Re: [PyMOL] isomesh for electrostatic potential
On Tue, 18 Apr 2006, Chun Tang wrote: Dear PyMoler, In the pymol apbs tool, there is an option to show the negative/positive isosurface (not the molecular surface) upon loading an electrostatic map. My question is if there is a way to show the electrostatic potential surface as mesh instead of solid surface, also if it is possible to show the potential as a series of contours. Thank you. Chun The plugin doesn't allow you to show a mesh, but it would be a good idea to build that in. You can do it from the command line with the isomesh command. If you're using the plugin to do everything, you can do something like this: isomesh iso_pos_mesh, apbs_map, 0.5 color blue, iso_pos_mesh If you're not using the plugin, change 'apbs_map' to whatever your map is called. the idea of showing a series of contours is probably a good one. I'm not sure how to make a nice GUI interface for it, though. I recently switched to a Mac. It was broken for quite a while, but I think I finally got things working properly this weekend. I'll try to put out a new version of the plugin soon. At the moment, here's what I'm planning to add: - the ability to use pdb2pqr to generate pqr files - the ability to display the APBS version - the ability to display isomeshes in addition to isosurfaces any other big suggestions? -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mler...@umich --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Producing publication quality images
It's not pretty, and this is easy enough to do by hand, but I've had enough people ask me about this that I hacked up a little rendering plugin just now. Can someone grab it from http://www-personal.umich.edu/~mlerner/PyMOL/rendering.py put it in $PYMOL_PATH/modules/pmg_tk/startup/ (or whatever it is you do on your OS of choice) and tell me what you think? -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mler...@umich On Tue, 21 Mar 2006, Warren DeLano wrote: Terry, The trick is to render large and then reduce. With recent versions, you can do something like this # To get a 300 dpi PNG file for a 4 inch by 3 inch image... # Ray-traced: ray 1200,900 png hires_ray.pdb, dpi=300 # OpenGL: draw 1200,900 png hires_ogl.pdb, dpi=300 Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Terry Jones Sent: Tuesday, March 21, 2006 12:43 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Producing publication quality images Hi. I'm wondering if there's a way to make pymol produce high-quality images suitable for publication. I've used ray/png to produce images, but the person I pass them on to tells me they're only 50 to 100 dpi, and they're wanting 300 dpi if possible. Is there a way to do this in pymol? Or can I export image data and use some other tools to get to a 300dpi image? BTW, I'll try to make sure that pymol gets credited in the paper. Thanks, Terry --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720; dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] ball-and-sticks, controlling bond color
set stick_color, grey the image looks a little more like set stick_color, grey90 but I can't quite tell. -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mler...@umich On Wed, 15 Feb 2006, matthew.frank...@imclone.com wrote: pymol-users-ad...@lists.sourceforge.net wrote on 02/15/2006 05:36:51 PM: Hi all, There is a beautiful ball-and-stick image on pymol-wiki that I am trying to replicate (http://www.pymolwiki.org/index.php/Ball_and_Stick). The wiki image has grey bonds and light blue balls for carbon, dark blue for nitrogen, and red balls for oxygen. My problem is that all my bonds and balls are the same color, and I can't figure out how to make the bonds a grey color, distinct from the atom ball colors. And I'm trying to script this. Hi Marilyn - You probably can't do it all with one object. Create another object which is a duplicate of the one you're working with, then show spheres on object #1 and sticks on object #2. You can then color the balls and the sticks separately, since each object gets its own set of colors. For example: PyMOLcreate obj1, 1FLT and chain w Selector: found 797 atoms. Executive: object obj1 created. PyMOLcreate obj2, 1FLT and chain w Selector: found 797 atoms. Executive: object obj2 created. PyMOLcolor gray, obj2 Executive: Colored 797 atoms and 1 object. PyMOLcolor green, obj1 Executive: Colored 797 atoms and 1 object. PyMOLshow spheres, obj1 PyMOLshow sticks, obj2 PyMOLset stick_radius, 0.1 Setting: stick_radius set to 0.1. PyMOLset sphere_scale, 0.25 Setting: sphere_scale set to 0.25000. This gives a ball-and-stick of one chain where the balls are all green and the sticks are all gray. Modify as needed - Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you. --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Multiple origins possible?
I was going to suggest the same thing. FWIW, I have a version that you can run from your .pymolrc on my webpage here: http://www-personal.umich.edu/~mlerner/PyMOL/mg_pymol_utils.py -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mler...@umich On Mon, 20 Feb 2006, Grégori Gerebtzoff wrote: Hi Jon, I don't know if this is possible, but Warren posted some weeks ago two scripts you can run on two PyMOL sessions, in order to synchronize the view on both visualization windows. Have a look at these two links: http://sourceforge.net/mailarchive/message.php?msg_id=14392630 and http://sourceforge.net/mailarchive/message.php?msg_id=14394927 It might do the trick for you. Cheers, Greg -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Jon Manning Sent: vendredi, 17. février 2006 19:59 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Multiple origins possible? Hi all, I'm new new to PyMol, but have a question so would appreciate any pointers people have. I currently read in a molecule to pymol, 'copy' it, and color the two copies at different positions. I set a single origin, being the centre of gravity of the combined molecules. Ideally, I'd like to be able to set two origins, and have the molecules rotate synchronously side-by-side rather than as one object, so I can compare more easily. Is this possible with PyMol? Thanks, Jon -- Smart Bomb: Cogito Ergo Boom. ### Jonathan Manning PhD Student Barton Group School of Life Sciences University of Dundee Scotland, UK Tel +44 1382 388707 --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Can I use the mouse to control multiple windows?
Warren-
I never even noticed the -l option. That's awesome!
Thanks,
-michael
--
www.umich.edu/~mlerner |_ |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan
it's a cheer-ocracy. | - against HTML email X | Biophysics
-Torrence, Bring It On| / \ | mler...@umich
On Fri, 6 Jan 2006, Warren DeLano wrote:
NOTE: Bug fix for receive.py
# BEGIN receive.py
from pymol import cmd
from time import sleep
import os
filename = view.txt
while not sleep(0.2):
if os.path.exists(filename):
try:
cmd.set_view(eval(open(filename,'r').read()))
os.unlink(filename)
except: # if the file isn't yet complete
pass
# END receive.py
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
-Original Message-
From: Warren DeLano
Sent: Friday, January 06, 2006 2:54 PM
To: 'Michael George Lerner'; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] Can I use the mouse to control multiple windows?
Michael,
Of course -- use ansynchrous Python threads to automate the
process. For example:
pymol test.pdb -l send.py
pymol test.pdb -l receive.py
with the scripts below. Note use of the lowercase L option
to launch PyMOL Python scripts in their own asynchronous thread.
Cheers,
Warren
# BEGIN send.py
from pymol import cmd
from time import sleep
import os
last_view = cmd.get_view()
filename = view.txt
while not sleep(0.2):
cur_view = cmd.get_view()
if last_view != cur_view:
if not os.path.exists(filename):
open(filename,'w').write(str(cur_view))
last_view = cur_view
# END send.py
# BEGIN receive.py
from pymol import cmd
from time import sleep
import os
filename = view.txt
while not sleep(0.2):
if os.path.exists(filename):
try:
cmd.set_view(eval(open(filename,'r').read()))
os.unlink(filename)
except: # if the file isn't yet complete
pass
# END receive.py
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf
Of Michael
George Lerner
Sent: Friday, January 06, 2006 1:56 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Can I use the mouse to control multiple windows?
Longshot, but ..
I'm looking at a structure under two different sets of
conditions, so
I have two PyMOL windows open. I'm constantly get_view and
set_view[*] to synchronize the two windows. Is there some
way to set
things up so that I can drag things around in one window
and have the
scene in the other window automatically follow along?
Thanks,
-michael
[*] actually, I'm a bit lazier than that .. I now have this
run via my
.pymolrc:
VIEW_FILENAME = '/tmp/currentview.txt'
def gv():
'''write current view to a file (default
/tmp/currentview.txt)'''
# '...%s...'%VIEW_FILENAME doesn't end up as gv.__doc__
f = file(VIEW_FILENAME,'w')
f.write(str(cmd.get_view()))
f.close()
def sv():
'''read current view from a file (default
/tmp/currentview.txt)'''
# '...%s...'%VIEW_FILENAME doesn't end up as sv.__doc__
f = file(VIEW_FILENAME)
cmd.set_view(f.read())
f.close()
cmd.extend('gv',gv)
cmd.extend('sv',sv)
so I can type 'gv' in one window and 'sv' in the other.
--
www.umich.edu/~mlerner |_ |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan
it's a cheer-ocracy. | - against HTML email X | Biophysics
-Torrence, Bring It On| / \ | mler...@umich
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Re: [PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?
On Wed, 21 Dec 2005, William Scott wrote: Dear Michael: Thanks. It works great. Sorry that I stupidly didn't think to check it. No problem. I'm glad it works. Almost everything should be the same. APBS has a new required parameter, sdens (Vacc sphere density) that I've added to the configuration pane. As far as I've heard, the default setting of 10.0 should be fine for most uses. If you permit me one whine, I still need to use pdb2pqr (new version of that too) in order to do this with nucleic acids. Allowing the plugin to use pdb2pqr is at the top of my PyMOL-related todo list. -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mler...@umich On Tue, 20 Dec 2005, Michael George Lerner wrote: There's a new version on my website (http://www.umich.edu/~mlerner/PyMOL/). Please feel free to try it out and let me know if it works. I've tested it on a few systems that I work with, and it seems fine. One person has reported some difficulties, but these may not be related to my plugin. Thanks, -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mler...@umich On Tue, 20 Dec 2005, William Scott wrote: I'm not getting very far... parsePBE: Warning -- parsed deprecated calcforce 0 statement. parsePBE: Please use calcforce no instead. PBEparm_check: SDENS not set! NOsh: MG parameters not set correctly! Error while parsing input file. --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?
There's a new version on my website (http://www.umich.edu/~mlerner/PyMOL/). Please feel free to try it out and let me know if it works. I've tested it on a few systems that I work with, and it seems fine. One person has reported some difficulties, but these may not be related to my plugin. Thanks, -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mler...@umich On Tue, 20 Dec 2005, William Scott wrote: I'm not getting very far... parsePBE: Warning -- parsed deprecated calcforce 0 statement. parsePBE: Please use calcforce no instead. PBEparm_check: SDENS not set! NOsh: MG parameters not set correctly! Error while parsing input file. --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] How can I get the color ramp to show up in raytraced images?
Hi, When I use the APBS plugin to look at electrostatic potentials, I get a color ramp at the bottom of the window (e.g. red and -1 on the left, blue and +1 on the right) that shows the color scale that I'm using. When I raytrace, that ramp goes away. How can I make it show up in the raytraced image? Thanks, -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mler...@umich
Question about commandline -d option (was RE: [PyMOL] displaying protein with propeptide)
This is awesome. It looks like this has been a valid setting for a *long*
time, but I've never seen it. I look at a lot of MCSS-type structures,
and I have some really painful scripts that get the bonds right once the
structure is loaded in PyMOL. Now, I can just stamp the CONECT records at
the end of the file and load things up in connect_mode=1 world and
everything works. Speaking of which, I made a little bash shell script to
launch PyMOL this way:
pymol -d cmd.set('connect_mode',1) $@
It took me a couple of tries to get that right. The documentation for
command-line options says
-d string Run pymol command string upon startup.
so I first tried
pymol -d set connect_mode,1 $@
but that doesn't work. Is this a documentation typo? I thought a PyMOL
command string was anything you could type at the PyMOL command prompt.
-michael
--
www.umich.edu/~mlerner |_ |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan
it's a cheer-ocracy. | - against HTML email X | Biophysics
-Torrence, Bring It On| / \ | mler...@umich
On Thu, 17 Nov 2005, Warren DeLano wrote:
I'm not sure how version-dependent this is, but setting connect_mode to 1
before loading the PDB should disable distance-based connectivity determination.
set connect_mode, 1
load CONECT_only_pdb.pdb
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Eric Zollars
Sent: Thursday, November 17, 2005 5:36 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] displaying protein with propeptide
Is there a similar command to force PyMOL to use only CONECT
lines in the pdb file instead of generating connectivity by distance?
Eric
Warren DeLano wrote:
A quick fix is to use the retain_order setting.
set retain_order
which will force PyMOL to honor the order of ATOMs in the
PDB file over the numeric ordering of residue identifiers.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Joel
Tyndall
Sent: Thursday, November 17, 2005 12:15 PM
To: Anne Mølgaard; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] displaying protein with propeptide
Hi Ann,
I would change the chain id of the propeptide in a text
editor, to say
P and remove the P from after the residue numbers.
J
Anne Mølgaard wrote:
Hi,
I am having problems displaying proteins with unusual residue
numbering, such as proteins with propeptides. An example is
1cs8, which
starts off like
this:
ATOM 1 N SER A 1P-32.762 23.978 22.929 0.00 34.26
N
ATOM 2 CA SER A 1P-32.360 24.645 21.660 0.00 34.08
C
ATOM 3 C SER A 1P-32.303 26.162 21.821 0.00 33.91
C
ATOM 4 O SER A 1P-32.838 26.712 22.786 0.00 33.82
O
ATOM 5 CB SER A 1P-33.338 24.274 20.541 0.00 34.28
C
ATOM 6 OG SER A 1P-34.684 24.406 20.971 0.00 34.36
O
.
.
.
And later on comes the sequence corresponding to the
mature protein:
ATOM 1060 N ALA A 1 11.470 66.852 16.148 1.00 22.69
N
ATOM 1061 CA ALA A 1 11.282 65.561 15.491 1.00 20.80
C
ATOM 1062 C ALA A 1 10.621 65.677 14.113 1.00 20.33
C
ATOM 1063 O ALA A 1 9.920 66.649 13.835 1.00 18.43
O
ATOM 1064 CB ALA A 1 10.451 64.636 16.393 1.00 19.50
C
Etc.
If I open 1cs8 with PyMol, I can see everything in the lines,
sticks and surface representation, but in ribbon or
cartoon mode
only part of the protein is shown. What do I have to do to
show the whole sequence?
How do I select residues with a P appended to the residue
number? If
I say select resi 1P-5P I get both 1P-5P and 1-5.
Any help will be appreciated! (I am using PyMol version 0.98
for Windows).
- Anne
Anne Mølgaard, Ph.D.
Center for Biological Sequence Analysis BioCentrum-DTU,
Building 208
DK-2800 Lyngby
Email: a...@cbs.dtu.dk
Phone: (+45)4525 2472
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Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #996 - 2 msgs
On Tue, 13 Sep 2005, surendra negi wrote: check this link! http://www.csb.yale.edu/userguides/graphics/pymol/electro.html That page is actually quite out of date. I emailed them about it a few months ago, but didn't get a response. You don't need to go through any of that hassle to use the APBS plugin these days .. it comes included with PyMOL. Yay for open source! :) -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mler...@umich Hope it wud help. best sn --- pymol-users-requ...@lists.sourceforge.net wrote: Send PyMOL-users mailing list submissions to pymol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ad...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than Re: Contents of PyMOL-users digest... Today's Topics: 1. Displaying an electrostatic potential on msms (Anna Feldman-Salit) 2. Re: Displaying an electrostatic potential on msms (Peter Adrian Meyer) --__--__-- Message: 1 Date: Mon, 12 Sep 2005 11:25:39 +0200 From: Anna Feldman-Salit anna.feldman-sa...@eml-r.villa-bosch.de To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Displaying an electrostatic potential on msms Dear All, I have a 0.98 PyMol version with APBS and Iso_Sliders plugins. However, my aim is not just visualize isosurfaces of electrostatic potential at certain values, but to display/map it on molecular surface. Would you be so kind to share your knowledge with me on this subject? I'd appreciate any help or advice of yours! Thanks, Anna. --__--__-- Message: 2 Date: Mon, 12 Sep 2005 12:03:54 -0400 (EDT) Subject: Re: [PyMOL] Displaying an electrostatic potential on msms From: Peter Adrian Meyer pa...@cornell.edu To: Anna Feldman-Salit anna.feldman-sa...@eml-r.villa-bosch.de Cc: pymol-users@lists.sourceforge.net Hi Anna, I generally run apbs seperately (due to difficulties with Alphas), but use the plugin to display with pymol. apbs will produce two output files, acc.dx and pot.dx. acc.dx is the electrostatic potential mapped to the solvent accessible surface; pot.dx is the electrostatic potential over the grid. What I generally do is to load acc.dx into pymol, and they use the plugin-apbs-display to show the surface (not sure of the exact sequence; pymol's doing a ray-tracing job for me at the moment so I can't check). Hope this helps...I've never tried the iso_sliders plugin. I believe the author of the apbs plugin is on this list, and will probably give you clearer answers. Pete Dear All, I have a 0.98 PyMol version with APBS and Iso_Sliders plugins. However, my aim is not just visualize isosurfaces of electrostatic potential at certain values, but to display/map it on molecular surface. Would you be so kind to share your knowledge with me on this subject? I'd appreciate any help or advice of yours! Thanks, Anna. --- SF.Net email is Sponsored by the Better Software Conference EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile Plan-Driven Development * Managing Projects Teams * Testing QA Security * Process Improvement Measurement * http://www.sqe.com/bsce5sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Pete Meyer Fu Lab BMCB grad student Cornell University --__--__-- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users End of PyMOL-users Digest __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --- SF.Net email is Sponsored by the Better Software Conference EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile Plan-Driven Development * Managing Projects Teams * Testing QA Security * Process Improvement Measurement * http://www.sqe.com/bsce5sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Setting transparency for CGOs
Quoting tanri...@stud.uni-frankfurt.de: # Hi everybody, # # i've just created many CGOs, which show up solid surfaces like spheres and # ellipsoids. Is it possible to set the transparency of some CGO's to i.e. 0.5 # and leave the others solid? # I've checked out the reference and the manual, and found something like: # # set transparency=0.5, object # # But this actually does not work for CGO's. # Any ideas # # Yusuf The last time I looked at this, it seemed like the easiest (only?) way to do this was to tweak the transparency at creation time. So, I typically have functions that look like this: def makeSphere(name,x,y,z,r,transparency=0,...): ... obj = [] ... obj.extend([cgo.ALPHA,1-transparency]) obj.extend([cgo.SPHERE,x,y,z,r]) ... cmd.load_cgo(obj,name,1) I don't know how to change it later, though. Hope that helps, -michael # # # -- # Yusuf Tanrikulu # Bioinformatics Diploma Student # Department of Biosciences # Johann-Wolfgang-Goethe Univerity Frankfurt # Siesmayerstrasse 70 # 60326 Frankfurt am Main # - Germany - # tanrik...@bioinformatik.uni-frankfurt.de # #
Re: [PyMOL] Mix pml script and PDB file
On Mon, 18 Jul 2005, Sebastien Moretti wrote: Hello, Is there a way to get one file with pymol commands (pml script) and with the structure (PDB file) ? I can get this with Rasmol and the ras script file. Can I get the same kind of file with PyMOL ? You can use the read_pdbstr command, like so: delete all cmd.read_pdbstr(HETATM 1985 O00 MOH 132 18.797 6.477 -12.112 0.00 0.00 O\ HETATM 1988 H03 MOH 132 18.437 7.229 -11.665 0.00 0.00 H\ HETATM 1989 C04 MOH 132 17.737 5.662 -12.563 0.00 0.00 C\ HETATM 1990 H05 MOH 132 18.129 4.785 -13.080 0.00 0.00 H\ HETATM 1991 H06 MOH 132 17.096 6.211 -13.253 0.00 0.00 H\ HETATM 1992 H07 MOH 132 17.130 5.322 -11.722 0.00 0.00 H,mymolecule) show sticks ... don't forget the trailing backslashes. There's another example here: http://chips.csb.ki.se/pymol/msg02104.html if you're curious. -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mler...@umich Thanks -- Sébastien Moretti http://www.igs.cnrs-mrs.fr/ CNRS - IGS 31 chemin Joseph Aiguier 13402 Marseille cedex --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77alloc_id492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Setting grid boundaries in APBS
On Tue, 12 Jul 2005, Miguel Alejandro Pabon Sanclemente wrote: APBS-users in PyMOL: The APBS plugin is not setting the grid boundaries correctly. Segments of the proteins I have been working on are not included in the calculations because they are outside of the grid boundaries. Even if I try to set the boundaries manually the plugin still does the calculations as if I had not changed any parameter. Im puzzled Can you send me an example PDB file that causes this problem? I haven't seen this behavior before, and I'd like to see if there are any bugs in the APBS Plugin itself. Thanks, -michael Any explanation as to how the program automatically set the grid is welcome. Thanks beforehand, Alejandro --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Pymol/ABPS
On Sun, 12 Jun 2005, Dyda wrote: I'd like to know what charges Pymol uses when generates a pqr file from a pdb. The follow-up would be is whether there was a way to change this, say if one wanted to use charmm charges rather than amber. PyMOL uses amber99 charges and radii. This is taken care of in pymol/modules/chempy/champ/amber99.py. It would be possible to add a different forcefield by using that as a template and changing a few things in pymol/modules/chempy/champ/assign.py, but it would take more free time than I have right now. It seems that APBS hates chain IDs. Is that really so, or just my imagination? This is true, but has been fixed in the current version of the PyMOL/APBS Plugin. Warren has added a couple of other nice features to the current version. Here's a copy of a message that I just sent to the APBS list: Hi all, This is fixed in the current PyMOL source tree, and it'll be fixed in the next released version of PyMOL. In the meantime, you can download the current version here: http://www-personal.umich.edu/~mlerner/PyMOL/apbs_tools.py There are installation instructions at the top of http://www-personal.umich.edu/~mlerner/PyMOL/ but it boils down to replace your $PYMOL_PATH/modules/pmg_tk/startup/apbs_tools.py with the current one. There are a few other new features, including: - More reasonable starting dielectric constants - The ability to set a maximum number of grid points - The ability to display solvent accessible surfaces as well as molecular surfaces - Better warnings when PyMOL is unable to generate appropriate parameters in the PQR file. Sometime soon, I'll probably also change the .in file to say things like bcfl sdh instead of bcfl 1 etc. Given that the PyMOL/APBS Plugin is getting updated a bit, please let me know if there are any features/changes you'd like. thanks, -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mler...@umich
[PyMOL] saving commands created by cmd.extend() in session files
hi,
i have some scripts that load a bunch of files and do various smart things to
make it easy to work with my data. in particular, they define functions and
use cmd.extend() to register those functions. the setup takes a long time, and
is therefore inconvenient. i'd like to go through it once and save a session
file for the future.
i understand that saving commands created by cmd.extend() is a serious security
hole. is it serious enough that it's unacceptable even if the user turns the
security features off (i.e. set security,0 or pymol -o foo.pse)?
for what it's worth, my version of cmd.py now has this right before
def extend...
_extended_commands = {}
def session_save_extended_commands(session):
session['extended_commands'] = {}
for name,function in _extended_commands.iteritems():
print SAVING FUNCTION:,name
session['extended_commands'][name] = function
def session_restore_extended_commands(session):
if 'extended_commands' in session:
for name,function in session['extended_commands'].iteritems():
if pymol.invocation.options.security:
print NOT RESTORING FUNCTION,name,FOR SECURITY REASONS
else:
print RESTORING FUNCTION:,name
extend(name,function)
return 1
if session_save_extended_commands not in pymol._session_save_tasks:
pymol._session_save_tasks.append(session_save_extended_commands)
if session_restore_extended_commands not in pymol._session_restore_tasks:
pymol._session_restore_tasks.append(session_restore_extended_commands)
and this at the end of the definition of extend:
_extended_commands[name] = function
it happens that i don't really use cmd.alias() so much, but the same thing
should work for saving aliased commands.
thanks,
-michael
--
www.umich.edu/~mlerner |_ |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan
it's a cheer-ocracy. | - against HTML email X | Biophysics
-Torrence, Bring It On| / \ | mler...@umich
Re: [PyMOL] saving commands created by cmd.extend() in session files
ack! the code i sent works with some simple functions, but not with
everything. i'll toy around with it some more, but i'll still have the
same question: would it be possible for pymol to save the results of
cmd.extend in session files and restore them if security is turned off?
thanks,
-michael
--
www.umich.edu/~mlerner |_ |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan
it's a cheer-ocracy. | - against HTML email X | Biophysics
-Torrence, Bring It On| / \ | mler...@umich
On Mon, 11 Apr 2005, Michael George Lerner wrote:
hi,
i have some scripts that load a bunch of files and do various smart things to
make it easy to work with my data. in particular, they define functions and
use cmd.extend() to register those functions. the setup takes a long time,
and is therefore inconvenient. i'd like to go through it once and save a
session file for the future.
i understand that saving commands created by cmd.extend() is a serious
security hole. is it serious enough that it's unacceptable even if the user
turns the security features off (i.e. set security,0 or pymol -o
foo.pse)?
for what it's worth, my version of cmd.py now has this right before
def extend...
_extended_commands = {}
def session_save_extended_commands(session):
session['extended_commands'] = {}
for name,function in _extended_commands.iteritems():
print SAVING FUNCTION:,name
session['extended_commands'][name] = function
def session_restore_extended_commands(session):
if 'extended_commands' in session:
for name,function in session['extended_commands'].iteritems():
if pymol.invocation.options.security:
print NOT RESTORING FUNCTION,name,FOR SECURITY REASONS
else:
print RESTORING FUNCTION:,name
extend(name,function)
return 1
if session_save_extended_commands not in pymol._session_save_tasks:
pymol._session_save_tasks.append(session_save_extended_commands)
if session_restore_extended_commands not in
pymol._session_restore_tasks:
pymol._session_restore_tasks.append(session_restore_extended_commands)
and this at the end of the definition of extend:
_extended_commands[name] = function
it happens that i don't really use cmd.alias() so much, but the same thing
should work for saving aliased commands.
thanks,
-michael
--
www.umich.edu/~mlerner |_ |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan
it's a cheer-ocracy. | - against HTML email X | Biophysics
-Torrence, Bring It On| / \ | mler...@umich
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Re: [PyMOL] combine distance objects
On Tue, 8 Mar 2005, Robert Campbell wrote:
Hi,
Daniel Farrell [Monday, March 07, 2005 1:23 PM] wrote:
I want to create a lot of distance objects (in the hundreds)
between particular atomic pairs. Obviously I can make a
script like the following, inserting the exact atomic
selections that I want:
distance distobj12 = (atom1), (atom2)
distance distobj34 = (atom3), (atom4)
... etc.
But in fact one *can* still turn them on and off, with the enable or
disable command on the command line:
enable _dist1
disable _dist1
And it would be straightforward to put those commands within a loop:
# turn them all off:
for i in range(100):
cmd.disable(_dist1%s % i)
# turn them all on:
for i in range(100):
cmd.enable(_dist1%s % i)
Change 100 to whatever is appropriate.
I was just about to write something like this. In fact, I have tons of
files called something like x.py sprinkled around that do things like
-
from pymol import cmd
num_dist = 100
def show_dist():
show all of my distance objects
for i in range(num_dist):
cmd.enable('_dist%s'%i)
def hide_dist():
hide all of my distance objects
for i in range(num_dist):
cmd.disable('_dist%s'%i)
cmd.extend('sd',show_dist)
cmd.extend('hd',hide_dist)
-
You could also try something cute like
def show_dist():
dists = [name for name in cmd.get_names() if cmd.get_type(name) ==
'object:distance']
for name in dists: cmd.enable(name)
etc.
if you don't want to have to keep track of how many there are.
-michael
--
www.umich.edu/~mlerner |_ |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan
it's a cheer-ocracy. | - against HTML email X | Biophysics
-Torrence, Bring It On| / \ | mler...@umich
Cheers,
Rob
--
Robert L. Campbell, Ph.D. r...@post.queensu.ca
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
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Re: [PyMOL] Getting Closer to Wiki Time!
On Tue, 15 Feb 2005, Douglas Kojetin wrote: While we're throwing out all these ideas and possibilities: Is it ... possible? ... relatively painless? ... difficult? ... to use BioPython modules in PyMOL scripts? if you compile python from source (it's pretty easy on most linux systems (i had a lot of trouble with gentoo recently, though)), you can just point it at a version of python that already has biopython installed. pymol works just fine with python 2.4, by the way. -michael Doug --- SF email is sponsored by - The IT Product Guide Read honest candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595alloc_id=14396op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Getting Closer to Wiki Time!
On Tue, 15 Feb 2005, Douglas Kojetin wrote: While we're throwing out all these ideas and possibilities: Is it ... possible? ... relatively painless? ... difficult? ... to use BioPython modules in PyMOL scripts? if you compile python from source (it's pretty easy on most linux systems (i had a lot of trouble with gentoo recently, though)), you can just point it at a version of python that already has biopython installed. pymol works just fine with python 2.4, by the way. -michael Doug --- SF email is sponsored by - The IT Product Guide Read honest candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595alloc_id=14396op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] apbs error ObjectMapLoadDXFile-Error: Unable to open file! / multiple electrostatics maps overlapping
Hi, I've been meaning to update APBS tools so that some of the warnings are larger and better explained. WARNING: 53 atoms did not have properties assigned means that PyMOL couldn't automatically assign properties for 53 atoms in yoru molecule. This is usually because you have non-standard protein residues (or because you're not using a protein at all). In this case, you'll need to teach PyMOL about your molecule (via chempy .. it's a little involved. I think Warren posted something about it recently) or use another program to generate the PQR file. If you can get a good PQR file from another source (e.g. there's an APBS web portal at https://gridport.npaci.edu/apbs/ that probably understands more molecules than PyMOL), then you can use APBS tools directly with that PQR file. For your second question, you'll have to have to make the surfaces yourself, as the APBS Plugin only supports one molecule/map at a time right now. Have you looked at the help information for isosurface? You may also have to create two different dx maps and load them in by hand so that they have different names. You can use the 'Configuration' pane of the APBS plugin to make sure that they get reasonable names when you create them (then you just use PyMOL's load command to load them). Is that enough to get you started? -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Mon, 7 Feb 2005, Sabuj Pattanayek wrote: Dear Pymol users, I'm trying to run APBS v0.3.2 with pymol 0.98beta27, by first clicking the Set grid button, then clicking run APBS, but I get the error message shown below. coarsedim is [119.03399429321288, 109.91349792480469, 143.63640098571776] finedim is [90.019996643066406, 84.654998779296875, 104.49200057983398] center is [105.73299789428711, 140.44650268554688, -1.454237060547] finegridpoints is [193, 193, 225] radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr WARNING: 53 atoms did not have properties assigned ObjectMapLoadDXFile-Error: Unable to open file! Another problem I've come across when trying to load phi maps exported from Grasp is described below: 1) Load a pdb x 2) Load Grasp phi map for x 3) Run APBS tools, visualize, set phi map x to correlate with molecule x, set values for say -16kt/e, 0, 16 kt/e, and show the surface, this looks as it should. 4) Now load pdb y which is in the vicinity of x 5) Load Grasp phi map for y. 6) Run APBS tools, visualize, set phi map y to correlate with molecule y, set values for say -16kt/e, 0, 16 kt/e, and show the surface, this looks as it should for pdb y but the remaining isosurface from phi map y gets mapped onto pdb x and the x surface no longer looks like it should. ..so is there anyway to load two phi maps and map them to the surfaces of their correlating molecules without exceeeding their respective surface boundaries? Thanks, Sabuj Pattanayek --- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag--drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] apbs error ObjectMapLoadDXFile-Error: Unable to open file! / multiple electrostatics maps overlapping
Hi, On Mon, 7 Feb 2005, Sabuj Pattanayek wrote: Dear Mr. Lerner, Thanks for letting me know about the PDB2PQR server. I was able to generate a pqr from the NBCR website that then works with APBS to generate the dx map. I'm not sure how to get the same electrostatic gradient effect on the molecule surface generated using APBS tools using the isosurface command. I really like the potential mapping to molecular surface visual and it would be nice if it could be done with more than one molecule (from separate pdb files). I guess I can just render one molecule at a time and then crop multiple images into a single document so it looks like one system. Oops .. my fault. I was reading quickly, and I thought you wanted different isosurfaces for each molecule, not different molecular surfaces. The APBS plugin can't handle what you want, but you can do it. You need to load a map and a molecule, create a ramp that controls the coloring and attach that ramp to the molecule's surface. Here's an example (assuming you have pdb files firstmol.pdb and secondmol.pdb and dx maps firstmap.dx and secondmap.dx): -- begin -- # load the molecules and maps load firstmol.pdb load firstmap.dx load secondmol.pdb load secondmap.dx # create the ramps and show the surfaces ramp_new firstramp, firstmap, [-10,0,10] set surface_color, firstramp, firstmol show surface, firstmol ramp_new secondramp, secondmap, [-10,0,10] set surface_color, secondramp, secondmol show surface, secondmol --- end --- This is kind of ugly, though: it creates both of the ramps in the same place, and i don't know how to move them. So, if you want to change the scales, you probably need to delete the ramp and give a new set of ramp_new, set and show commands. Does that help? Question: do people want the APBS plugin to support multiple molecules? I can probably put something in, but it would take a bit of work (and I'll have to think about how to keep the interface small enough for normal screen sizes). -michael Thank you very much, Sabuj Pattanayek Michael George Lerner wrote: Hi, I've been meaning to update APBS tools so that some of the warnings are larger and better explained. WARNING: 53 atoms did not have properties assigned means that PyMOL couldn't automatically assign properties for 53 atoms in yoru molecule. This is usually because you have non-standard protein residues (or because you're not using a protein at all). In this case, you'll need to teach PyMOL about your molecule (via chempy .. it's a little involved. I think Warren posted something about it recently) or use another program to generate the PQR file. If you can get a good PQR file from another source (e.g. there's an APBS web portal at https://gridport.npaci.edu/apbs/ that probably understands more molecules than PyMOL), then you can use APBS tools directly with that PQR file. For your second question, you'll have to have to make the surfaces yourself, as the APBS Plugin only supports one molecule/map at a time right now. Have you looked at the help information for isosurface? You may also have to create two different dx maps and load them in by hand so that they have different names. You can use the 'Configuration' pane of the APBS plugin to make sure that they get reasonable names when you create them (then you just use PyMOL's load command to load them). Is that enough to get you started? -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Mon, 7 Feb 2005, Sabuj Pattanayek wrote: Dear Pymol users, I'm trying to run APBS v0.3.2 with pymol 0.98beta27, by first clicking the Set grid button, then clicking run APBS, but I get the error message shown below. coarsedim is [119.03399429321288, 109.91349792480469, 143.63640098571776] finedim is [90.019996643066406, 84.654998779296875, 104.49200057983398] center is [105.73299789428711, 140.44650268554688, -1.454237060547] finegridpoints is [193, 193, 225] radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr WARNING: 53 atoms did not have properties assigned ObjectMapLoadDXFile-Error: Unable to open file! Another problem I've come across when trying to load phi maps exported from Grasp is described below: 1) Load a pdb x 2) Load Grasp phi map for x 3) Run APBS tools, visualize, set phi map x to correlate with molecule x, set values for say -16kt/e, 0, 16 kt/e, and show the surface, this looks as it should. 4) Now load pdb y which is in the vicinity of x 5) Load Grasp phi map for y. 6) Run APBS tools, visualize
[PyMOL] combining models in a biounit
hi, i want to combine the models in a biounit file. for example, ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/divided/ky/1kyw.pdb2.gz has two models. so, i - load it - split_states on it - save everything into a pdb file but .. the pdb file ends up empty (it's just an END line). am i doing something wrong? is there a workaround? thanks, -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
[PyMOL] Re: APBS plugin - warnings generating pqr files (and a question for Warren)
Peter - I can't remember if you sent this to the whole list or not (I only have one sent to me, but if you send it to both places, I get two coppies, and I often delete one of those), so I appologize in advance if you only sent it to me. On Mon, 22 Nov 2004, Peter Haebel wrote: On Monday 22 November 2004 20:29, you wrote: Hi, I've heard this from a few people, and the answer seems to be that the new version of APBS doesn't like chain information in the PyMOL-generated PQR files. I'll release a new version of the plugin that fixes this soon, but in the meantime, the easy solution is to remove the chain information from the PDB file before you start the APBS calculation. how does apbs handle oligomeric proteins if it does not support chain ids? i think pymol is not happy, if you have residues with identical chain (or no chain) and identical resi. - apbs just cares about points in space with radii and charge. in fact, some of the test cases that come with apbs actually have duplicate residue ids. - i think apbs probably supports chain ids pretty well; i think there's just a mismatch in file formats between pymol-generated pqr files and the latest apbs. - i think (this one i haven't tried, but i'm pretty sure) that if you load the protein up in pymol and then remove the chain ids, pymol will be just fine. - PyMOL couldn't assign charges/radii to some of your atoms. Do you have a non-standard protein residue? If not, it may be that you have a terminal residue that PyMOL/champ doesn't understand. Can you look at the PQR file to see which residues ended up with radii and charges of 0? i have simply attached the original pdb file after refinement with CNS and the converted pqr file. there seem to be two problems with a) C-terminus OT1 and OT2 b) Ser, Thr, Try OH-groups this is by the way not the original pdb file 1ini, which i only used to verify whether or not original pdb files work. i think the OH groups are fine. those have non-zero radii, so i think it's just that the standard set of parameters don't put a charge on the hydrogen there. the terminal THRs, though, are trouble. i think this is a question for warren: can champ handle terminal THRs? (i'm really busy right now, so i don't quite have time to check .. if you don't get an answer from warren soon, though, i'll double-check). the first two and last two residues of the chain look like this in the pqr file: ATOM 1 N LEU A 6 26.067 12.507 58.949 0.101 1.824 ATOM 2 CA LEU A 6 25.986 11.536 57.819 0.010 1.908 ATOM 3 C LEU A 6 25.209 10.280 58.196 0.612 1.908 ATOM 4 O LEU A 6 24.704 9.579 57.322 -0.571 1.661 ATOM 5 CB LEU A 6 27.394 11.138 57.356 -0.024 1.908 ATOM 6 CG LEU A 6 28.271 12.223 56.726 0.342 1.908 ATOM 7 CD1 LEU A 6 29.621 11.630 56.341 -0.411 1.908 ATOM 8 CD2 LEU A 6 27.578 12.796 55.501 -0.410 1.908 ATOM 9 HD23 LEU A 6 27.308 11.986 54.823 0.098 1.487 ATOM 10 H3 LEU A 6 26.642 12.122 59.684 0.215 0.600 ATOM 11 HA LEU A 6 25.454 12.034 57.009 0.105 1.100 ATOM 12 HB2 LEU A 6 27.282 10.342 56.620 0.026 1.487 ATOM 13 HG LEU A 6 28.430 13.025 57.446 -0.038 1.487 ATOM 14 HD13 LEU A 6 29.914 12.001 55.359 0.098 1.487 ATOM 15 HD22 LEU A 6 28.250 13.487 54.993 0.098 1.487 ATOM 16 H2 LEU A 6 25.140 12.687 59.306 0.215 0.600 ATOM 17 HB3 LEU A 6 27.916 10.861 58.272 0.026 1.487 ATOM 18 HD12 LEU A 6 29.546 10.543 56.312 0.098 1.487 ATOM 19 HD21 LEU A 6 26.677 13.327 55.809 0.098 1.487 ATOM 20 H1 LEU A 6 26.475 13.371 58.621 0.215 0.600 ATOM 21 HD11 LEU A 6 30.369 11.923 57.078 0.098 1.487 ATOM 22 N ASP A 7 25.123 9.988 59.492 -0.516 1.824 ATOM 23 CA ASP A 7 24.402 8.804 59.946 0.038 1.908 ATOM 24 C ASP A 7 22.955 8.814 59.477 0.537 1.908 ATOM 25 O ASP A 7 22.238 9.804 59.631 -0.582 1.661 ATOM 26 CB ASP A 7 24.450 8.684 61.470 -0.030 1.908 ATOM 27 CG ASP A 7 25.795 8.193 61.972 0.799 1.908 ATOM 28 OD1 ASP A 7 26.303 7.191 61.420 -0.801 1.661 ATOM 29 OD2 ASP A 7 26.339 8.801 62.917 -0.801 1.661 ATOM 30 HB2 ASP A 7 23.679 7.983 61.791 -0.012 1.487 ATOM 31 H ASP A 7 25.563 10.594 60.170 0.294 0.600 ATOM 32 HA ASP A 7 24.899 7.940 59.506 0.088 1.387 ATOM 33 HB3 ASP A 7 24.284 9.678 61.886 -0.012 1.487 ATOM 3218 N LEU A 227 17.723 -10.762 41.310 -0.416 1.824 ATOM 3219 CA LEU A 227 18.730 -10.979 42.344 -0.052 1.908 ATOM 3220 C LEU A 227 19.890 -11.839 41.842 0.597
[PyMOL] wire-mesh spheres?
Hi, I want to draw a bunch of spheres of various sizes and colors. I'm currently using cgos for this. No problem. Now, I also want to draw wire-mesh spheres. Does anyone have a script for making these? While I'm at it, is there a way to make cgos transparent? Thanks, -Michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
Re: [PyMOL] still abou surfaces
Hi, Did you get an answer to this already? I've been swamped recently, so I haven't answered many PyMOL/APBS questions. Anyway .. I don't know anything about MSMS data and plotting surfaces, but I know a bit about PyMOL + APBS. APBS calculations (like a lot of other electrostatics calculations) require a PQR file. This is just a PDB file that also has information about the charge and radius of each atom. There are good sets of standard parameters for generating PQR files for standard amino acids, so PyMOL can automatically generate PQR files most proteins. However, it can't automatically generate PQR files for non-standard protein residues. It also can't generate PQR files for non-proteins. From your question, I think you already know this, which brings me to the little bit of help that I might be able to provide: I don't know how you do your electrostatics calculataions, but if you generate a PQR file somewhere along the way, you can tell the APBS plugin to use that PQR file (and then you can use the APBS plugin to do your electrostatics calculations and show the results with the APBS plugin, etc.). If you don't use PQR files, or if you don't want to use APBS to do your electrostatics calculations, you can still probably convert your results to a format that PyMOL understands. The DX format is a particularly easy one to read and write .. you can find some documentation here http://agave.wustl.edu/apbs/doc/html/user-guide/x2539.html and I can probably help you out with it if that's not enough. If you can convert things to a PyMOL readable format, you can use the APBS plugin to show the electrostatic potential (or you can just use the built-in PyMOL commands like isosurf, isomesh, etc.). I get the feeling that I've said a lot, none of which will actually be useful .. sorry about that if it's true! thanks, -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Sat, 16 Oct 2004, Alan Wilter Sousa da Silva wrote: Hi List! I was wondering why PyMol does not do the same as VMD about importing data from MSMS and plotting surfaces. So, I would not have problems anylonger about making surface of drugs or ligands that are not based in residues. Moreover, I finally could use apbs plugin to draw electrostatic surface of some drugs that we have been studied here. How about it? Or is there another alternative? Thanks in advance for any commentary. Cheers, -- -- Alan Wilter Sousa da Silva -- D.Sc. - IBCCF/UFRJ Projeto BioPAUA - HP/LNCC Petrópolis (RJ), Brasil www.lncc.br/~alan --- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] long loading times as the number of existing objects increases
On Tue, 7 Sep 2004, Warren DeLano wrote:
In relation to this, I just noticed something very important:
If you set auto_zoom, off before loading a series of structures, you'll
boost PyMOL's loading performance dramatically: by 10X at least...perhaps
much more. Just zoom once manually after everything is loaded in.
That's great!
I meant to chime in earlier .. I have a bunch of ugly scripts that
- create objects 1 through N
(I found 50 to be a good number for both my laptop (Linux+256MM of
memory) and our SGIs (IRIX + something like 512MB))
- save them to a file
- remove/delete everything
- load that file (now the first N objects are all one object)
- create another N objects, etc.
I poked around a bit to see if there was anything obvious that I could
speed up in PyMOL's guts, realized once again how big PyMOL's guts are,
wrote my ugly scripts and forgot about it. I'm looking forward to trying
out the auto_zoom thing in the morning!
thanks,
-michael
--
This isn't a democracy;|_ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
cmd.set(zoom,off)
# now load your structures
...
# now zoom
cmd.zoom()
This change makes it possible to load hundreds of structures containing
hundreds of thousands of atoms in a reasonable amount of time. For example,
on my dual 1 GB G5 with Shark-optimized G5 beta code, I loaded 800 PDB
structures containing a total of 1.4 million atoms in just over 426 seconds
-- apparently the situation isn't nearly as bad as I'd feared.
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-Original Message-
From: Ben Allen [mailto:benal...@caltech.edu]
Sent: Tuesday, September 07, 2004 2:48 PM
To: Warren DeLano
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] long loading times as the number of
existing objects increases
Warren-
Thanks for your prompt response!
Given the fundamental issues you mentioned, I think I will
change my script so that it loads files only when they are
needed and deletes the associated objects when they are no
longer being displayed. Initially, I rejected this solution
as less efficient, but apparently the specific situation with
pymol actually makes it more efficient!
Although the current version of my script uses a lot of
outside information to determine which files are loaded, how
they are colored, and how they are aligned (and so I haven't
included it), the following illustrates what I'm talking about:
#!/usr/bin/env python
from glob import glob
from time import time
if __name__ == 'pymol':
from pymol import cmd
t1 = time()
for pdb in glob('*.pdb'):
print pdb
cmd.load(pdb)
t2 = time()
print t2-t1
If (from pymol) I cd to a directory that has 50 pdb files and
run this script, it takes about 105 sec to complete. If I
include simple alignment and color commands, as follows:
#!/usr/bin/env python
from glob import glob
from time import time
if __name__ == 'pymol':
from pymol import cmd
t1 = time()
objects = []
for pdb in glob('*.pdb'):
print pdb
cmd.load(pdb)
objects.append(pdb[:-4])
cmd.fit(objects[-1]+' and name ca',objects[0]+' and name ca')
cmd.color('wheat',objects[-1]+' and elem c')
t2 = time()
print t2-t1
, it still takes same amount of time as before. This is only
one data point (50 structures), because I didn't want to
repeat the benchmarks for larger sets of structures, but it
seems to indicate that the limiting step is the actual
loading of the pdb files, and not the subsequent
aligning/coloring steps.
Thanks again for letting me know which direction I should go.
I'll let you know if I get any insight into the origin of the
original issue.
-Ben
On Sep 7, 2004, at 11:51 AM, Warren DeLano wrote:
Ben,
Thanks for the great benchmarks! PyMOL is definitely
showing non-linear
behavior when it comes to loading a lot of objects...I
don't know why this
is exactly, but I can tell you that I didn't originally
envision (and thus
optimize PYMOL for) loading of so many objects.
As it currently stands, there are a number of places
where PyMOL does things
using lists when it should be using hashes, and there
are many tasks (such
as selecting of atoms) that are linearly dependent (or
worse) on the total
number of atoms and coordinate sets present in the
system. All of these
issues will be addressed in time, but it may take a
considerable work to
correct them. Unfortunately, these are more than just
bugs -- they are
limitations in the original design. Such limitations
are now the bane of my
Re: [PyMOL] running APBS plugin on macG5
Hi, I don't have a Mac, so I can't really help you here .. I know there are quite a few people on the PyMOL list who've gotten APBS to work on Macs, though, so maybe one of them will chime in. If you don't get help here, you can probably get some more advice on the APBS mailing list. In case you didn't sign up when you downloaded APBS, the webpage is http://cholla.wustl.edu/mailman/listinfo/apbs-users Once you get APBS installed, the APBS+PyMOL plugin should just work (it doesn't really need APBS's psize.py). But .. can anyone who has installed APBS on this platform tell me where APBS puts psize.py? I'd like to list that on my webpage. Thanks, -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Wed, 1 Sep 2004, Ann Mullin wrote: Hi, All I want to do is be able to create an electrostatic surface representation of a simple molecule. I am seriously overwhelmed by the information for compiling and setting APBS on their website. I was happy to fine a link to download a package with an installer, but when I run it it fails at the very end and tells me to try installing again. Also, is there any place that I should be installing this? I tried in the Applications folder and in the folder I made to surround PyMOL and it's user manual. I also notice that there is a binary ready to use for G5 on the website, but where do I put this to work, and where is the psize.py file. I rarely work on a UNIX platform and I have a very hard time switching from macOS to UNIX and back, since macOS is almost all point and click. Thanks for any help. Ann Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amul...@tulane.edu
Re: [PyMOL] help compiling/ running APBS plugin on macG5
I also notice that the same place that has APBS has this site that computes electrostatics from a PDB file and returns a PQR file. This would be lovely for people like me to use for the calculations. Now how can I use the PQR file to create an electrostatic surface with pymol? A PQR file is like a PDB file, but it includes charge and radius information that is used by programs like APBS to generate electrostatic potential surfaces. PyMOL can generate PQR files (e.g. via the APBS Plugin), as can the PDB2PQR web portal that you found on the APBS website. If you can't get APBS installed locally, you may be able to use the APBS web portal (https://gridport.npaci.edu/apbs/) to run the APBS calculations. I don't think that's as convenient as APBS+PyMOL, but it's definately an option if you can't get APBS installed. Hopefully, some Mac-savvy person will be able to help you with the Fortran problems. -michael Ann Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amul...@tulane.edu On Sep 1, 2004, at 5:26 PM, Alex W. Smith wrote: Ann: The first question is do you have the Apple X11 and Developer tools installed. If you don't you will have to get them installed before you do anything. If you have them installed then the directions below should help out. I just got through doing all this for my G4 AlPB. Turns out I need more memory but everything works fine. It may seem like a lot at first but installing from source (especially on a OS X box) is probably the best bet. I tried the binary for G4 and had some library problems. Below are two links that helped me a lot. The first is directions for installing from source. Be sure to get the MALOC (link is on the first webpage) tar file as well as the APBS. Start out with the Installation directories. Be sure to list the directory name properly (i.e. change export FETK_SRC=/home/soft/src to the directories you want to install to. Then just move both tar files to the /home/soft/src (or whatever you call it) directory. Then just follow the directions for MALOC. For APBS, just follow the directions for unpacking APBS. Then follow Bill Scott's tweak (http://chips.csb.ki.se/pymol/msg02192.html). It should not take that long to compile them both. Once APBS is installed you can use the plugin to find the binary, which will be in the apbs/bin directory. Don't let the source code install scare you. They are easy enough to beat after a bit. Hope this helps. Alex http://agave.wustl.edu/apbs/doc/html/user-guide/x122.html http://chips.csb.ki.se/pymol/msg02192.html On Sep 1, 2004, at 2:12 PM, Ann Mullin wrote: Hi, All I want to do is be able to create an electrostatic surface representation of a simple molecule. I am seriously overwhelmed by the information for compiling and setting APBS on their website. I was happy to fine a link to download a package with an installer, but when I run it it fails at the very end and tells me to try installing again. Also, is there any place that I should be installing this? I tried in the Applications folder and in the folder I made to surround PyMOL and it's user manual. I also notice that there is a binary ready to use for G5 on the website, but where do I put this to work, and where is the psize.py file. I rarely work on a UNIX platform and I have a very hard time switching from macOS to UNIX and back, since macOS is almost all point and click. Thanks for any help. Ann Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amul...@tulane.edu
[PyMOL] Capturing a selection with a plugin
Hi, With the old wizard interface, I could capture selection actions with the do_select method. Is there a similary way with the Plugins? (I'm willing to write more code, I just don't know quite where to start.) Thanks, -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
[PyMOL] A faster way of unbonding things?
Hi,
I have a file which contains a protein and a bunch of ligands. The
ligands come from a Monte Carlo simulation where they were allowed to talk
to the protein, but not to eachother. So, lots of the ligands overlap.
When PyMOL sees this, it draws bonds between the ligands. Every time I
load up one of these structures, I have to unbond things with something
like
for i in range(160,660):cmd.do('unbond resi %s, not resi %s'%(i,i))
which takes a *really* long time. Is there a faster way to do this? I
once hacked up the PyMOL source so that HETATMS with resi N didn't get
bonded to anything else in the first place, but that's obviously a bad way
to do things (and I can't seem to compile things myself on our SGIs, so
it doesn't work there anyway).
Thanks,
-michael
--
This isn't a democracy;|_ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
Re: [PyMOL] displaying electrostatic maps
Hi, I'm am a very new PYMOL user. I'm trying to calculate and display and electrostatic map, similar to what I used to get in GRASP. I haven't used GRASP, but I wrote the PyMOL APBS plugin, soI'll see if I can help :). I displayed my molecule. From the 'Plugin' drop down I selected 'APBS tools'. In 'APBS Location' tab I entered the path for apbs_tools.py for the APBS binary location (is that correct?). Nope. APBS is a separate program for calculating electrostatics potentials. You can find it at http://agave.wustl.edu/apbs/ and you'll need to install it on your machine. I left the APBS psize.py location blank. After 'set grid' and 'run APBS', I was told I needed to load a map, so I loaded my CNS 2FomFc map. No need to load an external map here .. once you have APBS installed, you'll be able to generate everything from within PyMOL. Also, I think a 2FomFc map is an electron density map .. the Visualization tab can help you visualize any kind of map, but maybe it should say please load an electrostatic potential map just to make things more clear. 'Run APBS' ran just fine, I went to the 'Visualization' tab. Actually, Run APBS didn't do what it was supposed to .. since you don't have APBS installed, it actually didn't do anything. I should change the APBS Plugin so that it warns you if it can't actually run APBS. In any case, you need to download and install APBS. Then, you can set it up and run it from within the APBS Plugin. Also, if your protein has any non-standard residues, you'll probably want to check the PQR file that PyMOL generates to make sure that all of the charges look reasonable. good luck, -michael At this point I'm confused. I've hit various 'update' buttons, the 'Molecular Surface' on show is completely white. I've toggled values on the visualization tab, and nothing seems to happen (even after hitting the 'update' buttons). I'm hoping there is something basic I'm missing and would appreciate any pointers. Many thanks, Marilyn Marilyn D. Yoder Division of Cell Biology and Biophysics 5007 Rockhill Rd. University of Missouri-Kansas City Kansas City, MO 64110-2499 phone: 816-235-1986 fax: 816-235-1503 -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
[PyMOL] A couple of quick PyMOL + APBS notes
Hi all, I've been getting two questions about APBS from a few people, so I thought I'd send the answers here: 1) Does APBS take a lot of memory? APBS can certainly take a lot of memory. In addition, my plugin sets up a grid that's a little finer than the APBS default (more grid points == better calculation, but more memory). You can point my plugin at APBS's version of psize.py for a grid setup that'll use less memory, and I'll add some more options in the next version of the plugin that'll make it easier to set up a coarser grid. 2) Does it work on a Mac? My plugin should work with Macs just fine. And Nathan Baker just posted this to the APBS list: Hi All -- Thanks to Michael Grabe (UCSF), temporary Mac G4 and G5 binaries are available from the APBS download website while we try to get our G5 up and running. So it sounds like it should be much easier to set things up now! Thanks, -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
Re: [PyMOL] Plug-in Menu
Hi, There's some example code in pymol/modules/pmg_tk/startup/__init__.py. You can see how it works by copying it (uncommented) into a new file and placing that file in pymol/modules/pmg_tk/startup. You'll see the new plugins the next time you start PyMOL. I have a larger plugin that I've written .. I'll be sending out an announcement about it later today. -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Wed, 14 Jul 2004, Charles Moad wrote: I am interested in developing some simple plugins for the new release, and I was wondering if there was a document or api specifying how to go about this. As the subject says, for example, how do you add a plugin entry to the new menu bar list. Thanks, Charles Moad Scientific Data Analysis Lab Indiana University --- This SF.Net email sponsored by Black Hat Briefings Training. Attend Black Hat Briefings Training, Las Vegas July 24-29 - digital self defense, top technical experts, no vendor pitches, unmatched networking opportunities. Visit www.blackhat.com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Electronic density maps
On Tue, 22 Jun 2004, Konrad Hinsen wrote: Bad news. My map has a grid spacing of 2 angstrom, I need better resolution than that for placing it. So now I am trying chempy.brick. If you're using the CVS version of PyMOL, you might try DX multigrid formatted files. You can find some brief documentation here http://agave.wustl.edu/apbs/doc/html/user-guide/x2539.html and there's sure to be more at opendx.org (you probably won't need more, though). -michael I just installed NumPy into the internal Python (business as usual). However, while I can generate bricks, any isomesh I make from them always has zero lines. This is true already for the example script (brick01.py), which generates eight meshes that are all empty. Is this a bug? Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hin...@llb.saclay.cea.fr - --- This SF.Net email sponsored by Black Hat Briefings Training. Attend Black Hat Briefings Training, Las Vegas July 24-29 - digital self defense, top technical experts, no vendor pitches, unmatched networking opportunities. Visit www.blackhat.com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Breaking down PDB files
I think that PyMOL can only align different objects, not different
selections. There may be a more elegant way, but ..
If your chains are A,B,C..H, try this from the PyMOL prompt to create
different objects:
for c in 'A B C D E F G H'.split():cmd.create(c+'_chain','chain '+c)
and this to align them to the first one:
for c in 'A B C D E F G H'.split(): cmd.align(c+'_chain','A_chain')
If you just want a main chain alignment, you can try this:
for c in 'A B C D E F G H'.split(): cmd.align(c+'_chain and name ca','A_chain
and name ca')
etc.
If you're going to do this in a script where you don't know what the
chains are in advance, you try something like this
from pymol import stored,cmd
stored.chains = {}
cmd.iterate('all','stored.chains[chain]=1')
stored.chains = stored.chains.keys()
first = stored.chains[0] + '_chain'
for c in stored.chains():
cmd.create(c+'_chain','chain '+c)
cmd.align(c+'_chain',first)
(that first part is a little slow for large files)
-michael
p.s. I just tried align A_chain,B_chain,object=thing for the first
time .. that's pretty cool.
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On Tue, 1 Jun 2004, Tony Giannetti wrote:
Hey everyone,
I know I should be past this, but I can't seem to figure out how to do
this. I have a couple of crystal structures that contain multiple copies in
the asymmetric unit, and I would like to superimpose each copy to see what
the differences are. One way is to break the PDB file into one file for
each chain, but I'm wondering if there's a better way to handle this in
PyMol? One file (1CX8) has 8 copies and the other (1DE4) had three. I
tried split_states but it didn't work. I also tried aligning say chain A
onto chain B directly but that failed too (as expected). Is there a
straightforward way to do this or do I begin splitting these 700 residues
proteins up by hand. I wouldn't ask except it's a recurring problem with
many of the structures we study so I'm wondering if a general solution or
script exists or can be made to deal with this.
Tony
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Re: [PyMOL] loading electrostatic maps generated with apbs
Hi,
(1) fresh, clean install of the pymol-0.95-1.rh90.py22 RPM, downloading
the various electrostatics.py, dx.py, etc. modules from your website and
then using the load_dx() function with DX maps already calculated in a
standalone APBS run...
This won't work. For now, PyMOL needs to be recompiled for my DX-related
code to work.
(2) rebuilding PyMOL 0.95 from CVS version, incorporating the new and
modified source such as ObjectMap.{h,c}, PMGApp.py, etc. exactly as
described on your website (the recompiled PyMOL works fine)...
(I think you mean the current CVS version of PyMOL .. the code on my
webpage is synchronized with that, rather than 0.95)
This, on the other hand, should work. The fact that the recompiled PyMOL
works is a good sign.
(3) both of the above steps with either a pre-calculated dx map or for
one generated on-the-fly in PyMOL via the apbs_tools wizard, for both a
small protein and a large one
Based on the ~60-sec delay and increased processor usage after issuing a
PyMOL command like 'load_dx(some_file.dx,mapa)', I think the DX file
is actually being read.
I think you're right.
However, the process invariably dies with the following error stream:
PyMOLload_dx some_file.dx
Traceback (most recent call last):
File modules/pymol/parser.py, line 139, in parse
result=apply(kw[nest][0],args[nest],kw_args[nest])
File /usr/lib/python2.2/site-packages/pymol/modules/pymol/dx.py,
line 1034, in load_dx
importing.load_object(importing.loadable.DX, thing, mapName)
AttributeError: class loadable has no attribute 'DX'
This is very strange. I know you said that you installed all of the files
I listed, but are you *sure* that you installed my version of importing.py
as modules/pymol/importing.py? The error here is that it can't find
importing.loadable.DX, but if you have my version of importing.py, that
shouldn't be a problem.
If really do have an up-to-date version of my code, we should probably
figure out what's wrong off-list.
Thanks,
-michael
The line 139 parser.py error sometimes shows up as line 255, and this
error behavior also results if I perform more explicit function calls
such as 'load_dx(some_file.dx,mapa)'.
If anyone has any ideas about solving this problem, please let me know
Thanks,
Cameron
PS. This is all on a Red Hat 9 Linux PC utilizing the following Python
packages:
CHEMCCA35:NFkB[8] rpm -qa | egrep -i python
python-2.2.2-26
python-optik-1.4-2
rpm-python-4.2-1
python-devel-2.2.2-26
gnome-python2-canvas-1.99.14-5
gnome-python2-gtkhtml2-1.99.14-5
gnome-python2-bonobo-1.99.14-5
python-numeric-devel-22.0-2mdk
libxml2-python-2.5.4-3.rh9
gnome-python2-1.99.14-5
python-numeric-22.0-2mdk
[PyMOL] trouble with Pmw?
Hi,
I don't know much abotu Pmw, but when I compile the CVS version of PyMOL
and the included version of PMW (1.1) with python 2.3, things break a bit.
When I run pymol, the main window shows up but the gui doesn't. I get a
traceback that ends with
File /home/mlerner/pymol/modules/Pmw/Pmw_1_1/lib/PmwMenuBar.py, line
188, in _addHotkeyToOptions
underline = string.atoi(menubutton.cget('underline'))
File /usr/lib/python2.3/string.py, line 220, in atoi
return _int(s, base)
TypeError: int() can't convert non-string with explicit base
I'm not sure what cget is supposed to do, but in this case, it's returning
0 rather than a string.
Upgrading to the most recent version of Pmw that I can find (1.2) fixes
the problem.
-michael
--
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it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
Re: [PyMOL] Selections
For example, I found a PDB online called 'pope.pdb' (a cool lipid
bilayer; http://moose.bio.ucalgary.ca/Downloads/) and simply wanted to
select all the hydrophobic tails and hydrophilic heads so that I may
apply different attributes to each. If I need to select the tails,
which in the PDB are labeled from C10 (or so) to C50 depending on the
molecule, can I use something like c10-c50 (experience tells me no) or
must I do c10+c11+c12...c50?
I don't know an easy way to do this .. like almost does what you want,
but not quite. You could do something like
select sol, resn sol
select heads, name
N4+C5+C6+O7+O9+O10+O11+C12+C13+O14+C15+O16+C32+O33+C34+O35+P8+H1+H2+H3
select tails, not sol and not heads
Or .. even easier .. drop this in a file called something like
select_names.py
---
#!/usr/bin/env python
from pymol import cmd,stored
def select_names(newSelectionName,selection):
Makes a new selection called newSelectionName comprised of
everything that has the same atom name as something in selection.
stored.selected_names = []
cmd.iterate(selection,'stored.selected_names.append(name)')
cmd.select(newSelectionName,'name %s'%'+'.join(stored.selected_names))
cmd.extend('select_names',select_names)
---
and type run selected_names.py from within PyMOL.
Now use the mouse to select one of the heads (I use shift+lb to put things
into the selection (lb).
Now type select_names heads, lb and you'll have a selection called
heads that has all of the heads.
Maybe someone who knows more about selections will know a better way,
though.
So, it comes down to: do you prefer the macro method or standard; and,
do you have any hints or tips for more accurate or powerful selections?
If you're going to be using PyMOL a lot, it's definately worth your time
to learn how to write Python scripts. I'd also recommend looking through
the PyMOL source itself. I don't have anything much to say about
selections, though .. I've always been quite happy with simple PyMOL
selections.
-michael
As an example, how could I select just the tails or just the heads in
the aforementioned pope.pdb file?
Thanks.
--
Jason Vertrees
BSCB Graduate Student @ UTMB, Galveston
javer...@utmb.edu :: http://www.bscb.utmb.edu
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Re: [PyMOL] embeding pymol in a web page
On Mon, 29 Mar 2004, Nat Echols wrote:
The downloaded script is then executed by Pymol, which can uses Python's
socket abilities to download PDB files and run Pymol commands on them.
H, I like this idea. Can PyMOL open files directly over the web? It
would be nice to simply type
PyMOL load http://server/1cll.pdb, calmodulin
Kristian Rother's rTools (http://www.rubor.de/bioinf/pymol_rubor.html)
comes with a pdb command that's similar:
pdb (pdb-id) - get PDB structure (pdb-id) from the local disk,
or from the PDB server.
which does everything that I want, but it might be nice to have PyMOL
parse urls like that. Shouldn't be hard, especially with read_pdbstr.
Hmmn .. in fact, if you feel like playing around a bit, you can go into
cmd.py and change the definition of _load. At the top, right after it
says 'r = 1', add this:
#print oname,oname,finfo,finfo,ftype,ftype
if ftype == loadable.pdb and finfo.startswith('http://'):
import urllib
from importing import read_pdbstr
print requesting file,finfo
pdbstr = urllib.urlopen(finfo).read()
r = read_pdbstr(pdbstr,oname,state,finish,discrete)
And change the 'if' on the next line to an 'elif'. That will make this
work with simple urls. For example, you can type something like
load http://www.umich.edu/~mlerner/1rx1.pdb
or
load http://www.umich.edu/~mlerner/1rx1.pdb, nifty
and it'll work. More complicated urls seem to break PyMOL's parser. If
you uncomment the print statement in my little code snippet above, you can
see what goes wrong with, e.g. a url from the PDB like this
http://www.rcsb.org/pdb/cgi/explore.cgi?job=download;pdbId=1RX1;page=opt=showformat=PDBpre=1
but I haven't played around with the parser at all.
-michael
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[PyMOL] How do I get PyMOL to keep TER cards?
Hi, I have a file called test.pdb that looks like this: ATOM 13268 O00 U00 1945 -18.065 -4.226 1.590 ATOM 13269 H03 U00 1945 -17.394 -4.877 1.447 ATOM 13270 C04 U00 1945 -19.175 -4.837 2.212 ATOM 13271 H05 U00 1945 -19.963 -4.104 2.383 ATOM 13272 H06 U00 1945 -18.888 -5.266 3.173 ATOM 13273 H07 U00 1945 -19.576 -5.633 1.583 TER ATOM 13274 O00 U01 1946 -18.452 -3.459 2.224 ATOM 13275 H03 U01 1946 -17.636 -3.864 1.971 ATOM 13276 C04 U01 1946 -19.108 -4.290 3.158 ATOM 13277 H05 U01 1946 -20.055 -3.842 3.462 ATOM 13278 H06 U01 1946 -18.491 -4.429 4.047 ATOM 13279 H07 U01 1946 -19.314 -5.268 2.722 TER ATOM 13280 O00 U02 1947 -5.561 -17.187 5.362 ATOM 13281 H03 U02 1947 -5.123 -17.493 6.143 ATOM 13282 C04 U02 1947 -6.904 -17.622 5.389 ATOM 13283 H05 U02 1947 -7.428 -17.283 4.495 ATOM 13284 H06 U02 1947 -7.419 -17.223 6.263 ATOM 13285 H07 U02 1947 -6.953 -18.711 5.424 TER If I do this from PyMOL: delete all load test.pdb save test2.pdb I end up with a file that is missing TER cards .. like this: ATOM 1 O00 U00 1945 -18.065 -4.226 1.590 0.00 0.00 O ATOM 2 C04 U00 1945 -19.175 -4.837 2.212 0.00 0.00 C ATOM 3 H03 U00 1945 -17.394 -4.877 1.447 0.00 0.00 H ATOM 4 H05 U00 1945 -19.963 -4.104 2.383 0.00 0.00 H ATOM 5 H06 U00 1945 -18.888 -5.266 3.173 0.00 0.00 H ATOM 6 H07 U00 1945 -19.576 -5.633 1.583 0.00 0.00 H ATOM 7 O00 U01 1946 -18.452 -3.459 2.224 0.00 0.00 O ATOM 8 C04 U01 1946 -19.108 -4.290 3.158 0.00 0.00 C ATOM 9 H03 U01 1946 -17.636 -3.864 1.971 0.00 0.00 H ATOM 10 H05 U01 1946 -20.055 -3.842 3.462 0.00 0.00 H ATOM 11 H06 U01 1946 -18.491 -4.429 4.047 0.00 0.00 H ATOM 12 H07 U01 1946 -19.314 -5.268 2.722 0.00 0.00 H ATOM 13 O00 U02 1947 -5.561 -17.187 5.362 0.00 0.00 O ATOM 14 C04 U02 1947 -6.904 -17.622 5.389 0.00 0.00 C ATOM 15 H03 U02 1947 -5.123 -17.493 6.143 0.00 0.00 H ATOM 16 H05 U02 1947 -7.428 -17.283 4.495 0.00 0.00 H ATOM 17 H06 U02 1947 -7.419 -17.223 6.263 0.00 0.00 H ATOM 18 H07 U02 1947 -6.953 -18.711 5.424 0.00 0.00 H END How can I convince PyMOL to give me the TER cards? The only obvious-sounding setting I could find was pdb_use_ter_records, but that doesn't seem to do what I want. Thanks, -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
Re: [PyMOL] how to search PyMOL-users archive?
hi, i posted one answer to this before, but i guess you'd need to know how to search for it before you could find it :) anyway, here's what i wrote before: Sourceforge has one here: http://sourceforge.net/mailarchive/forum.php?forum_id=60 (there's a search box in the top left corner) but it doesn't always seem to work for me. There's another archive here: http://chips.csb.ki.se/pymol/ where the searches seem to actually work. I have no idea who runs that site, though. I just google for pymol + the phrase I'm looking for. -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Thu, 5 Feb 2004, Cameron Mura wrote: hi, simple/stupid question -- is it possible to search the archives of this mailing list?? If so, how does one go about it? I tried looking at http://sourceforge.net/mailarchive/forum.php?forum=pymol-users, but didn't see an obvious search mechanism... Thanks, Cameron --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Surface coloring with ChemPy bricks?
Does surface coloring work with ChemPy bricks? I took the script in examples/devel/brick01.py and changed it to make a ChemPy brick that goes from [0,0,0]--[5,5,5] like so ... examples/devel/brick01.py ... brik.setup_from_min_max( [0.0,0.0,0.0], [5.0,5.0,5.0], [0.5,0.5,0.5]) ... examples/devel/brick01.py ... and then loaded up a pdb file with one hydrogen in that box (briktst.pdb) ATOM 1H H 1 2.000 2.50 2.00 H and then tried to color the surface with using the ChemPy brick ramp_new e_lvl, brick, [-0.5, 0.0, 0.5] set surface_color, e_lvl, briktst show surface, briktst but the surface seems to stay white no matter what I do. Any idea what I'm doing wrong? thanks, -michael Background: I wrote some code to make APBS and PyMOL play nicely with eachother. I wanted to play around with PyMOL's internals a bit, so I wrote some chunks of that in C. Now that other people are actually using that code, it turns out that making sure my source is always up to date with the CVS source (and ditto for other folk's source) is a bit of a pain. So, I tried to rewrite everything in Python and turn APBS's DX maps into ChemPy bricks. I get nice isosurfaces, etc, but I can't color the surface by electrostatic potential. :(. -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
Re: [PyMOL] Help for user-defined functions
Hi,
I haven't seen this documented anywhere, so I have no idea if it's the
Right Way to do things, but I think all you need to do is add
cmd.help_sc.append('some_func')
after the cmd.extend('some_func',some_func) call. should this be built in
to cmd.extend()?
-michael
--
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On Thu, 22 Jan 2004, Gareth Stockwell wrote:
Does anyone know if it is possible to add 'help' documentation to my own
user-defined functions? What I want is to be able to define a new PyMOL
command by executing the following script:
#--
def some_func:
'''
Some help docs here...
'''
# Python code here...
cmd.extend(some_func, some_func)
#--
... and then type 'help some_func'.
Gareth
--
Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics Institute
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[PyMOL] Plugging APBS into PyMOL for electrostatics
Howdy, So, I got PyMOL+APBS working over the holidays. It's not quite ready for prime time, though, as you have to recompile PyMOL first. I also made a wizard that guides you through the electrostatics calculations and makes it easy to visualize the results. If you want to see it now, check out http://www.umich.edu/~mlerner/Pymol for the details. I'll post again when you can use this without recompiling PyMOL. Please let me know if you try it out! This was a lot of fun, but it left me with a few questions and comments. I'll just put them all in this message instead of sending lots of little messages. General questions/comments: - I want to draw a surface 10A away from a protein. Is there an easy way to do this in PyMOL? Right now, I'm cheating by looping through all of the atoms in the protein and adding something to the vdw radii, but this doesn't work when the vdw radii get above 6, and it starts to look ugly when you add more than 2 or 3A. - I want to iterate across every point on a surface to do something like find the point with the electrostatic potential. Any easy way to do this? - Transparency seems a little strange .. if I have an inner surface and an outer surface, and I set the transparency on the outer surface to 0.8 and the transparency on the inner surface to 0.0, I can still see through the inner surface. This problem goes away when I ray-trace things. - Anyone have any scripts to let PyMOL read/write PQR files? I hacked some stuff together, but only enough to get by. I don't know how to read in files that want to change the charge and radius of each atom. - How do I make PyMOL update the colors on a surface? I have a ramp that controls the surface coloring, and if I change the max,medium,min values on the ramp, it seems that I have to either middle-click and drag the ramp or type 'sort' to get the surface to actually update (actually, what I do is make a new ramp each time the values change and use cmd.set to set the surface color, followed by a 'sort' to get the colors to update on the screen). (I have some stuff in my Wizard that sets the ramp parameters and I'd like it to work instantly .. is 'sort' really the way to go?). - It would be nice if I could just drop wizards into modules/pymol/wizard and have them work automatically. Maybe something could iterate through every .py (or .so) file there and load them as wizards. I tried doing that (I gave each wizard a WizardName attribute that I used as the label), but I kept getting security warnings. This isn't a big deal, but I thought I'd mention it before I forgot it. - PyMOL seems to work just fine with more recent versions of Python (2.3). That's what I compiled all of this with. Also, the ext library is out of sync with the PyMOL sources, as I mentioned in a previous email. Not-so-general questions: - Warren: any chance of folding the changes to the PyMOL source into PyMOL proper? I can give it to you under the PyMOL license (the only licensing questions are about the dx reading and writing code, which lives in apbs_electrostatics.py). The versions on my webpage are up to date with the current CVS, but I can send you diffs, etc. - I'm still not sure what ObjectMapState-Field-Points is exactly. In particular, I don't understand why ndim is 4. - I'm still not sure what's supposed to go into ObjectMapState-Dim. As I mentioned before, it looks to me like maps generated with cmd.map_new(map,gaussian,0.1,methanol) have random values there. My code seems to work just fine even though I don't know what this is supposed to be. - It looks like I have to make a Crystal for things to work, so I do. I can't reproduce the kinds of Crystals PyMOL generates for gaussian maps (like above), though. In particular, Norm and RecipDim look like they have nonsense values in them and making a Crystal from a PyList doesn't let me set RealToFrac and FracToReal to anything interesting. None of this seems to actually matter, though. Thanks, -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
Re: [PyMOL] searchable archive?
Sourceforge has one here: http://sourceforge.net/mailarchive/forum.php?forum_id=60 (there's a search box in the top left corner) but it doesn't always seem to work for me. There's another archive here: http://chips.csb.ki.se/pymol/ where the searches seem to actually work. I have no idea who runs that site, though. I just google for pymol + the phrase I'm looking for. -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Mon, 5 Jan 2004, Mark Wilke wrote: Is there a searchable archive of this newsgroup? - Mark --- This SF.net email is sponsored by: IBM Linux Tutorials. Become an expert in LINUX or just sharpen your skills. Sign up for IBM's Free Linux Tutorials. Learn everything from the bash shell to sys admin. Click now! http://ads.osdn.com/?ad_id=1278alloc_id=3371op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (almost working)
Hi again, I've gotten the code much closer to working. Also, I think it's factored well enough that most of it should be non-GPL-contaminated. After I actually get it working completely, I'll email the APBS folks to see if they care about licensing issues. Right now, I can generate isomeshes and isosurfaces for methanol that look reasonable (yay!). But I can't get the surface coloring to work. If I do this: load methanol.pdb show surface, methanol run cleanerDxMap.py # loads up my APBS-generated map ramp_new e_lvl, map, [-10,0.00,10] set surface_color, e_lvl, methanol isosurf surfneg, map, -0.1 isomesh meshpos, map, 0.1 color red, surfneg color blue, meshpos I get a good looking mesh, a good looking isosurface, and a completely white surface around methanol. dragging the limits on the map around to really small things or really large things doesn't seem to help either. Any quick guesses? In case you have a little bit of spare time, I have two dumb sounding questions: 1) What exactly is supposed to go into ObjectMapState-Dim? At first, I thought it was just a list of three integers giving the map dimensions (in grid points), but that doesn't seem to be the answer. When I take a map that PyMOL generates for me (e.g. with cmd.map_new(map,gaussian,0.1,methanol)) and print it out as a Python list (using ObjectMapAsPyList, etc.), I get different results each time the program is run. 2) What exactly is supposed to go into ObjectMapState-Field-Points? I think it's just the x,y,z coordinates of the points starting at minCorner and working up through maxCorner by incrementing z then y then x ([x1,y1,z1,x1,y1,z2,...]. But, when I first tried to set points myself, I got a few things wrong .. it looks like n_dim is supposed to be 4. I had guessed 3. It also looks like Dim should be four ints, the grid dimensions followed by the number 3. Finally, it looks like stride should be the normal stride followed by the base_size. What am I missing here? Why is points a four-dimensional thing while data is a three-dimensional thing? thanks, -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Thu, 11 Dec 2003, Warren L. DeLano wrote: Michael, Impressive! I think you're one of the few people to delve into PyMOL's source like this. Obviously I'd be the best person to look at your code, but I'm crunched right now getting ready for this upcoming trip. Also, if the code is GPL-contaminated, then it can't be useful in the main version, but perhaps we can rewrite this cleanly later on. I can probably help you in January. What you've written sounds right... One thing I'd suggest for debugging in the meantime is that you use the isomesh or isosurface routines to explore what data is ending up in the Map, before trying to use the color ramps. There may also be some code in the chempy brick stuff which could serve as an example for populating the list. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
Re: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (almost working)
What's the problem? Both PyMOL and APBS are licensed under the GPL so I see no problems there. Well, pymol isn't obviously. Note to self: Don't post about licensing stuff after an evening of mulled wine. I've had an evening of nice port .. we'll see how a port-influenced evening compares to a mulled-wine-influenced evening :). Still, as long as the pymol license is GPL-compatible (which I believe it is, but I'm no lawyer), and the additional code is licensed under the same license, it should be alright, as I understand it. The potential problem is this: once I get this working, I want to give it to PyMOL. That way, I don't have to care about maintainance :). If I'm going to give it to PyMOL, I think it needs to use the PyMOL license, not the GPL. The license thing is probably not a big deal anyway. On the one hand, I'm not sure that anything I've done is actually forced to be GPL'd. On the other hand, it would probably take Warren all of an hour to re-create everything I've done. It took me a while because in addition to writing something that parses DX files, I had to figure out some of the PyMOL internals. And I'm slow :). Playing around with PyMOL is definately fun, though. -michael
[PyMOL] Trying to plug APBS into PyMOL for electrostatics (not working yet)
NOTE: this doesn't actually work yet, so most people can probably ignore
this message completely .. but i'd love some help! :)
Hi,
I've been doing all of my electrostatics calculations in MOE, but I'd like
to switch to PyMOL. I looked/asked around a bit and found APBS
http://agave.wustl.edu/apbs/, a cool GPL'd Poisson Boltzmann solver. I
figured that the first step in plugging APBS into PyMOL would just be
getting PyMOL to read dx files (that's APBS's default output format). I
have this almost, but not quite, working. I haven't messed around
much with PyMOL's internals, so I'm sure I've done a few things the
wrong way. Here's what I did and where I'm stuck:
1) understand the dx file format - i was in a hurry here, so i just read
one of the APBS source files. i don't know much about licenses, and i
don't know if that means that part of my code now needs to be GPL'd
instead of released under the PyMOL license.
3) wrote some Python code to read in a dx file and turn it into a nice
class.
4) gave that class the ability to spit out a list that i *think* matches
PyMOL's PyList version of an electrostatics map (ObjectMapState in
ObjectMap.h/c)
5) added a function
ObjectMap *ObjectMapLoadFromPyList(ObjectMap *I,PyObject *list,int state,int
discrete);
to ObjectMap.h/c that should be able to load it.
Now, I wasn't sure exactly how I should get PyMOL to actually load the dx
files. The most promising way looked like importing.load_object, so ..
6) added dx to importing.loadable (loadable.dx = 31) and #define'd
cLoadTypeDxPyListMap to be 31 in Cmd.c. added a new case for
cLoadTypeDxPyListMap to the big switch in CmdLoadObject and made it call
through to ObjectMapLoadFromPyList.
7) made a little python script called dxMap.py that looks like this:
from pymol import importing
f = file('meoh.dx')
d = readDX(f)
f.close()
thing = d.getObjectMapState(asList=True)
importing.load_object(importing.loadable.dx, thing, 'map')
and a pml script that says
load methanol.pdb
show surface, methanol
run dxMap.py
ramp_new e_lvl, map, [-0.02,0.00,0.02]
set surface_color, e_lvl, methanol
At this point, things *almost* work. If I click on map in the main
PyMOL window, it shows a box around my molecule (methanol in case you
haven't guessed yet :)) that looks like the right size. But, the surface
is entirely white (and middle-clicking on the ramp and dragging doesn't
help). Even more disturbing, when I try something like isosurf surf1,
map, 0.008, PyMOL segfaults :(.
My guess is that I don't quite understand what PyMOL wants me to send to
ObjectMapLoadFromPyList or ObjectMapStateFromPyList. I've tried lots of
prinf debugging throughout ObjectMap.c, Isosurf.c and Field.c and
everything looks right.
Anyone have any quick guesses as to what I might be doing wrong? If I put
my little bit of Python and C code up on the web somewhere, would someone
be willing to take a look at it? I'm pretty sure the problem is in one of
my Python classes (ObjectMapState, Isofield and Field) or in my C code,
rather than in the dx parsing, so looking at those things shouldn't force
the GPL taint upon you :).
In case it matters, I'm using the CVS version of PyMOL, compiled to use
Python2.3 (i don't have Python2.2 on my system, the cvs version of PyMOL
wants Python2.2 and the ext package includes Python2.1 ..).
thanks in advance,
-michael
--
This isn't a democracy;|_ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
Re: [PyMOL] double bonds
On Mon, 9 Dec 2002, John Duperon wrote: Hello everyone, hopefully this is a question which is not answered in some FAQ that I missed...is it possible to have PyMol show double bonds in a simple manner not unlike what would be found in a high school text book? Just a black and white stick diagram? Or perhaps the same, but using the dotted notation? you can try going into lines mode and turning on the valence display: hide show lines set valence, 0.1 a higher value for valence spreads things out more. i don't know of a way to get the dotted notation. cheers, -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
[PyMOL] editing question
Hi,
I'm trying to cycle through the various protonation states of a Histidine
residue (HIE,HIP,HID). I have resn and the residue number stored as
'curr_state' and 'i' respectively. My first shot at a function looked
basically like this (the real function has a a doc string and some gunk to
set up curr_state and i):
cmd.remove('(hydro and neighbor %s/ND1,NE2)' % i)
if curr_state == 'HIE':
cmd.alter('%s/' % i,'resn=HID')
elif curr_state == 'HID':
cmd.alter('%s/' % i,'resn=HIP')
elif curr_state == 'HIP':
cmd.alter('%s/' % i,'resn=HIE')
cmd.h_add('(%s/)'%i)
cmd.sort()
After I run this, it looks like nothing has changed. I can use something
like
iterate (114/),print resn
to see that the resn has in fact changed, but the hydrogens end up right
where they were when I started.
I've tried progressively more complex things, like this:
cmd.remove('(hydro and neighbor %s/ND1,NE2)' % i)
if curr_state == 'HIE':
print Changing HIE to HID
cmd.alter('%s/' % i,'resn=HID')
cmd.alter('%s/ND1' % i,'formal_charge=1.0')
cmd.h_add('%s/ND1' % i)
cmd.alter('%s/NE2' % i,'formal_charge=0.0')
cmd.iterate('%s/ND1,NE2'%i,'print formal_charge,partial_charge')
elif curr_state == 'HID':
print Changing HID to HIP
cmd.alter('%s/' % i,'resn=HIP')
cmd.alter('%s/ND1' % i,'formal_charge=1.0')
cmd.h_add('%s/ND1' % i)
cmd.alter('%s/NE2' % i,'formal_charge=1.0')
cmd.h_add('%s/NE2' % i)
cmd.iterate('%s/ND1,NE2'%i,'print formal_charge,partial_charge')
elif curr_state == 'HIP':
print Changing HIP to HIE
cmd.alter('%s/' % i,'resn=HIE')
cmd.alter('%s/ND1' % i,'formal_charge=0.0')
cmd.alter('%s/NE2' % i,'formal_charge=1.0')
cmd.h_add('%s/NE2' % i)
cmd.iterate('%s/ND1,NE2'%i,'print formal_charge,partial_charge')
cmd.sort()
But I think I may just be on the wrong track. The last snippet *appears*
to work for NE2 (and not for ND1), but I think that's just because the his
was an HIE to begin with.
Any hints?
Thanks,
-michael
--
This isn't a democracy;|_ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
[PyMOL] Question about crystallographic symmetry
Hi, I'm looking at a PDB file which, due to symmetry, only provides me with part of the unit cell (in this case I'm looking at 1HHP, which is a dimer but only gives coordinates for the monomer, but I've run across the problem before). I'd like to see the full unit cell. I understand that I can use symexp to create symmetry related objects within a certain distance, but I'd like to be able to say give me the unit cell. I noticed that the online manual (http://pymol.sourceforge.net/html/S0400xtal.html#10) says Currently that information can only be provided to PyMOL as a CRYST1 record in the PDB file, which includes the correct space group identifier. However, it would be only a minor development task to add a means of assigning unit-cell and symmetry to any molecule object directly from the API. So, two questions: 1) Can PyMOL already do what I want? 2) If not, and if it's only a minor development task, could someone give me some pointers for how to do it so that I can code it up myself? thanks, -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
[PyMOL] Installing from source on a linux box
Hi, I have PyMol up and running on my windows partition .. the installation was super easy. Now, I want to set it up on my Linux partition. I have Mandrake 8.1 installed, which means that my default python version is 2.1. It also means that many things (Numeric, zlib, etc..) are pre-installed for me. So, I downloaded the PyMol sources and tried to install it. In the external packages bit, it looked like the only thing I need is glut. So, I changed the setenv BASE line in build.com to point to the right place (/home/mglerner/src/pymol/ext in my case) and changed the setenv PYMOL_TARGETS line to say glut-linux and did ./build.com. I also tried ./build.com glut-linux for variety .. both seemed to work. Then I went up a directory into the main pymol directory. I then moved Rules.linux to Rules.make and edited it. There were many instances of -lpython1.5 .. I changed all of them to -lpython2.1. It was still having some trouble finding libpython2.1, so I added -L/usr/lib/python2.1/config to the LIB_DIRS line. After typing make, things get pretty far, but it doesn't get far enough. I wasn't sure how many of the error messages to include, but I've tacked on the last screen or so of output at the end of this message. There were some things that made me think that various parts of this build process were really looking for python sources in the ext directory, so I placed a copy of the python 2.1 sources there just in case. It didn't seem to help. Sorry if this is a dumb question, -michael -- begin output from make -- make[2]: Entering directory `/home/mglerner/src/pymol/contrib/modules' rm -f *.o *~ rm -f *.a tags TAGS config.c Makefile.pre python sedscript rm -f *.so *.sl so_locations VERSION=`../../ext/bin/python -c import sys; print sys.version[:3]`; \ installdir=`../../ext/bin/python -c import sys; print sys.prefix`; \ exec_installdir=`../../ext/bin/python -c import sys; print sys.exec_prefix`; \make -f ./Makefile.pre.in VPATH=. srcdir=. \ VERSION=$VERSION \ installdir=$installdir \ exec_installdir=$exec_installdir \ Makefile /bin/sh: ../../ext/bin/python: No such file or directory /bin/sh: ../../ext/bin/python: No such file or directory /bin/sh: ../../ext/bin/python: No such file or directory make[3]: Entering directory `/home/mglerner/src/pymol/contrib/modules' make[3]: *** No rule to make target `/lib/python/config/Makefile', needed by `sedscript'. Stop. make[3]: Leaving directory `/home/mglerner/src/pymol/contrib/modules' make[2]: *** [boot] Error 2 make[2]: Leaving directory `/home/mglerner/src/pymol/contrib/modules' make[1]: *** [make-modules] Error 2 make[1]: Leaving directory `/home/mglerner/src/pymol/contrib' make: *** [.contrib] Error 2 -- end output from make -- -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
