Re: [PyMOL] Dot representation

/ On Dec 30, 2014, at 6:48 PM, Yarrow Madrona acacia.madr...@ucsf.edu wrote: 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

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 acacia.madr...@ucsf.edu wrote: Hi Brenton, I'm pretty sure you have to import python in your

Re: [PyMOL] Scripting attempts

/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Yarrow Madrona, Ph.D. *Postdoctoral Scholar* University of California, San Francisco Department of Pharmaceutical Chemistry Rm N551, 600 16th street San Francisco CA, 94143

[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

[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

[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

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] 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

[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

[PyMOL] trouble with sym exp

of 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

Re: [PyMOL] internal cavity lighting

://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, I saw a post on this sight a while back about how to move the lighting. However, I have not seen any

Re: [PyMOL] internal cavity lighting

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 of an internal cavity. I want the internal cavity to appear

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

/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

[PyMOL] [Pymol] plugins won't intitialize

, 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 -- Yarrow Madrona Graduate Student

[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

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/ On Mar 4, 2013, at 2:37 PM, Yarrow Madrona amadr...@uci.edu wrote: Thank you for your help Thomas, Using

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

/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 chimera you can limit the display surface within 0-X angstrom of a ligand. This allows you to see the surface

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

a 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

[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 Biochemistry Dept

Re: [PyMOL] changing ray_trace_line

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 the outline width of the ray_trace in ray_trace_mode, 1. I want to make it thicker so

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

of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

[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