Re: [PyMOL] save new coordinate
On Thu, Jul 21, 2011 at 1:21 AM, Thomas Holder spel...@users.sourceforge.net wrote: Hi Lina, transform_by_camera_rotation PyMOLtransform_by_camera_rotation Traceback (most recent call last): File /usr/local/lib/python2.6/dist-packages/pymol/parser.py, line 464, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1, in module NameError: name 'transform_by_camera_rotation' is not defined I don't know how achieve this part. Thanks again with best regards, sorry for not making this clear. You will find in the menu File Run... to run python scripts. Or type into the command line: run transform_by_camera_rotation.py After that, PyMOL knows the transform_by_camera_rotation command. For more details see: http://pymolwiki.org/index.php/Run http://pymolwiki.org/index.php/Running_Scripts Thanks very much for your advice, but I don't know which part is wrong, the new saved one is not the ideal one I wanted, which was supposed to be the one I saw from screen. do I need to modify the transfrom_by_camera_rotation scrips a bit. actually I don't get it very well. Thanks again, Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Best Regards, lina -- 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
[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
[PyMOL] euler-rod axis
hi, from the get_object_matrix output, i can use the euler-rodrigues transformation http://en.wikipedia.org/wiki/Euler%E2%80%93Rodrigues_formula and get the axis and angle of rotation. is there a way to place the axis? perhaps from the translation vector in the matrix? thanks jpd-- 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
