Re: [PyMOL] cropping the missing residues from other PDB file
Dear Joyce, It sounds like a question related to homology modeling. You could try http://salilab.org/modeller/download_installation.html or http://swissmodel.expasy.org/. In pymol, this may be a rough way: (1) align B to A, (2) create A_complete, A or ( the missing residues from B), (3) Now you got A_complete with homology residues in B. Mutate the homology residues to the corresponding ones in A. (4) Do some minimization in other molecular modeling software. However, remember that: pymol is a molecular visualization system and is not designed for molecular modeling. Regards, Zhijian Xu Joyce Tan wrote: Hi, A got a PDB file (let's name it A) while has about 90 missing residues. I found the other PDB file (let's name it B) which was from the homolog. Is there any way I could 'crop' the missing residues from B to A? Thanks. -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ 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 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ 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] Generating Image of Periodic System
Dear List I am trying to prepare a figure. I have a protein structure, enclosed by a rectangular box. Is it possible to copy/translate the enboxed structure for a given amount of times? This would end up as something as an illustration of a system with periodic boundaries. I attached a figure on my blog http://qmviews.blogspot.com/. If I cant come up with a PyMOL solution, then I guess I'll just try to find a Python solution. Thanks for any hints on this. -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev___ 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] Generating Image of Periodic System
Hi Martin, have a look at: http://pymolwiki.org/index.php/Supercell Run something like this: supercell 2,2,2, withmates=1 Your structure file needs a CRYST1 record that holds the box dimensions. Cheers, Thomas On 06/14/2011 11:55 AM, Martin Hediger wrote: Dear List I am trying to prepare a figure. I have a protein structure, enclosed by a rectangular box. Is it possible to copy/translate the enboxed structure for a given amount of times? This would end up as something as an illustration of a system with periodic boundaries. I attached a figure on my blog http://qmviews.blogspot.com/. If I cant come up with a PyMOL solution, then I guess I'll just try to find a Python solution. Thanks for any hints on this. -- Thomas Holder MPI for Developmental Biology -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ 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
