[PyMOL] morphing problem
I have two objects of the same protein in different conformational states and I want to show the conformational change using morph. Each object is a homopentamer, chains A-E. However, one object has the chains arranged in a clockwise direction and the second object has them arranged in a counterclockwise direction. When I morph them, I get a wierd twisty thing as a result of chains swapping with one another. I tried to fix this by changing the names of the chains (alter PDB1 and chain B, chain="E" ...and so on) so that now chain names A-E of both PDBs are clockwise. Although I succeed in renaming the chains, this has has no effect on the morphing. SO, I wondered if the segment identifer was the problem. Each chain also has a corresponding segment identifier (for example, originally PDB1/B/B which has now been changed to PDB1/B/E). I tried changing the segment identifier using the same syntax (alter PDB1 and segment B, segment="E"). Although the output message shows "modified 2667 atoms" the segment identifier in the sequencce window does not change and selection of segment E yields nothing and the morphing is unchanged. Sorry for the long narrative, but the main question is: what can I do to make this morphing work? Thanks. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] morphing with heteroatoms
Hi Karthik, Have you tried writing a script based on the "Morphing with Ligand" example? http://wiki.pymol.org/index.php/Morph#Morphing_with_Ligand Cheers, Thomas On 02 Oct 2015, at 09:50, Karthik Rajasekar wrote: > Hello all, > > I am trying to morph two structures using the commercial version of > Pymol. Pymol looses heteroatoms (zinc in my case) while morphing. Is > there any way around this? > > (I tried replacing zinc with water and linking it to the protein using > CONECT - didn't work) > > Thanks for your help. > Karthik -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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] morphing with heteroatoms
Hello all, I am trying to morph two structures using the commercial version of Pymol. Pymol looses heteroatoms (zinc in my case) while morphing. Is there any way around this? (I tried replacing zinc with water and linking it to the protein using CONECT - didn't work) Thanks for your help. Karthik -- ___ 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] morphing 3-states
Hi Jordan, morpheasy creates 30 states, which are mapped to 80 frames (forward play, pause, backward play). If you have multiple conformations, do morphs for each transition and join the results with "create". Consider this example which morphs 1 -> 2 -> 3 -> 1 # align conformations align conf2, conf1 align conf3, conf2 # do the morphs and forget about the movie frames morpheasy conf1, conf2 mstop; mset morpheasy conf2, conf3 mstop; mset morpheasy conf3, conf1 mstop; mset # append morph02 and morph03 to morph01 create morph01, morph02, 0, 31 create morph01, morph03, 0, 61 delete morph02 morph03 # if you want pauses between the morphs, use movie frames mset 1-30 30x10 30-60 60x10 60-90 Hope that helps. Cheers, Thomas On 11/25/2012 02:36 AM, Jordan Willis wrote: > Hi, > > I have 3 different conformations of the same structure and I was > wondering what is the easiest possible way to morph 3 conformations. > > Morpheasy works fantastic for two conformations, and this makes > around 80 frames. I can then reinitialize and do the other two > states. I have no idea how to link the two. > > Does anyone have any ideas or documentation on this? > > Thanks, Jordan -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] morphing 3-states
ImageMagick can easily append/adjoin animated gifs. Roger Rowlett On Nov 24, 2012 8:38 PM, "Jordan Willis" wrote: > Hi, > > I have 3 different conformations of the same structure and I was wondering > what is the easiest possible way to morph 3 conformations. > > Morpheasy works fantastic for two conformations, and this makes around 80 > frames. I can then reinitialize and do the other two states. I have no idea > how to link the two. > > Does anyone have any ideas or documentation on this? > > > Thanks, > Jordan > > > > > > > > -- > Monitor your physical, virtual and cloud infrastructure from a single > web console. Get in-depth insight into apps, servers, databases, vmware, > SAP, cloud infrastructure, etc. Download 30-day Free Trial. > Pricing starts from $795 for 25 servers or applications! > http://p.sf.net/sfu/zoho_dev2dev_nov > ___ > 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 > -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov___ 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] morphing 3-states
Hi, I have 3 different conformations of the same structure and I was wondering what is the easiest possible way to morph 3 conformations. Morpheasy works fantastic for two conformations, and this makes around 80 frames. I can then reinitialize and do the other two states. I have no idea how to link the two. Does anyone have any ideas or documentation on this? Thanks, Jordan -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] 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] morphing
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- -- 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] Morphing with mutations
Dear List, I'd like to morph a series of mutant proteins one into the other. I tried the Morph server and Moviemaker, but both of them cut the side chains of non-matching amino acids to ala. This means that I cannot see any mutations "taking place" in my movies, but only the side chain of the replacing alanines. Do you know, please, any alternative program or trick to transfom the side chain of a residues into its mutated counterpart, please, with a nice and smooth visual effect? Many many thanks, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _ Connect to the next generation of MSN Messenger http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline
Re: [PyMOL] Morphing movie
Hi there... If you want to generate your morph-pdbs with sensible geometry, try this script: http://www.molmovdb.org/molmovdb/morph/download/morph_dist.inp It requires CNS, but if you have start and end, it interpolates smoothly, using all atoms, without distorting geometry of side chains and so on. Can give very nice results, and is fully compatible with pymol. D On 28/02/07, Clara Marco wrote: Hi! I'm trying to build a morphing movie to show the transition between two conformational states of a protein. I've run morphing with program LSQMAN, which has generated intermediate pdb files between start.pdb and end.pdb.The problem is that to avoid geometry distortions I've used a LSQMAN option that only uses CA's and few side chains (selected by proximity of the ligand that induces the conformational change), and now, the intermediate pdbs only have CA's coordinates. Is there any possibility to represent these pdb's with pymol (cartoon/ribbon)? I've tried it but it only represents points/spheres corresponding to the CA's. If not, does anyone know how to calculate morphing intermediate pdb's suitable to be represented with pymol? Thank you very much. Clara Clara Marco-Marin Instituto de Biomedicina de Valencia Consejo Superior de Investigaciones Cientificas C/Jaime Roig, 11 46010 Valencia España - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- --- David Briggs, PhD. Father & Crystallographer www.dbriggs.talktalk.net iChat AIM ID: DBassophile
Re: [PyMOL] Morphing movie
Hi Clara Try set ribbon_trace_atoms, 1 or set cartoon_trace_atoms, 1 Daniel On Wed, 2007-02-28 at 10:10 +0100, Clara Marco wrote: > Hi! > I'm trying to build a morphing movie to show the transition between > two conformational states of a protein. I've run morphing with > program LSQMAN, which has generated intermediate pdb files between > start.pdb and end.pdb.The problem is that to avoid geometry > distortions I've used a LSQMAN option that only uses CA's and few > side chains (selected by proximity of the ligand that induces the > conformational change), and now, the intermediate pdbs only have CA's > coordinates. > Is there any possibility to represent these pdb's with pymol > (cartoon/ribbon)? I've tried it but it only represents points/spheres > corresponding to the CA's. > If not, does anyone know how to calculate morphing intermediate pdb's > suitable to be represented with pymol? > Thank you very much. > Clara > Clara Marco-Marin > Instituto de Biomedicina de Valencia > Consejo Superior de Investigaciones Cientificas > C/Jaime Roig, 11 > 46010 Valencia > España > > > - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.
[PyMOL] Morphing movie
Hi! I'm trying to build a morphing movie to show the transition between two conformational states of a protein. I've run morphing with program LSQMAN, which has generated intermediate pdb files between start.pdb and end.pdb.The problem is that to avoid geometry distortions I've used a LSQMAN option that only uses CA's and few side chains (selected by proximity of the ligand that induces the conformational change), and now, the intermediate pdbs only have CA's coordinates. Is there any possibility to represent these pdb's with pymol (cartoon/ribbon)? I've tried it but it only represents points/spheres corresponding to the CA's. If not, does anyone know how to calculate morphing intermediate pdb's suitable to be represented with pymol? Thank you very much. Clara Clara Marco-Marin Instituto de Biomedicina de Valencia Consejo Superior de Investigaciones Cientificas C/Jaime Roig, 11 46010 Valencia España
Re: [PyMOL] morphing between complexes
unfortunately I've already tried that server and I've seen that also in that case, the ligand is stripped out.I obtain movies with only the protein movements. I don't know if i have problems with my pdbs: I have 245 residues + 1 ligand (246). it has the ATOM and not the HETATM indication, could be this a problem? The server itself doesn't deal with heteroatoms, mostly because it makes dealing with the PDB even more of a nightmare than usual. The underlying CNS input file will handle any ligand you want as long as you have the correct topology and parameter files (e.g. from Gerard Kleywegt's HIC-UP server). I don't know of any program that will morph between *different* ligands, though. You can cheat by using a dummy ligand that has the conserved core, and adding in the rest manually once you have the interpolation. For instance, to show ATP hydrolysis, you use ADP in both PDB files, and later re-insert the original ATP in place of the ADP in the first frame(s). PyMOL makes this very easy. -Nat
Re: [PyMOL] morphing between complexes
Il giorno mar, 28/11/2006 alle 11.22 -0500, matthew.frank...@imclone.com ha scritto: > > Dear Andrea - > > You should try using the Gerstein Morph Server: > http://www.molmovdb.org/molmovdb/morph/ > > The core algorithm uses CNS, so if your structure is parsed properly by > CNS, it should emerge from the server looking OK. You'll get a small movie > back from the server, and you can also ask it to send you the PDB files > used for each frame, so you can make your own movies in Pymol. > Thanks a lot for your reply, unfortunately I've already tried that server and I've seen that also in that case, the ligand is stripped out.I obtain movies with only the protein movements. I don't know if i have problems with my pdbs: I have 245 residues + 1 ligand (246). it has the ATOM and not the HETATM indication, could be this a problem? > For making movies in complicated situations like this, I've usually used > script files to explicitly define each frame of the movie: > > load file1.pdb > (rendering commands) > ray 2400,2400 > png frame1.png > delete file1 > load file2.pdb > etc... > > You get a long script file, but you can use a text editor to copy & paste > the text blocks. I think that the resolution or quality could be a useful setting to add in the program to overcome this "manual" procedure. > > Hope that helps, > Thanks, it helped me Andrea
Re: [PyMOL] morphing between complexes
pymol-users-boun...@lists.sourceforge.net wrote on 11/28/2006 05:25:15 AM: > Hi all, > I'm new to this list and I'm a newbie of Pymol. > I'm trying to do some morphing movies between different complexes (same > protein but different ligands). I'm having troubles cause the morphed > structures (pdbs generated by lsqman (procedure taken by this page > http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html )) partially > lost the informations about the ligands (only the core of the similar > portion of each ligand is mantained, but the substituent are lost). Do > you know if there is a way to solve/overcome this problem? > Another related question is if was possible to set a ray resolution > (let's say ray 2400, 2400) for the creation of all the frames of the > movie (multiple png). I've been able to do that for one frame at time, > manually...is there the possibility to set a different resolution > recursively for all the image creation processes? > Many thanks in advance and sorry for the long message > Andrea > > Dear Andrea - You should try using the Gerstein Morph Server: http://www.molmovdb.org/molmovdb/morph/ The core algorithm uses CNS, so if your structure is parsed properly by CNS, it should emerge from the server looking OK. You'll get a small movie back from the server, and you can also ask it to send you the PDB files used for each frame, so you can make your own movies in Pymol. For making movies in complicated situations like this, I've usually used script files to explicitly define each frame of the movie: load file1.pdb (rendering commands) ray 2400,2400 png frame1.png delete file1 load file2.pdb etc... You get a long script file, but you can use a text editor to copy & paste the text blocks. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
[PyMOL] morphing between complexes
Hi all, I'm new to this list and I'm a newbie of Pymol. I'm trying to do some morphing movies between different complexes (same protein but different ligands). I'm having troubles cause the morphed structures (pdbs generated by lsqman (procedure taken by this page http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html )) partially lost the informations about the ligands (only the core of the similar portion of each ligand is mantained, but the substituent are lost). Do you know if there is a way to solve/overcome this problem? Another related question is if was possible to set a ray resolution (let's say ray 2400, 2400) for the creation of all the frames of the movie (multiple png). I've been able to do that for one frame at time, manually...is there the possibility to set a different resolution recursively for all the image creation processes? Many thanks in advance and sorry for the long message Andrea
