Re: [PyMOL] weird distance measurements when pdb file contains symmetric atoms
Hi Pascal, the problem is that PyMOL looks up atoms by ID, which are not unique in your structure. Possible workarounds: 1) disable dynamic measures: PyMOL unset dynamic_measures 2) assign unique atom IDs: PyMOL stored.ID = 0 PyMOL alter all, ID=stored.ID=stored.ID+1 Cheers, Thomas Pascal Auffinger wrote, On 07/30/12 15:24: Hi, I encounter a weird behavior when I measure distances for atoms in the attached pdb files. The distances that are measured are not associated with the picked atoms but to some that have been generated by using the pymol symmetry options, with segi activated. Any ideas ? Thanks a lot, Pascal -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Help auto interpolate
Hi Anke, we are currently trying to do movies and are running into some problems concerning the “auto interpolate” function of pymol. We realized that camera and molecule positions are always interpolated back to the position of frame 1 at the end of the movie. Autointerpolate is not the problem here. PyMOL likes to show smooth transitions from camera position A to camera position B over the intervening frames. So, the solution to your problem is to make sure there are no intervening frames: save your last camera position in the last frame. # create a 60-frame movie mset 1x60 # setup scene #1 scene 001, store # do something different to setup scene #2 # store scene #2 scene 002, store mview store, 1, scene=001 mview store, 60, scene=002 Now, the movie will not smoothly loop back to camera position 1. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Preparation of the pdb for MD simulation
Dear PyMol users! I have pdb structure wich I'd like to prepare for my MD simulation. In that case this structure consist of some non-standart residue ( chromophore) wich is covalently bonded to the protein's backbone. The main problem is that this structure has some missing residues on both of the C and N termi wich I'd like to rebuild ussing some homology-building teqnique. Could you advise me some web server wich could done such simple task? It's very important that I 'd kile to prevent deletion of the my heteroatomic groups after processing of my pdb into that server ( e.g servers like pdb2pqr delete heteroatomic group after processing ). Thanks for help James -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Ca sphere size from b-factor value
Hi Jason, Thanks -- is there any way to add some limits to the scaling, say to alter the vdw radius from a value of 1 to 5 based on a b-factor range of values? Doug On Jul 31, 2012, at 4:44 PM, Jason Vertrees wrote: Hi Douglas, You can do something as simple as this: # fetch a protein fetch 1ejg, async=0 # show as spheres as spheres, n. CA # set the vdw radii = some factor of the b-factor alter n. CA, vdw=b/5 rebuild Cheers, -- Jason On Tue, Jul 31, 2012 at 3:36 PM, Douglas Kojetin douglas.koje...@gmail.com wrote: Hi All, I would like to set the sphere size for each Ca atom proportional to the b-factor value (the larger the b-factor the larger the sphere size) and also color the sphere based on the b-factor value. Is there an easy way to adjust the sphere size according to b-factor value? Thanks, Doug -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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
