[PyMOL] [Rendering Problem] Pymol & VMD conflicts Coot

2013-02-18 Thread Chen Zhao
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

[PyMOL] Pymol 1.6 Cannot Run Scripts on Debian Wheezy (NVIDIA Q4000)

2013-05-29 Thread Chen Zhao
Dear Pymol Users, I am very pleased with my Debian system until today I found pymol cannot run scripts, which work fine on pymol-win. This is the initialization information: Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 4.20. Adapting to Quadro hardware. Det

[PyMOL] APBS error

2013-06-17 Thread Chen Zhao
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 Exception in Tk callback Function: at 0x33a6938> (type: ) Args: () Traceback (inne

Re: [PyMOL] APBS error

2013-06-18 Thread Chen Zhao
mol-users@lists.sourceforge.net/msg11148.html > > > > Troels Emtekær Linnet > > > 2013/6/18 Chen Zhao > >> 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, bu

[PyMOL] Off-topic: Crystallographic Symmetry Applications Available?

2013-07-31 Thread Chen Zhao
group, in which molecules are represented as dots, would be helpful. Thank you so much! Sincerely, Chen Zhao -- Get your SQL database under version control now! Version control is standard for application code, but databa

[PyMOL] Sphere display conflict with screen selection

2014-07-31 Thread Chen Zhao
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 h

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

2014-08-29 Thread Chen Zhao
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 and

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

2014-08-29 Thread Chen Zhao
> > -- > Jared Sampson > Xiangpeng Kong Lab > NYU Langone Medical Center > http://kong.med.nyu.edu/ > > > > > > > On Aug 29, 2014, at 12:25 PM, Chen Zhao wrote: > > Dear all, > > I am thinking whether it is possible to color a molecule by a spe

[PyMOL] [Error] Add morph into eMovie

2014-09-11 Thread Chen Zhao
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 Exception in Tk callback Function: >

[PyMOL] Slow down the frame rate

2014-09-12 Thread Chen Zhao
Dear all, I am now having a problem of changing the frame rate when saving the movie. Even if I set the frame rate by "Movie->frame rate", the frame rate will stay at the default value if I save the movie as MPEG file. I know there is another way to do this, in which I save all the frames as png f

Re: [PyMOL] Slow down the frame rate

2014-09-12 Thread Chen Zhao
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 wrote: > Dear all, > > I am now

[PyMOL] Pymol residue number disappear?

2014-09-15 Thread Chen Zhao
Hi all, I have a very weird problem: every time when I show sequence in pymol, the residue number just disappears. The changes I made recently before I spotted this problem are eMovie plug-in and freemol installation (in order to save mpg movies). I am using pymol 1.6.0.0 on a Debian Wheezy machin

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

2014-10-17 Thread Chen Zhao
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] Get the color code of each residue when using spectrum?

2014-10-19 Thread Chen Zhao
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 wrote: > Ni hao Chen Zhao, > >

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

2014-10-19 Thread Chen Zhao
ence. It's included in psico: > http://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 "

[PyMOL] Slow Pymol rendering

2016-05-06 Thread Chen Zhao
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] Slow Pymol rendering

2016-05-06 Thread Chen Zhao
y Notice | This e-mail message, including any attachments, > is for the sole use of the intended recipient(s) and may contain > confidential or proprietary information. Any unauthorized review, use, > disclosure or distribution is prohibited. If you are not the intended > recipient, immediately

[PyMOL] Definition cavities

2016-12-23 Thread Chen Zhao
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