Re: [ccp4bb] RMSD of dimers
Hi all, Just writing an update, as I have had two people contact me asking if I had found a solution and if I could share. I would like to apologize first for not phrasing my question to describe the situation simply. I had several suggestions that Coot, and PISA could do it but actually can not. Eugene Krissinel rephrased the question brilliantly. What is required, however, is optimal superposition on one pair of chains (one from each dimer) but measuring RMSD on the other pair of chains from same dimers. The solution was given by Thomas Holder and can be done in Pymol: Use rms_cur based on a sequence alignment obtained with align, try: # make sequence alignment object (optional: cycles=0) align A1B1 chain B, A2B2 chain B, object=aln, transform=0 # get current rms for this alignment rms_cur A1B1 aln, A2B2 aln, matchmaker=-1 This will give the RMSD for other pair of chains. Thanks Dan
Re: [ccp4bb] RMSD of dimers
Doesnt pisa give you some of this information? It lists all likely homodimers and I think gives RMSD too Eleanor On 24 February 2015 at 22:00, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Dan, gaps/insertions should be no problem for PyMOL's rms_cur command, as long as chain identifiers match (and all other atomic identifiers!). See http://pymolwiki.org/index.php/Fit for a description of the matchmaker argument. Cheers, Thomas On 24 Feb 2015, at 16:30, D Bonsor dbon...@ihv.umaryland.edu wrote: I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have superimposed using Chain A. Several programs will produce the RMSD of Chain A2, A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain B2, B3, B4... to Chain B1 when I have superimposed the structures relative to Chain A. I have tried using Pymol though there are gaps/insertions so rms/rms_cur will not work. Does anyone else have any other suggestions? Thanks in advance, Dan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
Re: [ccp4bb] RMSD of dimers
No, the question seems to be slightly different. While one can use either CCP4's SSM or GESAMT to superpose 2 dimers, these algorithms would balance RMSD between both chains and produce something optimal for both chains. What is required, however, is optimal superposition on one pair of chains (one from each dimer) but measuring RMSD on the other pair of chains from same dimers. Nothing impossible in principle but no corresponding option in general-purpose aligners (this requires something like masks/selections for residues to superimpose and residues to measure the RMSD on). If this were a common and frequent problem, we could have it implemented in SSM/GESAMT. Eugene On 26/02/2015 12:47, Eleanor Dodson wrote: Doesnt pisa give you some of this information? It lists all likely homodimers and I think gives RMSD too Eleanor On 24 February 2015 at 22:00, Thomas Holder thomas.hol...@schrodinger.com mailto:thomas.hol...@schrodinger.com wrote: Hi Dan, gaps/insertions should be no problem for PyMOL's rms_cur command, as long as chain identifiers match (and all other atomic identifiers!). See http://pymolwiki.org/index.php/Fit for a description of the matchmaker argument. Cheers, Thomas On 24 Feb 2015, at 16:30, D Bonsor dbon...@ihv.umaryland.edu mailto:dbon...@ihv.umaryland.edu wrote: I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have superimposed using Chain A. Several programs will produce the RMSD of Chain A2, A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain B2, B3, B4... to Chain B1 when I have superimposed the structures relative to Chain A. I have tried using Pymol though there are gaps/insertions so rms/rms_cur will not work. Does anyone else have any other suggestions? Thanks in advance, Dan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
Re: [ccp4bb] RMSD of dimers
Oops, sorry: lsqman gives you the rmsd between pairs not moleman. Additional comment: PDBSET should also give you the rmsd between B1 abd B2 using the coordinates generated by lsqman. Phil Philippe BENAS, Ph.D. X-ray diffraction and computing facilities manager Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 De : Philippe BENAS philippe_be...@yahoo.fr À : CCP4BB@JISCMAIL.AC.UK Envoyé le : Jeudi 26 février 2015 15h00 Objet : Re: [ccp4bb] RMSD of dimers Dear CCP4bbers, If I remember correctly you can do this in LSQMAN (EXPLICIT superimposition command if I remember well): the superimposition is made between residues of chain A2 onto those of chain A1, then you apply the rotation/translation to all the A2B2 dimer and moleman gives you the rmsd between the two pairs of dimers. Alternatively, I think LSQMAN allows you to calculate the rmsd between B1 and B2 after having applied the transformation to the all dimer.Have a look on GJK-DVD pages at http://xray.bmc.uu.se/usf/ . And finally isn't Coot doing this as well (using command lines) ? I think I did this once... HTS,Philippe Philippe BENAS, Ph.D. X-ray diffraction and computing facilities manager Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 De : Eugene Krissinel eugene.krissi...@stfc.ac.uk À : CCP4BB@JISCMAIL.AC.UK Envoyé le : Jeudi 26 février 2015 14h17 Objet : Re: [ccp4bb] RMSD of dimers No, the question seems to be slightly different. While one can use either CCP4's SSM or GESAMT to superpose 2 dimers, these algorithms would balance RMSD between both chains and produce something optimal for both chains. What is required, however, is optimal superposition on one pair of chains (one from each dimer) but measuring RMSD on the other pair of chains from same dimers. Nothing impossible in principle but no corresponding option in general-purpose aligners (this requires something like masks/selections for residues to superimpose and residues to measure the RMSD on). If this were a common and frequent problem, we could have it implemented in SSM/GESAMT. Eugene On 26/02/2015 12:47, Eleanor Dodson wrote: Doesnt pisa give you some of this information? It lists all likely homodimers and I think gives RMSD too Eleanor On 24 February 2015 at 22:00, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Dan, gaps/insertions should be no problem for PyMOL's rms_cur command, as long as chain identifiers match (and all other atomic identifiers!). See http://pymolwiki.org/index.php/Fit for a description of the matchmaker argument. Cheers, Thomas On 24 Feb 2015, at 16:30, D Bonsor dbon...@ihv.umaryland.edu wrote: I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have superimposed using Chain A. Several programs will produce the RMSD of Chain A2, A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain B2, B3, B4... to Chain B1 when I have superimposed the structures relative to Chain A. I have tried using Pymol though there are gaps/insertions so rms/rms_cur will not work. Does anyone else have any other suggestions? Thanks in advance, Dan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
Re: [ccp4bb] RMSD of dimers
Dear CCP4bbers, If I remember correctly you can do this in LSQMAN (EXPLICIT superimposition command if I remember well): the superimposition is made between residues of chain A2 onto those of chain A1, then you apply the rotation/translation to all the A2B2 dimer and moleman gives you the rmsd between the two pairs of dimers. Alternatively, I think LSQMAN allows you to calculate the rmsd between B1 and B2 after having applied the transformation to the all dimer.Have a look on GJK-DVD pages at http://xray.bmc.uu.se/usf/ . And finally isn't Coot doing this as well (using command lines) ? I think I did this once... HTS,Philippe Philippe BENAS, Ph.D. X-ray diffraction and computing facilities manager Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 De : Eugene Krissinel eugene.krissi...@stfc.ac.uk À : CCP4BB@JISCMAIL.AC.UK Envoyé le : Jeudi 26 février 2015 14h17 Objet : Re: [ccp4bb] RMSD of dimers No, the question seems to be slightly different. While one can use either CCP4's SSM or GESAMT to superpose 2 dimers, these algorithms would balance RMSD between both chains and produce something optimal for both chains. What is required, however, is optimal superposition on one pair of chains (one from each dimer) but measuring RMSD on the other pair of chains from same dimers. Nothing impossible in principle but no corresponding option in general-purpose aligners (this requires something like masks/selections for residues to superimpose and residues to measure the RMSD on). If this were a common and frequent problem, we could have it implemented in SSM/GESAMT. Eugene On 26/02/2015 12:47, Eleanor Dodson wrote: Doesnt pisa give you some of this information? It lists all likely homodimers and I think gives RMSD too Eleanor On 24 February 2015 at 22:00, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Dan, gaps/insertions should be no problem for PyMOL's rms_cur command, as long as chain identifiers match (and all other atomic identifiers!). See http://pymolwiki.org/index.php/Fit for a description of the matchmaker argument. Cheers, Thomas On 24 Feb 2015, at 16:30, D Bonsor dbon...@ihv.umaryland.edu wrote: I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have superimposed using Chain A. Several programs will produce the RMSD of Chain A2, A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain B2, B3, B4... to Chain B1 when I have superimposed the structures relative to Chain A. I have tried using Pymol though there are gaps/insertions so rms/rms_cur will not work. Does anyone else have any other suggestions? Thanks in advance, Dan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
[ccp4bb] RMSD of dimers
I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have superimposed using Chain A. Several programs will produce the RMSD of Chain A2, A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain B2, B3, B4... to Chain B1 when I have superimposed the structures relative to Chain A. I have tried using Pymol though there are gaps/insertions so rms/rms_cur will not work. Does anyone else have any other suggestions? Thanks in advance, Dan
Re: [ccp4bb] RMSD of dimers
Hi Dan, gaps/insertions should be no problem for PyMOL's rms_cur command, as long as chain identifiers match (and all other atomic identifiers!). See http://pymolwiki.org/index.php/Fit for a description of the matchmaker argument. Cheers, Thomas On 24 Feb 2015, at 16:30, D Bonsor dbon...@ihv.umaryland.edu wrote: I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have superimposed using Chain A. Several programs will produce the RMSD of Chain A2, A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain B2, B3, B4... to Chain B1 when I have superimposed the structures relative to Chain A. I have tried using Pymol though there are gaps/insertions so rms/rms_cur will not work. Does anyone else have any other suggestions? Thanks in advance, Dan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
