Re: [PyMOL] morph issues

is still messed up. It > seems to take two of the four chains and rotate them around a circle instead > of morphing them, the other two chains morph okay. > >> On Apr 26, 2016, at 6:29 AM, Honegger Annemarie > <mailto:honeg...@bioc.uzh.ch>> wrote: >> >>

Re: [PyMOL] morph issues

Hi Adam This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the atoms in the two endpoints of the morph. If you eliminate the alternative conformations (remove (not alt “”+A)) or restrict the selection to t

Re: [PyMOL] pymolrc location (harold steinberg)

The dot in .pymolrc is optional - if you prefer to have your pymolrc file visible in the finder, leave out the dot and call the file “pymolrc” - The leading dot is optional, so everything that starts with .pymolrc or pymolrc will be found by PyMOL. Files with dot take precedence over file

Re: [PyMOL] shadows commands

Hi Adam: The commands for shadow rendering are: util.ray_shadows('black') util.ray_shadows('heavy') util.ray_shadows('medium') util.ray_shadows('light') util.ray_shadows('none') How to find out what commands a menu item corresponds to: Set a log file (Pull-down Menu File:Log…). As you select di

Re: [PyMOL] running python scripts from within python loops in a pymol scripts

Yes, this works! Thank you very much for your help! Annemarie > On 01 Apr 2016, at 15:17, David Hall wrote: > > I think you can use cmd.do > > cmd.do("com /DARPin2//A/37-135/CA, object=com2”) > > -David > > >> On Apr 1, 2016, at 8:48

[PyMOL] running python scripts from within python loops in a pymol scripts

Hi! I am trying to automate some model building tasks this loop in my pml script works just fine, it generates models in which two protein domains are joined by a shared helix and highlights backbone steric clashes python for i in range(1, 25): cmd.fit('/DARPin2//C/15-22/CA','/helix1//B/%d

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

Thanks Jared, this worked. Since I only have the extracellular domains of the receptors, i used the center-of-mass of all extracellular domains as one point, and the centre-of-mass of the alpha atoms closest to the membrane for all receptor moleculees as a second point, then shifted copies of

[PyMOL] Transformation of cgo objects

//www.bioc.uzh.ch/plueckthun/nanowelt > > On Mon, Feb 1, 2016 at 10:57 PM, Julian Heinrich wrote: > Hi Annemarie, > > Have you tried the following? > cmd.translate([x,y,z], object='membrane') > > replace x,y,z with your translation vector. > > Cheers,

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

I am trying to show some cell surface receptors and to indicate their position relative to the membrane. I thought to indicate the plane of the membrane by a flat disk, a ago cylinder. x1,y1,z1 = 0, -1, 0 # start point r1,g1,b1 = 1, 1, 0 # color (yellow) x2,y2,z2 = 0, -2, 0 # end point r2,g2,b2

Re: [PyMOL] PyMOL-users Digest, Vol 115, Issue 7

> On Fri, Dec 11, 2015 at 8:19 AM, Smith Liu > wrote: > >> Dear All, >> >> Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close B.pdb >> and have only A.pdb displayed? >> >> Smith >> > > -- > Tsjerk A. Wassenaar, Ph.D. > Date: Fri, 11 Dec 2015 08:53:

Re: [PyMOL] PyMOL-users Digest, Vol 114, Issue 7

I like the way the Protein-Ligand Interaction Profiler (PLIP, https://projects.biotec.tu-dresden.de/plip-web/plip/index , https://pypi.python.org/pypi/plip , http://nar.oxfordjournals.org/content/early/2015/04/14/nar.gkv315.full ) highlights different interactions in its PyMol output file, suc

[PyMOL] creating a virus capsid using supercell.py (Marcelo Marcet)

> Hi Everyone, > > I have been trying to build a virus capsid using pymol. The biological unit > for the complete structure is not available. :( > > My first attempt at getting this done was by using the ?rotate? and > ?translate? commands. Unfortunately, these commands can only move objects >

Re: [PyMOL] PyMOL-users Digest, Vol 107, Issue 14

Hi Wenfu Getting a putty representation out of a series of MD snapshots should be equivalent to producing a putty representation from an NMR ensembles: Multiple models in one pdb files, and you want the putty width to represent the structural variation between the models. This site https://k