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
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
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
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
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
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
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
>
> --
> 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
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: >
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
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
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
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
--
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,
>
>
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 "
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:
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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
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