Re: [PyMOL] extra bonds
Hi Jianghai, by default PyMOL does a distance based bonding (basically when the VDW radii of two atoms overlap, they get connected). To prevent that, you need two settings: # before saving the correctly bonded but distorted structure set pdb_conect_all # before loading set connect_mode, 1 http://pymolwiki.org/index.php/connect_mode Cheers, Thomas Jianghai Zhu wrote, On 04/30/13 02:39: Hi, In my trajectory movie, there are some minor distortions of some of the residues, but the sticks presentation in pymol seems fine. However, after I loaded the trajectory pdb file use discrete=1, extra bonds would be shown in sticks in those slightly distorted residues. Is there is way to avoid those extra bonds? Thanks a lot. --Jianghai -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ 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] sorting pdb ensembles based on rmsd
Dear PyMol users! I have a set of conformations extracted from the MD trajectory (on the equal time-steps). After loading of all that pdb's into pymol (each conformer= separate pdb file) I want to sort that structures based on the RMSD relative to the reference conformer (e.g step0.pdb ) in the selected range (e.g select and sort only structures with RMSD = 0.5 to the 0.pdb. So if I have 100 conformers I want that pymol select only 5 structures with rmsd (measured by TMalign plugin for instance) to reference equal to 0.5, 1, 1.5, 2.0, 2.5 and 3.0 Angstroms, respectively). Does it possible to make such sorting ? James -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1___ 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] Labels not showing in 1.6
Hi pymolers.
I have this strange problem, that labels
are not showing, unless I use the ray command.
Anyone experience the same?
image1: http://snag.gy/fhk3J.jpg
image2: http://snag.gy/0143z.jpg
fetch 1lev, async=0
preset.publication(selection='all')
remove chain F
select substrates, organic
select f6p, resn F6P
zoom f6p
util.cbac('f6p')
select act_site, byres f6p around 3.5
show sticks, act_site
distance pol_cont, f6p, act_site, mode=2
select cli, /1lev//A/CLI # OR: select cli, resn CLI
select mn, name MN # OR: select mn, symbol Mn # OR: select mn, inorganic
show spheres, mn
label act_site and name CB, resn+resi
zoom pol_cont
viewport 1024,768
bg_color white
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test.pml
Description: Binary data
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