedral of this amino acids. When I've tried make it by means of DYNOPLOT plugin the rest of the alpha helix was distorded. Is there any possible ways to make this conversion ? James -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Set values for dihedral angles
Dear Thomas, Jed! Firstly, thanks for the advise in further days I'll try Modeller software! But also I've tried to use above advises in PyMol and in general I was satisfy with the results. I have just only several questions 1- What exactly is the Sculpping ? As I've understood its something like real-time minimisation of the edited structure. Is what cases this might be better than rigid rotation\edition of the selected bonds/ angles by mouse-mode editing ? :) 2- I'm looking for the possible way to set the values for psi and phi dihedral-angles. As I understood the commands like torsion or set dihedrals need in the definition of the edited angles. Is there more trivial way to set values for the pre-defined backbone dihedrals like set phi value, sele, 120 ? :) Something like this I can do via DynoPlot plugin where I can move point on the graph wich correspond to the pair of psi-phy angles but I need in more accuracy way to define the exactly values of this dihedrals. Thanks again, James 2012/1/26 Jed Goldstone jedg...@gmail.com James- I think you need to seriously consider using software that's actually designed to compute and refine protein models, such as Modeller. There are forcefield and structural constraints that PyMol is just not designed to do, and your results may not have the scientific validity you require. Jed Thomas Holder wrote: Hi James, the modeling capabilities of PyMOL are rather limited, there are probably more powerful tools for such tasks. Without guaranty that the result will be reasonable, try this: # lock all but the STG tripeptide protect not pepseq STG # activate sculpting sculpt_activate all set sculpting # switch to edit mode edit_mode Now drag atoms with the mouse or pick bonds and use commands like torsion. Hope that helps. Cheers, Thomas James Starlight wrote, On 01/26/12 13:45: Dear PyMol users! I'm looking for the possible way to change some backbone didedral values in my peptide and dont perturbe the secondary structure of the rest of the peptide. E.g I have alpha-helix with sequence x-S-T-G-xI want to make turn motif in the STG tripeptide only by changing dihedral of this amino acids. When I've tried make it by means of DYNOPLOT plugin the rest of the alpha helix was distorded. Is there any possible ways to make this conversion ? James -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Access to pymolwiki
No. :-) Works as a charm now. It was a temporary thing for 10 minutes. Maybe my internet solution from the uni was a little strange. /T 2012/1/27 Jason Vertrees jason.vertr...@schrodinger.com Hi Troels, I can get to it. Still having problems? Cheers, -- Jason 2012/1/26 Troels Emtekær Linnet tlin...@gmail.com: I am not able to reach the site? Is it down? Troels Emtekær Linnet -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
