[PyMOL] Running pymol without launching window in batch

I'm trying to run pymol in batch mode without launching the window. I am running PyMOL 3.1.1. Here is my code for an example script (test.py). I'm trying to run before running the real script. In the command line I enter: pymol -cq test.py from pymol import cmd import time def main(): print("St

Re: [PyMOL] Scripting attempts

Sorry, I didn't read the other entries. Thanks for the "python end" code. I have had this problem with loops a lot in pymol and this solves it. -Yarrow On Tue, Jan 6, 2015 at 9:21 AM, Yarrow Madrona wrote: > Hi Brenton, > > I'm pretty sure you have to import pyt

Re: [PyMOL] Scripting attempts

el.sourceforge.net > ___ > 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 > -- Yarrow

Re: [PyMOL] Dot representation

ab > NYU Langone Medical Center > http://kong.med.nyu.edu/ > > > > > > > On Dec 30, 2014, at 6:48 PM, Yarrow Madrona > wrote: > > Hell Pymolers, > > 1. Does anyone know what the dot representation for a residue > represents? Is it the van der waals radii? >

[PyMOL] Dot representation

Hell Pymolers, 1. Does anyone know what the dot representation for a residue represents? Is it the van der waals radii? 2. Is there a way to draw transparency for the dots? -Yarrow -- Yarrow Madrona, Ph.D. *Postdoctoral Scholar* University of California, San Francisco Department of

Re: [PyMOL] surface stuck on one color

Hi Pymolers I have solved my problem. I am using surface cavity_mode, 3. I need to change the ray_interior_color instead of the surface color. I guess this is because pymol is visualizing the interior of the surface not the exterior. -Yarrow On Thu, Jul 24, 2014 at 11:08 AM, Yarrow Madrona

[PyMOL] surface stuck on one color

I think the problem may have to do with the surface_cavity_mode being set to 3. I try to change the surface_cavity_mode but I still detect cavities instead of the surface. It seems like any option related to the surface is locked. -Yarrow ---

[PyMOL] surface transparency not chaning

Hello Pymol users, As anyone experienced an instance where the surface transparency remained stuck in one color? I changed it to pink a while back. However, now issuing the comand: set surface_color, green, object1 does nothing. Object1 is the object I want to color. Even if I try to change the

Re: [PyMOL] Portein cross section

Thanks for all of your help. I came out with dome nice figures On Fri, May 30, 2014 at 11:16 AM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > On 30 May 2014, at 14:05, Takanori Nakane wrote: > > However, showing intact spheres above the clip plane for the surface > > can be difficult

[PyMOL] Portein cross section

Hello, I have previously cut my protein in half with a solid cross section using a series of steps (including photoshop) but I am wondering if there is something simpler. I would like to make a figure similar to this: https://www.dropbox.com/s/bxpz6v4xly5fsee/MMI_7243_f6.gif This can be done pr

[PyMOL] script with arguments.

Hello, I am making a script that loads in two molecules as arguments in the command line. I want to then align these molecules and make a pretty picture of the molecules that were input as arguments in the comand line but I am not sure how to name them as objects. I don't know how to select the ne

[PyMOL] trouble with sym exp

pymol? Can I feed it the symmetry operators instead? -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- This

Re: [PyMOL] internal cavity lighting

" and very difficult. Still maybe worth it. -Yarrow > On 13-05-28 14:11, Yarrow Madrona wrote: >> Hi, >> >> I saw a post on this sight a while back about how to move the >> lighting. However, I have not seen any information on how to change >> the lighting

Re: [PyMOL] internal cavity lighting

pymol sponsor, visit this page: > http://pymol.org/dsc/dokuwiki/doku.php?id=media:ambient_occlusion > > Hope that helps. > > Cheers, > Thomas > > Patrice Peterson wrote, On 05/29/13 13:37: >> On 13-05-28 14:11, Yarrow Madrona wrote: >>> Hi, >>>

[PyMOL] internal cavity lighting

coming from inside the object that brightens it up. Does anyone know how to change the internal lighting of a cavity when shown in surface representation? Thanks. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm

[PyMOL] internal surface

help me with this? -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Learn Graph Databases - Download

[PyMOL] trouble with fading for sticks in a movie

but not sure how to implement it in pymol. Thanks! - Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 --

Re: [PyMOL] Can CAVER be run iteratively through a python script?

ing 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 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. Universi

[PyMOL] [Pymol] plugins won't intitialize

p.py", line 320, in initializePlugins mod.__init__(self) TypeError: module.__init__() argument 1 must be string, not instance Error: unable to initialize plugin 'movs'. I guess there is something wrong with the code but this seems strange. It looks o.k. Thanks. -Yarrow -- Ya

[PyMOL] How to ray trace clipped image without clipping spheres.

Hi, Does anyone know how to ray trace an image of an active site in sphere representation that is clipped, without getting a weird result that I assume comes from clipping the spheres? It looks like unfilled circles. Thank you -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and

Re: [PyMOL] [PyMol] How to visualize surface within a given radius

;> -- >> Jared Sampson >> Xiangpeng Kong Lab >> NYU Langone Medical Center >> Old Public Health Building, Room 610 >> 341 East 25th Street >> New York, NY 10016 >> 212-263-7898 >> http://kong.med.nyu.edu/ >> >> >> >> >> O

Re: [PyMOL] [PyMol] How to visualize surface within a given radius

> See also: > http://pymolwiki.org/index.php/Selection_Algebra > Hope that helps. > Cheers, > Thomas > Yarrow Madrona wrote, On 03/03/13 18:34: >> Hello, >> Does anyone know how to visualize a surface within a given radius from a >> ligand binding site? In c

[PyMOL] [PyMol] How to visualize surface within a given radius

new selection of residues around a ligand and show this surface but I wondered if there are any other ways of doing this. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

[PyMOL] How to visualize an active site pocket using specific residues?

Hello, I have some output from the CASTp server-pymol plugin. I have the residues selected surrounding an active site pocket. I would like to make a shape with these atoms as vertices that I can color transparent from the atom selection. Is there a way to do this in pymol? Thank you. -- Yarrow

[PyMOL] ccp4 map sigma setting

Hi, When I display ccp4 maps in pymol they look a bit larger than I am used to seeing in coot for a given sigma setting. Is it common for users to increase the sigma setting when displaying maps in pymol? -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University

Re: [PyMOL] changing ray_trace_line

; -- Jason > > On Thu, May 17, 2012 at 8:46 PM, Yarrow Madrona wrote: >> Hi Thomas, >> >> I have tried this. It works well for sticks but puts a lot of cross >> hatching patterns in the cartoon representation. I would like to >> ray_trace >> a transparen

Re: [PyMOL] changing ray_trace_line

g for the "ray_trace_gain" setting. > > http://pymolwiki.org/index.php/Ray_Trace_Gain > > Cheers, >Thomas > > Yarrow Madrona wrote, On 05/17/12 21:11: >> Hello, >> >> This seems to be a simple problem but I can't figure out how to change >>

[PyMOL] changing ray_trace_line

Hello, This seems to be a simple problem but I can't figure out how to change the outline width of the ray_trace in ray_trace_mode, 1. I want to make it thicker so that when I ray_trace it doesn't look so small. -- Yarrow Madrona Graduate Student Molecular Biology and Biochem

[PyMOL] suface display protein-protein interactions...residues getting bleached.

help me with this. Thanks! Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Benefiting from Server

[PyMOL] installing_running vasco

1 ;3152 ; ; Finish: time:16 sec Thank you for your help. -Yarrow -- Yarrow Madrona Graduate Student Molecu

Re: [PyMOL] Visualizing two surfaces using APB2tools2.1

USD value)! >> Finally, a world-class log management solution at an even better >> price-free! >> Download using promo code Free_Logger_4_Dev2Dev. Offer expires >> February 28th, so secure your free ArcSight L

[PyMOL] Visualizing two surfaces using APB2tools2.1

Hello, Does anyone know how to visualize the surface potentials of two molecules simoutaneously using the APBS Tools2.1 plugin? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA