Hello:
I just got a question: can we use the open source version of pymol for
commercial usage? Or can we develop some commercial tool based on Pymol?
thank you very much.
Albert
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Hello:
I notice that my screen resolution is too high that the font of pymol
GUI looks extremely small. I am just wondering is it possible to
increase them?
thank you very much.
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Hello:
I've installed pymol git repo following steps:
http://www.pymolwiki.org/index.php/Git_install
However, when I start pymol, it always showed the following messages:
No module named tkintertable.Tables
Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui).
No module
wondering is it possible for pymol give alternative
rotamer conformation of a protein residue?
thanks a lot
Albert
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Hello:
Does anybody know whether Nvidia GTX980Ti support Pymol active stereo
3D? I saw someone said that some GTX graphic card may also work, but I
am not sure for this one.
Thx a lot
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I think the major concern is how Pymol depicts the pi-pi stacking Of
course we can identify such interaction immediately as soon as we open
the system in Pymol.
However there is no any components to indicate this, eg: we can depict
the H-bond with a dash between two atoms but how could
?
thanks a lot
Albert
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Hello:
I am trying to calculate the protein surface electstatic properities by
APBS plugin in pymol. But it always failed with messages:
Could not find/tmp/1.dx so searching for /tmp/1-PE0.dx
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does '/tmp/1-PE0.dx' exist?
Does
thanks a lot for reply.
Problem solved after I specify the maloc library path explicitly in my
tcsh environment.
setenv FETK_LIBRARY /home/albert/install/apbs/apbs-1.4.0/lib
On 10/08/2015 05:02 PM, Andreas Forster wrote:
Hi Albert,
I apologize that I take your email for a grumpy old
://istar.cse.cuhk.edu.hk/iview/
and here is script for this tool
https://github.com/HongjianLi/istar/tree/master/public/iview
Thank you very much.
Albert
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Dear Osvaldo:
Thanks a lot for further information.
I just run the command
|set pse_export_version, 1.72 |
before I load anything to pymol, then followed the step for exporting.
But it still failed with messages:
Traceback (most recent call last):
File "/home/albert/install/
Hello:
I noticed that there is a plugin called
exportToWeb.py
I try to rum it with command:
python exportToWeb.py test.pse
However, no any new file generated I am just wondering how shall we
use this script correctly?
thanks a lot
Albert
Thanks a lot for further advice.
Here is what I got:
PyMOL> run exportToWeb.py
PyMOL>exportToWeb my
Traceback (most recent call last):
File "/home/albert/install/pymol-1.7.6/modules/pymol/parser.py", line
256, in parse
self.result=apply(layer.kw[0],layer.args,layer
Hello:
I've colored object1 in various color in different regions. I am just
wondering how can we copy the color scheme for object1 to object2?
Object 2 is the same protein with object1 but with different conformations.
Thank you very much
Albert
Hello:
I am just wondering is there any hotkey in Pymol so that we can center
in the Ligand automatically? For instance:
If I press keyboard "L", Pymol zoom to ligand binding pocket
automatically
Thanks a l
Hello:
I've got a 3D coordinate in 3D. I am just wondering is it possible to
show it in 2D diagram in Pymol for a ligand so that we can get more
clear idea how exactly the ligand looks like?
thanks a lot
Albert
Hello:
Does anybody have any idea whether pymol could label the absolute
configuration (R/S) for a chiarity atom?
Thank you very much.
Albert
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Dear:
I've compiled pymol-1.8.0 under my Linux X64 OS. I found that Pymol can
start by command:
pymol
without any complaints or erros. However, when I try to load a .pdb file
into pymol, pymol always failed with following messages:
just click the b.pdb on the Pymol object manager bar to undisplay it.
That's the basic of basic usage of Pymol. Wouldn't it be nice if you
spend a few minutes to go through Pymol manual?
On 12/11/2015 08:19 AM, Smith Liu wrote:
Dear All,
Suppose by pymol I have opened A.pdb abd B.pdb. Is
Hello:
I noticed that if we run command:
fetch 2ac1
to get PDB into pymol in Version 1.8.0, it downloaded .cif file by
default. I am just wondering is it possible to change the default format
as .pdb file?
thanks a lot
Albert
it, and cannot find any helpful information
thanks again
ALbert
On 11/18/2015 11:16 PM, Thomas Holder wrote:
> Hi Albert,
>
> These messages come from third-party plugins that you have installed, see:
> http://pymolwiki.org/index.php/MtsslDock
> http://pymolwiki.org/index.php/M
the ligand). There is a "optimize" plugin
in Pymol, maybe the developer can consider merge them together?
Thank you very much
Albert
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you very much
Albert
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Hi Thomas:
thanks a lot for helpful advice.
May I ask is there any superior features of mmCIF format against PDB format?
regards
Albert
On 11/22/2015 04:15 PM, Thomas Holder wrote:
> Hi Albert,
>
> Unfortunately the default fetch type can't be configured. But you can
> overri
Yes, I also really love this function. However, for the sake of
accuracy, I believe many users will also strongly demand for introducing
forcefield for minimization..I am looking forward to see that
"optimize" plugin would somehow merged into "Molecular Sculpting".At
least, it is very
Hello:
Does anybody have any idea whether PyMol support Virtual Reality (VR)?
Can we use the following VR devices to visualize PyMOl in computer?
http://www.polygon.com/2016/1/5/10719326/nvidia-virtual-reality-performance-power
https://www.youtube.com/watch?v=U4JPhUr_d7g
If yes, will any VR
Hello:
I would like to know the XYZ information of a specific atom. I am just
wondering how can we do this? Is there any command line?
thank you very much
Albert
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Hello,
I've got a pymol .pse file and I am just wondering how can we convert it
with a Linux command line directly to a .html file without opening pymol
GUI?
Thank you very much.
Albert
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File "/home/albert/install/pymol/Pymol-script-repo/pymol2glmol.py",
line 152, in dump_rep
int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2])))
IndexError: tuple index out of range
Do you have any idea what's the problem?
THX again.
On 01/25/2017 10:46 PM, Thomas Ho
Hi Thomas,
Thanks a lot for your information. I know this command and that's what I
needed.
However, I don't what to open the PyMOL GUI. Is it possible that we run
PyMOL with a text mode and convert the .pse file directly to a .html file?
Thanks again.
Albert
On 01/25/2017 10:46 PM
fantastic job!!
Thanks a lot.
Albert
On 01/16/2017 10:16 PM, Sampson, Jared M. wrote:
Dear PyMOL Users,
I am pleased to introduce a new plugin called PyMOLProbity
<https://github.com/jaredsampson/pymolprobity> which allows a PyMOL
user to visualize MolProbity-style structural vali
Hello:
I noticed that if I show my structure as cartoon, there would be a
"dashed loop" cartoon filling in the missing part of my structure. I am
just wondering how can we disable PyMol show the missing part automatically?
Thank you very mu
to solve this problem? I am using PyMOL-1.8.2.3.
I also tested in the latest 1.8.4, it has the same issue.
Thank you very much.
Albert
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I see.
It works very well now.
Thanks a lot
On 10/06/2016 10:32 PM, Thomas Holder wrote:
> Hi Albert,
>
> "internal_gui" is now a blacklisted setting not be stored or restored from
> session files.
>
> You can launch PyMOL without internal gui like this f
doesn't start and I didn't get any error messages from terminal
either.
I am just wondering how can we solve the problem?
Thx a lot
Albert
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Hello:
I am using openSUSE 13.2 X64 OS.
Pymol works fine without optirun in 1.8.4.
Here is output from ./pymol -c
PyMOL>python end
PyMOL: normal program termination.
However, when I type
optirun ./pymol -c
I didn't obtain any information.
regards
Albert
On 10/10/2016 08:46
ank you very much.
Albert
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Dear Tsjerk:
Thanks a lot for such prompt reply.
It works very well.
Cheers.
Albert
On 12/07/2016 08:46 PM, Tsjerk Wassenaar wrote:
Hi Albert,
You can do:
show cell
Cheers,
Tsjerk
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I think you can obtain it from your Linux terminal
On 01/13/2017 10:34 AM, Academic Research wrote:
Pymol Professionals I need your help,
I have the following command:
|iterate n. CA, print resi + ':' + ss |
I use this command in pymol to print out each residue number and its
code from the svn of the current version, 1.2-x.
Same results.
Hope someone can help me,
albert
. Saving into an obj file works
well when surface_type is set to 0, or 1. Any help?
Best,
Albert
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Dr Albert Solernou
EPSRC Research Fellow,
Department of Physics and Astronomy,
University of Leeds
the
trajectory if I simply:
align trj, pdb1
as it is told in:
http://www.pymolwiki.org/index.php/Align
However, I am unable to get the list of RMS values printed out. How
could I do that?
Thanks,
Albert
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Dr Albert Solernou
EPSRC Research Fellow
Thanks Thomas,
I was already printing k[i][3] (RMSD before refinement) instead of
k[i][0] (RMSD after refinement) but your cycles=0 looks cleaner.
Cheers,
Albert
On 05/06/2015 05:14 PM, Thomas Holder wrote:
Hi Albert,
Please pay attention to the difference between all-atom RMSD and RMSD
Oh, I see...
It looks like I'll need to end up writing a short script that does the
loop along the trajectory together with a correct RMS calculation.
Thanks for the tip, Carsten.
Cheers,
Albert
On 05/08/2015 04:11 PM, Schubert, Carsten [JRDUS] wrote:
Hi Al,
based on my experience running
Terribly useful Carsten!
I could easily do a loop and get the RMS along the trajectory:
k = []
for i in range(1,101): k.append(cmd.align(trj,pdb1,mobile_state=i))
for i in range(100): print k[i][0]
Cheers,
Albert
On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote:
Hi Al,
you
be very grateful if you could give me some hints on the code
structure, and on how to tackle the inclusion of this new feature.
Cheers,
Albert
On 04/08/2016 09:18 PM, Thomas Holder wrote:
> Hi Albert,
>
> This is currently not possible and adding this would be a very major project.
&g
Dear All,
I was wondering if there is a way to select faces, vertices and/or edges
from a CGO either using the mouse or the command line. How difficult
would be to add this, and how would you do that?
It would be very useful for us if we could get that working.
Thanks,
Albert
Dear All,
I was wondering if there was a way to load a PDB file stored in memory
instead of disk, i. e., a memory file, defined through StringIO or
tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could
handle an open file instead of a file?
Thanks,
Albert
Hi Jordan,
I still don't figure out how to do that with "load_object". What is the
"type" for a file handler? Would be "object" the file handler itself?
Albert
On 10/26/2016 10:58 AM, Jordan Willis wrote:
> Probably could use load_object instead.
>
>
>
That's lovely, David.
Thanks,
Albert
On 10/26/2016 11:56 AM, David Hall wrote:
> https://pymolwiki.org/index.php/Read_Pdbstr
>
> -David
>
> On Oct 26, 2016, at 3:55 AM, Albert Solernou <a.soler...@leeds.ac.uk
> <mailto:a.soler...@leeds.ac.uk>> wrote:
>
Dear All,
we have been writing a plugin for PyMOL during the last years, released
as GPL. I would like to support PyMOL2, but need to know whether the
code will be made accessible or not. Is PyMOL2 still free software? And
if so, can we get access to the source code?
Thanks,
Albert
OK,
I found the answer myself, googling in this email list. Sources will be
released early next year, I understood. I'll wait patiently :)
Cheers,
Albert
On 22/11/17 11:49, Albert Solernou wrote:
Dear All,
we have been writing a plugin for PyMOL during the last years, released
as GPL. I
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