[PyMOL] hydrogen bonds delete
Hi, when I use dist selename, select1, select2, mode=2 which produced one hydroge bond between oxygen of residues with anothe oxygen of phosphate groups. I wonder, Which reason cause dist recognize the O-O forming hydrogen bonds in pymol? Another question, are there some simple ways to just get those contact residues output into a file simply, without examine one by one using eyes. Thanks for any answer, lina -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___ 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] Ray tracing problems
When I ray trace a surface, the colors on the surface appear to have a smaller color depth. In other words, there are finite boundaries between different shades of colors rather than a smooth gradient. Could the problem be color-dependent? Has anyone seen this? Any ideas how to fix it? Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/ -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___ 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] Problems with set solvent_radius
I am trying to change the solvent radius for the surface of about 20 objects in my scene simultaneously. I set solvent_radius, 4 and pymol seems to take the time to do all the calculations, but at the end of the processing the surface only displays for one out of the 20 objects. rebuild does not fix the issue. Any suggestions would be very helpful. -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___ 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
