From: sasi k. <sbk...@gm...> - 2011-12-27 00:37:27
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dear pymol users, i have a homodimer, with two identical monomers. i would like to know the rmsd of each residue in the first monomer with respect to each residue in the second monomer. i guess pair_fit should give the rmsd. is there a better command to look at the per residue rmsd. thank you. sasi |
From: Thomas H. <sp...@us...> - 2011-12-27 10:49:27
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Hi Sasi, for "pair_fit" you have to match all atom pairs manually. I guess what you want is "align" on the full monomers and then "rms_cur" (or just distance measure) on each CA pair. Have a look at the "rmsd_b.py" script from http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ It writes per residue deviation to the b-factor column. Example: fetch 2hv1, async=0 extract mono2, chain B align mono2, 2hv1, cycles=0, object=aln rmsd_b mono2 & aln, 2hv1 & aln iterate mono2 and name CA, print (resi,b) Hope that helps. Cheers, Thomas sasi kodathala wrote, On 12/27/11 01:37: > dear pymol users, > > i have a homodimer, with two identical monomers. i would like to know > the rmsd of each residue in the first monomer with respect to each > residue in the second monomer. > > i guess pair_fit should give the rmsd. > > is there a better command to look at the per residue rmsd. > > thank you. > > sasi -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Oganesyan, V. <Oga...@Me...> - 2011-12-27 16:42:28
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I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to extract the sequence info. I'm typing "save objectname.fasta" in old version and get the fasta file. In 1.4.1 it complains ========================= Traceback (most recent call last): File "C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py", line 254, in parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 535, in save st = _self.get_fastastr(selection) File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 178, in get_fastastr if seq.has_key(obj): AttributeError: 'str' object has no attribute 'has_key' ========================= Is there now a different way of extracting sequence info in PyMOL? Thank you. Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. |
From: Jason V. <jas...@sc...> - 2012-07-24 13:52:24
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Hi Vaheh, Thanks for pointing this out. I just fixed this, am testing, and will push the changes shortly. Cheers, -- Jason On Tue, Dec 27, 2011 at 11:15 AM, Oganesyan, Vaheh <Oga...@me...> wrote: > I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to extract the sequence info. > I'm typing "save objectname.fasta" in old version and get the fasta file. In 1.4.1 it complains > ========================= > Traceback (most recent call last): > File "C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py", line 254, in parse > self.result=apply(layer.kw[0],layer.args,layer.kw_args) > File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 535, in save > st = _self.get_fastastr(selection) > File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 178, in get_fastastr > if seq.has_key(obj): > AttributeError: 'str' object has no attribute 'has_key' > ========================= > > Is there now a different way of extracting sequence info in PyMOL? > > Thank you. > > Vaheh > To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. > > ------------------------------------------------------------------------------ > Write once. Port to many. > Get the SDK and tools to simplify cross-platform app development. Create > new or port existing apps to sell to consumers worldwide. Explore the > Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join > http://p.sf.net/sfu/intel-appdev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Oganesyan, V. <Oga...@Me...> - 2011-12-27 19:20:07
|
Never mind. After restarting the computer fasta file is being written. Vaheh -----Original Message----- From: Oganesyan, Vaheh [mailto:Oga...@Me...] Sent: Tuesday, December 27, 2011 11:16 AM To: pym...@li... Subject: [PyMOL] sequence file extraction I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to extract the sequence info. I'm typing "save objectname.fasta" in old version and get the fasta file. In 1.4.1 it complains ========================= Traceback (most recent call last): File "C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py", line 254, in parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 535, in save st = _self.get_fastastr(selection) File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 178, in get_fastastr if seq.has_key(obj): AttributeError: 'str' object has no attribute 'has_key' ========================= Is there now a different way of extracting sequence info in PyMOL? Thank you. Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. ------------------------------------------------------------------------------ Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. |
From: Stefano M. <s....@un...> - 2012-07-24 10:08:50
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I have got the same problem with pymol 1.5.0.4 and restarting the computer is not fixing it. Any help please? Thanks Stefano Le 27/12/2011 20:19, Oganesyan, Vaheh a écrit : > Never mind. After restarting the computer fasta file is being written. > > Vaheh > > > > > -----Original Message----- > From: Oganesyan, Vaheh [mailto:Oga...@Me...] > Sent: Tuesday, December 27, 2011 11:16 AM > To: pym...@li... > Subject: [PyMOL] sequence file extraction > > I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to extract the sequence info. > I'm typing "save objectname.fasta" in old version and get the fasta file. In 1.4.1 it complains > ========================= > Traceback (most recent call last): > File "C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py", line 254, in parse > self.result=apply(layer.kw[0],layer.args,layer.kw_args) > File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 535, in save > st = _self.get_fastastr(selection) > File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 178, in get_fastastr > if seq.has_key(obj): > AttributeError: 'str' object has no attribute 'has_key' > ========================= > > Is there now a different way of extracting sequence info in PyMOL? > > Thank you. > > Vaheh > To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. > > ------------------------------------------------------------------------------ > Write once. Port to many. > Get the SDK and tools to simplify cross-platform app development. Create > new or port existing apps to sell to consumers worldwide. Explore the > Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join > http://p.sf.net/sfu/intel-appdev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. > > ------------------------------------------------------------------------------ > Write once. Port to many. > Get the SDK and tools to simplify cross-platform app development. Create > new or port existing apps to sell to consumers worldwide. Explore the > Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join > http://p.sf.net/sfu/intel-appdev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Dr. Stefano MARZI UPR 9002 CNRS-ARN Université De Strasbourg IBMC 15 Rue René Descartes 67084 Strasbourg-France Phone +33 (0)3 88417051 Fax: +33 (0)3 88602218 E-mail: s....@ib... http://www-ibmc.u-strasbg.fr/arn/Romby/ |
From: Thomas H. <sp...@us...> - 2012-07-24 11:49:10
|
Hi Stefano, this is a known bug and it has not been fixed yet. A workaround is to only save one object at a time to fasta format. See bug report: http://sourceforge.net/tracker/?func=detail&aid=3466472&group_id=4546&atid=104546 Cheers, Thomas On 07/24/2012 12:08 PM, Stefano Marzi wrote: > I have got the same problem with pymol 1.5.0.4 and restarting the > computer is not fixing it. > > Any help please? > > Thanks > > Stefano > > Le 27/12/2011 20:19, Oganesyan, Vaheh a écrit : >> Never mind. After restarting the computer fasta file is being written. >> >> Vaheh >> >> >> -----Original Message----- >> From: Oganesyan, Vaheh [mailto:Oga...@Me...] >> Sent: Tuesday, December 27, 2011 11:16 AM >> To: pym...@li... >> Subject: [PyMOL] sequence file extraction >> >> I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to extract the sequence info. >> I'm typing "save objectname.fasta" in old version and get the fasta file. In 1.4.1 it complains >> ========================= >> Traceback (most recent call last): >> File "C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py", line 254, in parse >> self.result=apply(layer.kw[0],layer.args,layer.kw_args) >> File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 535, in save >> st = _self.get_fastastr(selection) >> File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 178, in get_fastastr >> if seq.has_key(obj): >> AttributeError: 'str' object has no attribute 'has_key' >> ========================= >> >> Is there now a different way of extracting sequence info in PyMOL? >> >> Thank you. >> >> Vaheh -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Robert C. <rob...@qu...> - 2012-07-24 14:09:27
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Hi Thomas, On Tue, 2012-07-24 12:57 EDT, Thomas Holder <sp...@us...> wrote: > Hi Stefano, > > this is a known bug and it has not been fixed yet. A workaround is to > only save one object at a time to fasta format. > > See bug report: > http://sourceforge.net/tracker/?func=detail&aid=3466472&group_id=4546&atid=104546 Another bug (I guess I should report it via the bug tracker) is that if a structure has multiple conformations (at least at the CA atom), then the residue appears twice in the sequence. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |