[PyMOL] RMSD calculation sans alignment
Dear all, I'm attempting to align a series of structures using the CEAlign plug-in in PyMOL due to a lack of any detectable sequence homology. CEAlign does a good job of aligning and the fits are very reasonable. However, the RMSD that is calculated is based only on the c-alphas that were actually aligned, not based on the total number of c-alphas in the structure. After searching online I have been unable to find any software or servers that will simply calculate the RMSD of two structures as is, without aligning them first. I would think this would be a relatively straightforward thing to do, just to calculate RMSD from two existing structures without translation or rotation for alignment. Does anyone know of a way either in PyMOL or in general to simply calculate the RMSD between all c-alphas of two structures? Obviously it won't necessarily be a one-to-one ratio of c-alphas, but I can manually curate the pdb to include only the equivalent and aligned residues, even if not used in the CEAlign algorithm, so that there are the same number of c-alphas in both structures. Thank you for any help and suggestions, Tom -- 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/___ 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] RMSD calculation sans alignment
Tom- Try ProFit http://www.bioinf.org.uk/software/profit/ Jed Thomas Grant wrote: Dear all, I'm attempting to align a series of structures using the CEAlign plug-in in PyMOL due to a lack of any detectable sequence homology. CEAlign does a good job of aligning and the fits are very reasonable. However, the RMSD that is calculated is based only on the c-alphas that were actually aligned, not based on the total number of c-alphas in the structure. After searching online I have been unable to find any software or servers that will simply calculate the RMSD of two structures as is, without aligning them first. I would think this would be a relatively straightforward thing to do, just to calculate RMSD from two existing structures without translation or rotation for alignment. Does anyone know of a way either in PyMOL or in general to simply calculate the RMSD between all c-alphas of two structures? Obviously it won't necessarily be a one-to-one ratio of c-alphas, but I can manually curate the pdb to include only the equivalent and aligned residues, even if not used in the CEAlign algorithm, so that there are the same number of c-alphas in both structures. Thank you for any help and suggestions, Tom -- 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/ ___ 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 -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/ ___ 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] RMSD calculation sans alignment
PyMOL's rms_cur command will do what you want. E.g. fetch 1rx1 fetch 1ra1 # reports Executive: RMS = 34.329 (159 to 159 atoms) # because the structures still need to be translated and rotated rms_cur (1rx1 and name CA), (1ra1 and name CA) # reports Executive: RMS =0.862 (159 to 159 atoms) # because it calculates translated/rotated value, but does now # apply the translation/rotation to the molecules rms (1rx1 and name CA), (1ra1 and name CA) # reports Executive: RMS =0.391 (1026 to 1026 atoms) # standard PyMOL align, which also translates and rotates align 1rx1, 1ra1 # both of these report Executive: RMS =0.862 (159 to 159 atoms) # because the structures have now been translated and rotated rms_cur (1rx1 and name CA), (1ra1 and name CA) rms (1rx1 and name CA), (1ra1 and name CA) Cheers, -Michael On Fri, Jul 22, 2011 at 10:19 AM, Thomas Grant tgr...@hwi.buffalo.eduwrote: Dear all, I'm attempting to align a series of structures using the CEAlign plug-in in PyMOL due to a lack of any detectable sequence homology. CEAlign does a good job of aligning and the fits are very reasonable. However, the RMSD that is calculated is based only on the c-alphas that were actually aligned, not based on the total number of c-alphas in the structure. After searching online I have been unable to find any software or servers that will simply calculate the RMSD of two structures as is, without aligning them first. I would think this would be a relatively straightforward thing to do, just to calculate RMSD from two existing structures without translation or rotation for alignment. Does anyone know of a way either in PyMOL or in general to simply calculate the RMSD between all c-alphas of two structures? Obviously it won't necessarily be a one-to-one ratio of c-alphas, but I can manually curate the pdb to include only the equivalent and aligned residues, even if not used in the CEAlign algorithm, so that there are the same number of c-alphas in both structures. Thank you for any help and suggestions, Tom -- 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/ ___ 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 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) as of August 15th: Department of Physics and Astronomy Earlham College 801 National Road West Richmond, IN 47374-4095 -- 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/___ 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] RMSD calculation sans alignment
Thank you all for your help. Looks like both ProFit and rms_cur will do just what I needed. Thanks! Tom -- Thomas D. Grant Graduate Research Assistant Hauptman-Woodward Medical Research Institute 700 Ellicott St. Buffalo, NY 14203 On Fri, Jul 22, 2011 at 10:59 AM, Michael Lerner mgler...@gmail.com wrote: PyMOL's rms_cur command will do what you want. E.g. fetch 1rx1 fetch 1ra1 # reports Executive: RMS = 34.329 (159 to 159 atoms) # because the structures still need to be translated and rotated rms_cur (1rx1 and name CA), (1ra1 and name CA) # reports Executive: RMS =0.862 (159 to 159 atoms) # because it calculates translated/rotated value, but does now # apply the translation/rotation to the molecules rms (1rx1 and name CA), (1ra1 and name CA) # reports Executive: RMS =0.391 (1026 to 1026 atoms) # standard PyMOL align, which also translates and rotates align 1rx1, 1ra1 # both of these report Executive: RMS =0.862 (159 to 159 atoms) # because the structures have now been translated and rotated rms_cur (1rx1 and name CA), (1ra1 and name CA) rms (1rx1 and name CA), (1ra1 and name CA) Cheers, -Michael On Fri, Jul 22, 2011 at 10:19 AM, Thomas Grant tgr...@hwi.buffalo.eduwrote: Dear all, I'm attempting to align a series of structures using the CEAlign plug-in in PyMOL due to a lack of any detectable sequence homology. CEAlign does a good job of aligning and the fits are very reasonable. However, the RMSD that is calculated is based only on the c-alphas that were actually aligned, not based on the total number of c-alphas in the structure. After searching online I have been unable to find any software or servers that will simply calculate the RMSD of two structures as is, without aligning them first. I would think this would be a relatively straightforward thing to do, just to calculate RMSD from two existing structures without translation or rotation for alignment. Does anyone know of a way either in PyMOL or in general to simply calculate the RMSD between all c-alphas of two structures? Obviously it won't necessarily be a one-to-one ratio of c-alphas, but I can manually curate the pdb to include only the equivalent and aligned residues, even if not used in the CEAlign algorithm, so that there are the same number of c-alphas in both structures. Thank you for any help and suggestions, Tom -- 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/ ___ 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 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) as of August 15th: Department of Physics and Astronomy Earlham College 801 National Road West Richmond, IN 47374-4095 -- 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/___ 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
