Do you know about the fink builds of pymol?
http://pdb.finkproject.org/pdb/package.php/pymol-py26 . You might
have more success modifying that package to pull the source from
subversion.
-David
On Wed, Mar 24, 2010 at 11:48 AM, hari jayaram hari...@gmail.com wrote:
Hi ,
Because I wanted to
PyMol doesn't provide programmatic access to actual bond objects.
Instead, you have to do what was suggested 5 days ago:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07745.html
-David
On Tue, Mar 23, 2010 at 3:48 PM, hari jayaram hari...@gmail.com wrote:
Hi
I want to write
2010/3/22 Tatsiana Kirys nus...@mail.ru:
I've installed it. But i have even more errors now:
nus...@linux-3mpg:~/Download/trunk/pymol python setup.py build install
bunch of stuff
/usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld: cannot
find -lpng
collect2: ld
Looks like you don't have the python-devel package. This provides the
header files such as Python.h you need for compiling python modules.
-David
On Fri, Mar 19, 2010 at 5:50 PM, Tatsiana Kirys nus...@mail.ru wrote:
Dear All,
i'm trying to install pymol on suse. i've checked that i have
To: Jason Vertrees
Cc: pymol-users@lists.sourceforge.net; David Hall
Subject: Re: [PyMOL] PyMOL on the Mac
Hi Jason,
Along those lines, would it be possible to have a 'default' which can
be set to a list of settings related to appearance? That might be more
concise than to have everything
See http://www.pymolwiki.org/index.php/Intra_Rms#USER_EXAMPLES.2FCOMMENTS
comments that start with Fit, Rms, Rms_Cur are finicky and only
work... as that likely explains your problem and a possible solution.
But I agree that pymol's behavior with this command can be extremely annoying.
-David
I would be a fan of auto_show_cartoon. Also, if you set more than one of
these, it will auto show more th one representation. Coolness.
If anyone is curious, I just figured out what auto_show_selections appears to
do (it is on by default), so I'll try to document that tomorrow.
Thanks,
while I agree with many of the points in that article, I've found it
often penalizes members of a community who participate the most
strongly by having them:
a) receive a lot of private e-mail that should go to the list, meaning
they have to explain to a lot of people the purpose of lists and what
Can Jason set up the list as the automatic Reply-To: header? Would
make it a lot easier.
-David
On Mar 9, 2010, at 5:53 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
I never get used to Pymol doing reply-to-sender in stead of reply-to-
list :|
-- Forwarded message --
What are you using to create the xyz file (and why can that software
not write a pdb)? The command you have below is pretty simple. An
alternative is also the xyzpdb program that comes as part of tinker.
( eg: xyzpdb graphite.xyz charmm22.prm gives you graphite.pdb )
-David
On Tue, Mar 9, 2010
If you would like to use a server for protein-protein docking, you can
check out the nice list on the wikipedia page for CAPRI.
http://en.wikipedia.org/wiki/Critical_Assessment_of_PRediction_of_Interactions#List_of_predictions_servers_participating_in_CAPRI
If you're looking for actual pieces of
I don't think DynoPlot can't do this. Are there even callbacks to
watch for things like changing state in the Pymol GUI? Maybe that
should be a feature request as it would allow for a lot more powerful
plugins. Callbacks that we can bind to through TKinter to watch for
modifications in the
util.cbas for salmon
util.cbay for yellow
You can see how these are implemented in
http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/modules/pymol/util.py?view=markup
if you want to make your own custom versions.
-David Hall
On Tue, Feb 9, 2010 at 5:46 PM, Ariel Talavera talav...@cim.sld.cu wrote
During my editing of dynoplot.py, I noticed that there were some
whitespace issues. Normally I consider whitespace a bikeshedding
topic, but in python, it is significant, so it matters. When tabs and
spaces are mixed, our own personal settings for how tabs are displayed
in an editor makes a huge
You would have to work with the DynoPlot author to improve this.
So, I figured it would be nicer if I sent the author a patch instead of just
complaining, so I went to look at the code.
Right now, it uses integer math to try to find the residues before and after,
but I know from my mistakes
Alright, here's a feature request that might convince people who still don't
believe, despite your first commit to pymol trunk post-acquisition including
Fixed a GL build bug on OSX (see
http://pymol.svn.sourceforge.net/viewvc/pymol?view=revrevision=3887 )
A Pymol Quicklook plugin. My primary
On Thu, Jan 21, 2010 at 9:46 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Errm, that only makes sense if the viewport itself is resampled
somehow when you don't do raytracing, but I don't think it is.
I'm pretty sure it is resampled when you specify a width or height. All
this below is with
- Original Message
From: Adrian Schreyer ams...@cam.ac.uk
To: jason.vertr...@schrodinger.com; PyMOL-users@lists.sourceforge.net
Sent: Wed, January 20, 2010 10:00:03 AM
Subject: [PyMOL] New Feature Ideas
Something more challenging:
3) Export scenes as webGL.This is a bit more
That seems like a modification that makes it less flexible. Now I can't do:
ray 2.5in, 20cm, dpi=300
Don't ask me why I might want to use two different units, I just don't see a
reason to make it so I cannot. I'm frequently surprised by my desires.
And resolution is inconsistent with the png
1) I would love it if the PDB Loader Service Plugin would clean up what it left
in /tmp on pymol exit. I have a feeling this might be complicated though. I
just have a bad memory when I first entered this world and I had pymol open and
I was trying to load a pdb and the plugin just would not
In my incentive build, freemol is present with the following readme:
This is a binary distribution of the FreeMOL Open-Source Compilation.
The FreeMOL project home page can be found at:
http://bioinformatics.org/freemol
Complete source code for building FreeMOL and its various components
Matthias Haffke said:
Is there a way to extract the translation / rotation matrix out of the
super command or can I use another command to align both,
protein B and A and to apply the function on every symmetry mate?
In addition the commands mentioned by Jason, you can look at matrix_copy
How would someone get the list of groups in a pymol session? get_object_list
doesn't have them and the only commands I can find in cmd that have the word
group in them seems to be group and ungroup (if my quick regex search worked
right).
Thanks,
David
2. Is there any way to get the information about bonds, angles and dihedrals ?
I found the following command can display the bonds information, but can't
be assigned to a variable.
cmd.select('all')
atoms=cmd.get_model('sele')
print atoms.list()
I wanted to play around with Jymol free evaluation builds (
http://delsci.com/jymol/ ), but I'm having trouble with the instructions given
in the README.txt for using javac to compile the examples. I know almost
nothing about Java, so my problem may be something obvious.
When I run:
javac
Problem solved: it looks like I just had to use javac from openjdk instead of
javac from gcj.
-David
- Original Message
From: David Hall dwash59_2...@yahoo.com
To: pymol-users@lists.sourceforge.net
Sent: Sun, November 22, 2009 2:22:18 PM
Subject: [PyMOL] Jymol Question
I
Is there any documentation on getting information out of alignment objects into
scripts? I tried looking around the wiki, but I didn't see anything.
I'm just wondering things like if I have a residue in one object, finding the
residue in another object that has been aligned.
Thanks,
David
pymol.cmd.align(%s % name_struct1, %s % name_struct2)
should return a list, the first element of which is the rms, if I remember
correctly.
Warren can probably say what the rest of the elements are.
On this note, maybe we could start documenting on the wiki what exactly all
these commands
is it possible to put a link to these archives in the signature portion of the
mailing list? I would find that very helpful.
-David
- Original Message
From: Warren DeLano war...@delsci.com
To: pymol-users pymol-users@lists.sourceforge.net
Sent: Tuesday, April 28, 2009 11:52:28
If people really like this git stuff, it might be interesting to move the
scripts to using gist.github.com . I don't know how well that would work with
the current repo that Justin created. Also, it might be useless as wikipedia
already lets us track the history of the page.
I could see
I could see some use in being able to see forks off from the scripts
in the wiki to people's individual computers though.
this can be readily done via the repo
Can you show how I can clone a single file out of the repository? Or how I can
fork a single file from the repository? Or
Put the commands in your pymolrc file
See http://pymolwiki.org/index.php/Launching_PyMOL#Windows
-David Hall
- Original Message
From: Kelvin Luther klut...@ic.sunysb.edu
To: pymol-users@lists.sourceforge.net
Sent: Saturday, October 4, 2008 5:53:24 PM
Subject: [PyMOL] PyMol
? (where there might not be an atom)
origin position=[1.0,2.0,3.0]
center origin
At least it looked like it worked.
-David Hall
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