Re: [PyMOL] Angle between two structure upon alignment
Hi Appu, if I understand you correct then you have a structure with at least two domains. If you align two conformations of that structure, one domain does not get superposed nicely. Right? The psico module provides the command angle_between_domains, which is what you are looking for I guess. Example: (tilted domain spans residues 100 to 150) PyMOL align s1, s2 PyMOL select d1, s1 and resi 100-150 PyMOL select d2, s2 and resi 100-150 PyMOL angle_between_domains d1, d2 This requires numpy and psico installed. Download psico: https://github.com/speleo3/pymol-psico Hope that helps. Cheers, Thomas Appu kumar wrote, On 11/01/12 04:50: Dear user Can you please help me in finding the angle between two structure upon alingment. I have aligned two structure and one structure is not perfectly aligned on other. There is domain of two structure tilting outward upon alignment. IS there any way to find the angle between two structure. Thanks in advances. -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ 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] electron density map
Dear All, I am trying to create a electron density map for the pdb file which is not deposited in RCSB bank, however I do not find any option on http://eds.bmc.uu.se/eds/. Is there any way to get density map for the pdb files which are not deposited in pdb data bank? All the best, Mehdi -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ 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] electron density map
Hi mehdi. Look for inspiration here. http://www.pymolwiki.org/index.php/Dynamic_mesh fetch 1HWK, async=1 fetch 1HWK, 1hwk_map, type=2fofc, async=1 Best Den 01/11/2012 18.09 skrev Mehdi Talebzadeh Farooji mahdi...@yahoo.com: Dear All, I am trying to create a electron density map for the pdb file which is not deposited in RCSB bank, however I do not find any option on http://eds.bmc.uu.se/eds/. Is there any way to get density map for the pdb files which are not deposited in pdb data bank? All the best, Mehdi -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ 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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ 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
