Re: [PyMOL] Normalize ccp4 maps- problem
Hi Vasan, Changing the sampling of the map would require re-calculating it on a different (coarser or finer) grid. This would have only incidental effects on normalizing the map values. Hope this helps, Pete Srinivasan Rengachari wrote: Dear Pymol Users, I am a basic level user of the Pymol. I am trying to make a figure with my ligand showing electron density. In principle, the guide on the pymol wiki works and i get to show the map. But I wanted to lower the sampling of the mesh in the electron density and tried to unset normalizing ccp4 maps before loading the map and the pdb. After this, the isomesh map, mymap.map, 2.0, site, carve=1.6 updates the map but i dont see any electron density mesh on the screen. I request your help regarding this problem. The pymol version is 1.504. Many thanks in anticipation, Vasan -- 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 -- 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] Adding hydrogens
Dear PyMOL list I'm adding hydrogens to a crystal structure. Upon saving, however, I realize all hydrogens have been added to the beginning of the PDB file. Can PyMOL be configured such that the hydrogens are placed at the intuitively appropriate place in the PDB file? Thanks for any hints. Martin -- 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] Adding hydrogens
Hi Martin, do you have retain_order set to 1? This is not the default. Try: unset retain_order save file.pdb Cheers, Thomas Martin Hediger wrote, On 09/25/12 18:24: Dear PyMOL list I'm adding hydrogens to a crystal structure. Upon saving, however, I realize all hydrogens have been added to the beginning of the PDB file. Can PyMOL be configured such that the hydrogens are placed at the intuitively appropriate place in the PDB file? Thanks for any hints. Martin -- 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
[PyMOL] visualising superpositions in pymol
Hi there I am fairly new to pymol and am currently using it to visualise superpositions of 2 protein structures. However, I have noticed that a lot of structural detail is lost in regions where the structures are very similar and - instead of seeing two proteins nicely superimposed - I get fragments or some structural data missing altogether. Is there a way to counteract this problem please? All advice much appreciated!!! -- 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
