[PyMOL] Definition cavities

Dear pymol developers, I am sorry to bother you, but I am just wondering how the cavities is defined when I use the cavity mode of surface representation. Are there any references? Thank you very much and happy holiday, Chen

Re: [PyMOL] Slow Pymol rendering

intended > recipient, immediately contact the sender by reply e-mail and destroy all > copies of the original message. > > > > *From:* Chen Zhao [mailto:chenzhaoh...@gmail.com] > *Sent:* Friday, May 06, 2016 10:50 AM > *To:* pymol-users@lists.sourceforge.net > *Subject

[PyMOL] Slow Pymol rendering

Dear all, I recently upgraded to Debian 8 and I compiled the source code for pymol 1.8.2.0. However, the graphics is really slow. The information that pymol prints out is as follows: Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.30. OpenGL graphics engine:

Re: [PyMOL] Get the color code of each residue when using spectrum?

Dear Tsjerk, I just got a chance to test the code and it works great for me. Now my task becomes to how to convert RGB codes in an efficient way. Anyway, thank you so much! Best, Chen On Sat, Oct 18, 2014 at 2:43 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Ni hao Chen Zhao, This works

Re: [PyMOL] Get the color code of each residue when using spectrum?

://pymolwiki.org/index.php/psico Cheers, Thomas Chen Zhao wrote, On 10/19/14 09:52: Dear Tsjerk, I just got a chance to test the code and it works great for me. Now my task becomes to how to convert RGB codes in an efficient way. Anyway, thank you so much! Best, Chen On Sat, Oct

[PyMOL] Get the color code of each residue when using spectrum?

Dear all, Is it possible to get the color code of each residue if I color the whole molecule by B-factor using spectrum? I would like to make a figure with the same colors on the primary sequence. Thank you so much in advance. Best, Chen

Re: [PyMOL] Slow down the frame rate

I am sorry that I forgot to mention, the reason why I cannot make movie with more frames is that I am working on a morph from an external. That software has a maximum number of frames to output. Thank you, Chen On Fri, Sep 12, 2014 at 4:19 PM, Chen Zhao chenzhaoh...@gmail.com wrote: Dear all

[PyMOL] [Error] Add morph into eMovie

Dear all, I have a problem with adding morph into eMovie. I made a morph between two states using other softwares and load it into pymol by load previously created morph. But when I tried to add morph to eMovie, I got the following error message: Error: 2 type 'exceptions.UnboundLocalError'

[PyMOL] Other coloring strategies based on user-provided properties

Dear all, I am thinking whether it is possible to color a molecule by a specific property residue-wise or atom-wise like generally be done on B-factor? This property could be provided as numbers in a column. An obvious way might just be to change the B-factor column to the user-provided column

Re: [PyMOL] Other coloring strategies based on user-provided properties

://kong.med.nyu.edu/ On Aug 29, 2014, at 12:25 PM, Chen Zhao chenzhaoh...@gmail.com wrote: Dear all, I am thinking whether it is possible to color a molecule by a specific property residue-wise or atom-wise like generally be done on B-factor? This property could be provided as numbers

[PyMOL] Sphere display conflict with screen selection

Dear all, I am running pymol 1.6 on a Debian wheezy machine. I encountered a weird conflict of sphere display and mouse selection. When I show the ion in sphere, I cannot select residues by clicking it with mouse. Only after I hide the sphere am I able to accomplish click selection. Does anybody

Re: [PyMOL] APBS error

@lists.sourceforge.net/msg11148.html Troels Emtekær Linnet 2013/6/18 Chen Zhao chenzhaoh...@gmail.com Dear Pymol Users, I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian Wheezy machine. The initialization is successful, but when I hit set grid, I got the error

[PyMOL] APBS error

Dear Pymol Users, I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian Wheezy machine. The initialization is successful, but when I hit set grid, I got the error message below: *error: 1 type 'exceptions.UnboundLocalError' Exception in Tk callback Function: function lambda

[PyMOL] [Rendering Problem] Pymol VMD conflicts Coot

Hi all, I am a newbie in Linux, and recently installed Coot, Pymol and VMD on Ubuntu 12.04. It took me a while to figure out a strange conflict among them on my machine. If I remove the mesa-swx11 package, Coot becomes crazily slow. However, if I include that package, which requires the remove of