listinfo/pymol-users
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>
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IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909,
--
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
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>
ts.sourceforge.net)
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Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laborator
lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
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> Archives:
hat I can hide or show
> individually so I can switch off the ones not connected to a residue of
> interest. Even better (if possible) would be to only show dashes connected
> to a residue of choice.
>
> I hope that makes sense. Thank you for your help,
>
> Harry
>
>
>
The plan is to write this as a userland script first. If issues relating to
security and validation can be resolved, we'll see if the official builds
want to include it.
Cheers,
-Michael
--
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IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fis
een a real need for SSL. Jason would be
the real authority here, but I'd guess that SSL would be possible if it
there's a strong push for it.
-Michael
>
> Pete
>
>
> Michael Lerner wrote:
>
>> Hi all,
>>
>> I'm considering building in a
TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
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>
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Michae
cript is now working.
>
> Thank you again,
>
> Ivan Campeotto
>
>
> From: Tsjerk Wassenaar [tsje...@gmail.com]
> Sent: 26 May 2011 07:18
> To: Michael Lerner
> Cc: Campeotto, Ivan; pymol-users@lists.sourceforge.net
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MOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
\Python27\PyMOL\pymol.cmd which
>> executes python on C:\Python27\PyMOL\pymol-launch.py
>>
>> Happy pymoling.
>>
>> Best
>> Troels
>>
>
>
>
> --
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e. Splunk takes this
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Hi all,
If I have a surface representation, is there currently a way to write it
out as points (perhaps with a desired spacing) to a file? I know that the
answer used to be no, but I thought I'd check just in case there was a new
function that I didn't know about.
Cheers,
-Michael
-
rs@lists.sourceforge.net)
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>
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Michael Lerner
Department of Physics and Astronomy
Earlham College - Drawer 111
801 National Road West
Richmond, IN 47
7;m trying to use as
intermediates between the two is proving to be troublesome.
Cheers,
-Michael
--
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Department of Physics and Astronomy
Earlham College - Drawer 111
801 National Road West
Richmond, IN
ooks like it has the right shape, but is clearly offset
from 1rx1.
I have a feeling I'm doing something simple and obvious wrong, but I'm not
sure what.
Thanks,
-Michael
On Mon, Jun 11, 2012 at 10:47 PM, Michael Lerner wrote:
> Hi all,
>
> Tsjerk- Thanks. I'm not sure
edFaceSet(wrlname)
> f = file(ptsname,'w')
> f.writelines(points)
> f.close()
> pts2pdb(ptsname,pdbname)
> cmd.set_view(view)
>
> Cheers,
> Thomas
>
> Michael Lerner wrote, On 07/15/12 04:05:
>
>> I finally got back to this,
I have some stuff from an amber8 (sander) MD run that I'd like to
visualize in PyMOL. When I load it up, PyMOL says something like
"assuming amber6 format" and dies. I'm using fink/pymol-py24 on an
intel macbook pro. I always forget how to load amber files anyway, so
I could easily be screwing
I have a crystal structure that contains two conformations for a
flexible loop. They're both in the crystal structure, but have
occupancies less than one. When I look at the structure in PyMOL, I
see only one conformation. Is there a command similar to split_states
that will allow me to view b
Oh, if it helps, the residues are all named things like ACYS and BCYS
for the different conformations.
On 7/25/06, Michael Lerner wrote:
I have a crystal structure that contains two conformations for a
flexible loop. They're both in the crystal structure, but have
occupancies less tha
This is not a great answer, but do you know about the object parameter
for the align command? I often type something like
align struct1, struct2, object=alignment
and then just look at which things were included/excluded.
-michael
On 8/3/06, Marc Bruning wrote:
hello,
is there any way to f
I think he means for you to have a "Load" button as part of your
plugin. That button would first record the path to the file and then
call through to cmd.load().
On 8/19/06, Ron Jacak wrote:
Peter,
>> I'm working on a plugin that reads information appended to the end of
>> PDB files to draw C
Thank you,
-Michael Lerner
--
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner http://lernerclan.net
Raúl,
I don't have time to look at this in detail right now, but .. what
exactly do you mean that the potentials change between frames? What
happens if you draw isosurfaces? Do they change?
-michael
On 1/7/07, Raúl Mera wrote:
Dear all,
Two things.
First, I just written a small plugin that
have this question,
-michael
On 1/9/07, Michael Lerner wrote:
Raúl,
I don't have time to look at this in detail right now, but .. what
exactly do you mean that the potentials change between frames? What
happens if you draw isosurfaces? Do they change?
-michael
On 1/7/07, Raúl Mera wr
nds
bound, different parts of a dynamics run, etc.
In your case, you might need to align all of the structures to one reference
structure first, so that the views are similar.
Hope this helps,
-Michael Lerner
On 25 Jan 2007 16:32:21 +, David F Burke wrote:
Pymol users,
I wish to com
ecall correctly, my problems with bricks were mostly that I
wasn't using them correctly, but I didn't figure out how to use them
correctly until after I'd already converted everything to DX.
-Michael Lerner
On 2/19/07, BuzB wrote:
Hi All,
Thanks to everyone and for the responses to and
Hi,
I'm using PyMOL to look at Amber trajectories. It would be really
useful if I could zoom around the movie with a slider, like in VMD.
Has anybody seen (or written) a plugin to do such a thing?
It would also be nice if I could say "each frame is 5ps and the movie
starts at time=500ps" and ha
Actually, I did this when I was developing the APBS Plugin. I put all
of the interesting code in a module called _apbs_tools. apbs_tools
was just a little wrapper where the init function would import and
reload _apbs_tools and then call through to it.
-Michael
On 2/24/07, DeLano Scientific wr
ools(thing):
reload(SomethingOrOtherTools)
return SomethingOrOtherTools.SomethingOrOtherTools(thing)
Let me know if you have any more questions.
-michael
On 2/24/07, Michael Lerner wrote:
Actually, I did this when I was developing the APBS Plugin. I put all
of the interesting code in a module called _apbs
On 3/3/07, se...@uniroma2.it wrote:
Dear all,
I'm new to this list and to the software.
I used PyMOL and APBS to calculate an electrostatic surface for a
small protein (I'm using the WindowsXP version) and everything seems fine.
Now I would like to visualize this surface AND the secondary stru
PyMOL doesn't know where the electrostatic potential map comes from.
If you load up a map and a structure, it will show the potential from
that map on that structure.
On 4/2/07, Gianluigi Caltabiano wrote:
YesI have already done as wrote
My question iswhat if I up load ligand surfa
The pseudoatom business looks very cool. I'll have to try it out.
In the meantime, I wanted to mention that you certainly can make
transparent CGOs. Here's some code that I wrote to visualize dock
output in our lab. The files it reads in have lines that look like
x y z r temp
Where x,y,z
Hi,
I feel like I'm missing something obvious here. How do I say
"Find me the distance between atom1 and atom2 in state 4"
or
"select all waters that are within 5.0 angstroms of residue 15 during state 7"
I'm trying to analyze various properties throughout the course of a
trajectory.
I made
Hi,
Can you try installing the most recent version of my plugin from
http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use
the normal Install Plugin menu option .. there's no need to do things
by hand anymore)? It fixes some problems and gives better error
messages on others.
Tha
In the past, I've had some strange issues with loading AMBER
trajectories (they might all be fixed by now), but the following has
always worked for me:
1) Rename your files so that they have the same filename and the
extensions .top and .trj. For instance, if you're studying the protein
1YCR, you
Hi,
I have a script that uses PyMOL to aid with a lot of calculations. So,
I run the script like this:
pymol -c script.py
The script has grown so that it has a lot of options. Right now, I
edit the script every time I want to change them. If it were a normal
Python script, I'd run it like
scrip
lt you think it might be to implement (that's not a
promise that I'll implement it .. just that I'll consider it :) ).
Thanks,
-Michael Lerner
--
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner
Hi,
I'm using PyMOL as a front end to a few scripts. So, I need to get my
hands on sys.argv to process the command-line arguments. On OS X,
everything works just like I'd expect. However, on Linux, I can't get
sys.argv. Here's a very simple Python script:
#!/usr/bin/env python
import sys
print di
You can do this with the isodot command.
Are you using the PyMOL-APBS plugin to generate or view electron
density maps? If so, would you like me to add dot representations to
the plugin in the next release?
Thanks,
-michael
--
Biophysics Graduate Student
Carlson Lab, University of Michigan
htt
endeavor!" -WLD
>
>
> > -Original Message-
> > From: pymol-users-boun...@lists.sourceforge.net
> > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
> > Of Michael Lerner
> > Sent: Tuesday, August 14, 2007 2:35 PM
> > To: pymol-users@l
It looks like quite a few people are actually still using the
electrostatics wizard, so I updated the code on my website
(http://www.umich.edu/~mlerner/PyMOL). For what it's worth, I just use
the visualization pane of the APBS plugin these days, but I understand
if the wizard is a little cleaner fo
Hi,
I have a Python script that sets a system up and then calls cmd.png()
to render an image. I use it to process several files at a time, and
there's no need to look at it while it's working, so I use
pymol -qcr myscript.py
to launch it. It works fine when I ray trace things, but if I just set
> I would like to use apbs from within PyMOL. I have downloaded and
> installed the latest version of apbs, and apbs_tools.py exists in
> $PYMOL_PATH/modules/pmg_tk/startup/. However, I find no "plugins" entry
> in any of the PyMOL menus.
I think that you need to rename the application bundle to
An object whose name begins with an underscore will not appear in the menu.
On Feb 11, 2008 3:13 PM, Toni Pizà wrote:
> Hi!
>
> When I create a distance in a pymol session, an object called "dist n"
> is created, and a label with there name is shown at the right of the
> screen, with the other ob
Hi,
First, the initial error you were seeing was a syntax error:
> from sys import argv
> my_argv =3D argv[argv.index("--"):]
> print my_argv[1], my_argv[2]
is failing because of the word "3D"
Second, that used to fail on Linux systems anyway (it worked on some
other systems). I tend to use opt
On Fri, Mar 7, 2008 at 5:04 PM, DeLano Scientific wrote:
> So from where I sit, the obvious open-source candidates are:
>
> APBS (electrostatics -- improve the current plugin)
Please let me know if anyone decides to do this. I have an
(unreleased) improved version, and several ideas for how to
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5635 Fishers Lane, Room T909
http://www.umich.edu/~mlerner
.
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Laboratory of Comput
heck out the new SourceForge.net Marketplace.
> >> It's the best place to buy or sell services for
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> >
> >
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>
> --
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5635 Fishers Lane, Room T909
Rockville, MD 20852
http://www.umich.edu/~mlerner
new SourceForge.net Marketplace.
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data to me).
However, PyMOL gives me errors when I try to load the resulting .xplor file.
This may not be directly related to PyMOL, but I'm hoping it's a common
enough task that someone can point me in the right direction.
Thanks,
-michael
--
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IRTA Pos
>
>
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ould someone help me please?
>
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Access to pymol.org has been restored.
On Fri, Dec 4, 2009 at 8:25 PM, Michael Lerner <
mglerner+sourcefo...@gmail.com > wrote:
> I have no idea why it's been blocked. I filed a ticket with the help desk
> (by clicking on the link in the middle of the "Access Denied"
---
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important issues
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ve the plugin window on top of your main PyMOL window
when you click "Ray". That doesn't seem to be necessary anymore, at least on
my MacBook Pro.
[image:
?ui=2&view=att&th=12651b51d47cc010&attid=0.1&disp=attd&realattid=ii_12651b51d47cc010&zw]
Cheers,
-Michael
Conference
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t ValueError:
print "Unknown units"
return
print 'width',width,'height',height
cmd.ray(width=width,height=height,**kwargs)
#cmd.png(self.filename.getvalue(), dpi=int(self.dpi.getvalue()))
cmd.extend('rayy',rayy)
On Thu, Jan 21, 2010 a
ht = todots(width,units,dpi),todots(height,units,dpi)
except ValueError:
print "Unknown units"
return
print 'width',width,'height',height
cmd.ray(width=width,height=height,**kwargs)
cmd.extend('rayy',rayy)
On Thu, Jan 21, 2010 at
i.org/index.php/User:Mglerner ). If you add it to your
.pymolrc, you will be able to type "rayy 3 in, 2 in, dpi=300" from the PyMOL
command line
4. Followed Luca Jovine's suggestion to change the order of rayy's
arguments.
Cheers,
-Michael
On Thu, Jan 21, 2010 at 11:29 AM, Micha
rocess for running external programs
* Deals with paths on Windows properly
* Gives better diagnostic information so that PyMOL/APBS developers can find
bugs more easily
* Lots of internal code cleanup
You can find this same information on the PyMOL wiki:
http://pymolwiki.org/index.php/User:Mglerner
Tha
W
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rated. Try
this series of commands from the PyMOL prompt:
gradient my_grad, pymol-generated
ramp_new my_grad_ramp, pymol-generated
color my_grad_ramp, my_grad
I'm considering building this into the next version of the plugin.
Cheers,
-Michael
--
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IRTA Postdoctoral
DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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dlines())
output_file.close() #windows doesn't do this automatically
if DEBUG:
print "Results were:"
print "Return value:",retcode
print "Output:"
print prog_out
return (retcode,prog_out)
during beta.
> http://p.sf.net/sfu/intel-sw-dev
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.sourceforge.net
>>
>
>
>
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel
or 3) set the APBS_BINARY_DIR environment variable.
It's worth noting that the environment variables weren't working in some
previous versions of the plugin.
Cheers,
-Michael
On Wed, Jul 21, 2010 at 2:56 PM, Michael Lerner <
mglerner+sourcefo...@gmail.com > wrote:
> Hi Daniel,
f.net/sfu/intel-thread-sfd
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> http://p.sf.net/sfu/intel-thread-sfd
> ___
> PyMOL-users mailing list (PyMOL-
deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
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> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> __
be more
> appreciated.
>
>
> Could you please attach your script in the above command, so that all the
> cluster_*.sdf is loaded and its polar contacts is displayed in one press.
>
>
> Thanks in advance
>
> Renuka.
>
>
> --- On *Wed, 22/9/10, Michael Lerner
>
rich applications that run
> across multiple browsers and platforms. Download your free trials today!
> http://p.sf.net/sfu/adobe-dev2dev
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izes are up for grabs.
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--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fish
management solution at an even better
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> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
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--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fell
Real-Time with Splunk
> Collect, index and harness all the fast moving IT data generated by your
> applications, servers and devices whether physical, virtual or in the
> cloud.
> Deliver compliance at lower cost and gain new business insights.
> Free Software Download: http://p.sf.net/sfu/splunk
g list (PyMOL-users@lists.sourceforge.net)
> >Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >
>
>
>
>
&
3
>> >Fax: <%2B49%20%280%29%20351%20463-40087>+49 (0) 351 463-40087
>> >E-Mail: hongbo.zhu at biotec
>> >Webpage: www.biotec.tu-dresden.de
>> >
>>
>>
>> >--
>> &
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Laboratory of Computational Biology NIH/NHLBI
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