RE: [PyMOL] measuring distances
Tara,
Use Python (and the run command with .py files).
from pymol import cmd
f=open('dist.txt','w')
dst=cmd.distance('tmp','mol1///25/ha','mol1///26/ha')
f.write("%8.3f\n"%dst)
f.close()
You could measure the whole protein this way by putting a loop around the
distance command:
from pymol import cmd
f=open('dist.txt','w')
atom = cmd.get_model("mol1ha").atom
for i in range(len(atom)-1):
sele1 = 'mol1///%s/HA'%atom[i].resi
sele2 = 'mol1///%s/HA'%atom[i+1].resi
dst=cmd.distance('tmp',sele1,sele2)
f.write("%14s %14s %8.3f\n"%(sele1,sele2,dst))
f.close()
The output "dist.txt" would then look like:
mol1///4/HAmol1///5/HA4.748
mol1///5/HAmol1///6/HA4.828
mol1///6/HAmol1///7/HA4.861
mol1///7/HAmol1///8/HA4.784
mol1///8/HAmol1///9/HA4.936
mol1///9/HA mol1///10/HA4.833
mol1///10/HA mol1///11/HA4.933
mol1///11/HA mol1///12/HA4.813
etc.
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 FAX:(650)-266-3501
> -Original Message-
> From: Tara Sprules [mailto:tspru...@ualberta.ca]
> Sent: Wednesday, January 08, 2003 3:20 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] measuring distances
>
>
> Hi,
>
> I have a file which measures a bunch of distances between
> atoms (of the
> form "distance (mol1///25/ha), (mol1///26/ha)"), and rather
> than having to
> look at the results on the screen I'd like to have the values output
> to a text file. Is it possible to do this?
>
> Thanks,
>
> Tara
>
> Tara Sprules
> Post-Doctoral Fellow
> Department of Chemistry
> University of Alberta
>
>
>
> ---
> This SF.NET email is sponsored by:
> SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See!
> http://www.vasoftware.com
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
Re: [PyMOL] x-windows pymol, fink and os x
> 0. Upgrade to 10.2.3 if you have not already done so. On a side note, did they fix NIS compatability again after breaking it in 10.2? I dropped OS X as soon as I discovered that, since that made it nearly useless for the environment I work in. If they got it working again, that and the new X server would be a huge incentive to get our G4s up and running. Nathaniel Echols Programmer n...@bioinfo.mbb.yale.eduGerstein Lab 203-589-6765 Yale University
[PyMOL] measuring distances
Hi, I have a file which measures a bunch of distances between atoms (of the form "distance (mol1///25/ha), (mol1///26/ha)"), and rather than having to look at the results on the screen I'd like to have the values output to a text file. Is it possible to do this? Thanks, Tara Tara Sprules Post-Doctoral Fellow Department of Chemistry University of Alberta
[PyMOL] x-windows pymol on OS X
Oh, and if you already have installed pymol with fink, you don't need to do anything apart from installing Apple's X-windows. William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax: +1-831-4593139 (fax)
[PyMOL] x-windows pymol, fink and os x
Awesome! I was hoping Apple's new release might have this impact. In my hands the X-windows version of pymol on OS X went from unusable to almost as fast as the native version. Apple's GLUT driver can now bind to the hardware drivers under X11 at the same time as the Tcl/Tk external GUI. It used to be an either/or situation. Apple has finally answered our requrests to support a fast 3D environment just like Linux and Windows, without requiring developers to specifically write to their user interface (which has taken me a lot of time, and I'm still not done)! Can you (or someone else knowledgable) please paste a quick summary for newbies as to how they would go about getting PyMOL running under Fink with the new OSX release? 0. Upgrade to 10.2.3 if you have not already done so. 1. Download X-windows from apple and install it (more details in the blue box here: http://chemistry.ucsc.edu/%7Ewgscott/xtal/page1.html ) currently free but once they get everyone addicted 2. Download Apple's December 2002 developer tools and install it (this includes compilers) http://developer.apple.com/tools/macosxtools.html Free but you have to register. 3. Download fink and install it (more details here: http://chemistry.ucsc.edu/%7Ewgscott/xtal/page3.html ) 4. type fink install pymol(this installs pymol and all of its dependencies like python). Thanks. Cheers, Warren William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax: +1-831-4593139 (fax)
Re: [PyMOL] 0.86 and MacOS X
To get the fink 0.86 version of PyMOL running hardware accelerated on Mac OS X using Apples newly released X11 you will need to install both Apples X11 public beta and their X11 software development kit available here: http://www.apple.com/macosx/x11/ You also need to get fink up and running. Detailed instructions for installing fink can be found here: http://fink.sourceforge.net/doc/bundled/install.php instructions for setting up fink to use Apples X11 XServer can be found here: http://fink.sourceforge.net/doc/x11/inst-xfree86.php#apple-binary once you have installed fink and apples X11, you will need to compile PyMOL I would recommend that newbies use fink commander to get their fink installation configured correctly. You need to enable the preference to use unstable packages in the Fink Commander preferences before you attempt to install PyMOL as the 0.86 release is not yet rated as stable (although it works fine for me). Fink commander can be found here: http://www.versiontracker.com/moreinfo.fcgi?id=15256&db=mac after getting fink up and running (with selfupdate-cvs) using the unstable tree and apples X11 all you need to do to get PyMOL 0.86 running is to type sudo fink install pymol in a terminal or just highlight the pymol package in Fink Commander and select the > source >install command from the menus) this should build PyMOL 0.86 and all required dependencies (~15 packages in all). This will take quite a while so don't be impatient. Finally launch Apples X11.app and under the applications menu select customize then add an item called PyMOL with the command /sw/bin/pymol and you should now be able to launch accelerated PyMOL from the applications menu Cheers and enjoy, Y On Wednesday, January 8, 2003, at 10:13 AM, Warren L. DeLano wrote: Awesome! I was hoping Apple's new release might have this impact. Apple's GLUT driver can now bind to the hardware drivers under X11 at the same time as the Tcl/Tk external GUI. It used to be an either/or situation. Apple has finally answered our requrests to support a fast 3D environment just like Linux and Windows, without requiring developers to specifically write to their user interface (which has taken me a lot of time, and I'm still not done)! Can you (or someone else knowledgable) please paste a quick summary for newbies as to how they would go about getting PyMOL running under Fink with the new OSX release? Thanks. Cheers, Warren On Wed, 8 Jan 2003, yuriwho wrote: I would like to report that 0.86 works fine under MacOS X 10.2.3 using Apples X11 version of xwindows. As far as I can tell it also has graphics acceleration (but I'm not sure as I haven't done any rigorous tests...seems dramatically faster than previous xwindows(fink) versions of pymol). I am using the latest fink package on a TiBook 800. Can anyone else comment about speed/features using 0.86 under X11 versus current/future MacOS X ports? It is nice to have the more full featured menus again. Y yuri...@mac.com
Re: [PyMOL] graphics performance
Hi Dirk This might actually be a hardware affect rather than a software effect. The GeForce4 is undoubtably quicker that the GeForce 2 bu there comes a time when the actual CPU is lagging behind in the amount of data it can pass to the GPU- this also includes other limitations such as the graphics apature size setting in the bios, the amount of RAM available to the machine and the speed of the AGP BUS. Putting a GeForce4 into a PIII means the GPU will be idling a lot probably upgrading the motherboard, RAM and CPU will yield improvements, better graphics cards most likely won't. Jules On Wed, 8 Jan 2003, Dirk Kostrewa wrote: > Dear Gordon, > > I assume that you changed the default "nv" driver in your XF86config(-4) file > to the Nvidia driver "nvidia". I've replaced on my private Pentium III (733 > MHz) PC a GeForce2 GTS against a GeForce4 Ti4200 and I also observe less > improvement than expected. Here are my observations: > 1. Under Windows98SE with 3DMark2001 I get a ~50 % higher score, which is > probably okay. > 2. Under Linux I get a ~ doubled frame rate for the simple OpenGL benchmark > program "gears" in full-screen mode and somewhat less than this in the > Vulpine OpenGL Mark, which is fine (Nvidia driver 31.23). > 3. But, puzzlingly with pymol and on-screen rendering of a complex secondary > structure sketch (without ray-tracing) I only get a moderate increase (~ 10 > %, or so) of the movie frame rate compared to a Geforce2MX440 running on a > Pentium III (450 MHz) in my office! Here, I would really expect a huge > difference in frame rate. I also don't understand this. A possible > explanation would be that pymol, upon automatic detection of the graphics > card, internally changes the complexity of the calculations resulting in a > slower but improved image? > > Best regards, > > Dirk. > > On Wednesday 08 January 2003 09:40, gordon wrote: > > Hi > > I recently upgraded from a geforce 2 to a geforce 4 ti4200, and I don't > > really notice a performance improvment (running linux). I judge this > > based on how smoothly large sized proteins can be rotated with spheres > > on. > > Just wondering why? >
Re: [PyMOL] 0.86 and MacOS X
Awesome! I was hoping Apple's new release might have this impact. Apple's GLUT driver can now bind to the hardware drivers under X11 at the same time as the Tcl/Tk external GUI. It used to be an either/or situation. Apple has finally answered our requrests to support a fast 3D environment just like Linux and Windows, without requiring developers to specifically write to their user interface (which has taken me a lot of time, and I'm still not done)! Can you (or someone else knowledgable) please paste a quick summary for newbies as to how they would go about getting PyMOL running under Fink with the new OSX release? Thanks. Cheers, Warren On Wed, 8 Jan 2003, yuriwho wrote: > I would like to report that 0.86 works fine under MacOS X 10.2.3 using > Apples X11 version of xwindows. As far as I can tell it also has > graphics acceleration (but I'm not sure as I haven't done any rigorous > tests...seems dramatically faster than previous xwindows(fink) versions > of pymol). I am using the latest fink package on a TiBook 800. > > Can anyone else comment about speed/features using 0.86 under X11 > versus current/future MacOS X ports? > > It is nice to have the more full featured menus again. > > Y > > yuri...@mac.com > > > > --- > This SF.NET email is sponsored by: > SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! > http://www.vasoftware.com > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] Script Box
Many thanks for the replies. I had forgotten the import statement (Doh!).
Now working fine again.
On a different note, one of the best features of 0.86, in my humble
opinion, is the new scrolling objects list. Previously I've created
sidechain objects to toggle individual sidechains on/off with one mouse
click using the following:
create MET1, (1/* & !n;N,C,O,H,HA,H03)
cmd.show("sticks","MET1")
util.cbaw("MET1")
cmd.disable('MET1') # disable at startup
and for small proteins it's not too time consuming to cut/paste/alter a
script to do this for every sidechain in the molecule (performance is a tad
slow on my old PII/NT machine but fine on faster PCs). Now I can toggle any
sidechain on/off with one mouse click and it doesn't matter how many
objects I have, similar to what you can do in SwissPDB viewer.
Any way my question is, can anybody think of a way to write a script that
would iterate through any pdb file and create individual objects MET1,
ALA2, ASP3... to AAn etc at the push of a scriptbox button?? My
python/scripting isn't so good but I'm learning!
Cheers,
Chris.
___
Dr Chris Winfield Lab: N317/318
Post-Doctoral Researcher Tel: +44 (0)1179 546 324
School of Chemistry Fax: +44 (0)1179 298 611
University of Bristol Mob: +44 (0)7866 550 518
Cantocks Closechris.winfi...@bristol.ac.uk
Bristol BS8 1TS
___
--On 08 January 2003 12:24 +0100 Kristian Rother
wrote:
Am Dienstag, 7. Januar 2003 11:08 schrieb Chris Winfield:
Has anybody managed to get ScriptBox working under Windows with v0.86??
Yes, me at least :-)
I'm
having trouble.
Here's my checklist:
1.) Did you write an 'import ScriptBox' statement into PMGApp.py?
2.) Is Scriptbox.py really in the pmg_tk directory (OK, You mentioned
that already)?
Hm, the people i know of had no problems further than this yet. Let me
know whether this works.
Kristian
I put ScriptBox.py in the appropriate placeplace and the following at the
end of the createMain(self) procedure in PMGApp.py in the usual manner:
ScriptBox.__init__(self)
But get the following error on loading PyMol:
NameError: global name 'ScriptBox' is not defined
If anyone has any suggestions they'd be most appreciated. I like
ScriptBox a lot so do you think there's any chance of incorporating this
into PyMol either as a GUI window or as its own dropdown scripts menu
that could also list all the scripts in a given directory??
Cheers,
Chris.
___
Dr Chris Winfield Lab: N317/318
Post-Doctoral Researcher Tel: +44 (0)1179 546 324
School of Chemistry Fax: +44 (0)1179 298 611
University of Bristol Mob: +44 (0)7866 550 518
Cantocks Closechris.winfi...@bristol.ac.uk
Bristol BS8 1TS
___
---
This SF.NET email is sponsored by:
SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See!
http://www.vasoftware.com
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] graphics performance
Dear Gordon, I assume that you changed the default "nv" driver in your XF86config(-4) file to the Nvidia driver "nvidia". I've replaced on my private Pentium III (733 MHz) PC a GeForce2 GTS against a GeForce4 Ti4200 and I also observe less improvement than expected. Here are my observations: 1. Under Windows98SE with 3DMark2001 I get a ~50 % higher score, which is probably okay. 2. Under Linux I get a ~ doubled frame rate for the simple OpenGL benchmark program "gears" in full-screen mode and somewhat less than this in the Vulpine OpenGL Mark, which is fine (Nvidia driver 31.23). 3. But, puzzlingly with pymol and on-screen rendering of a complex secondary structure sketch (without ray-tracing) I only get a moderate increase (~ 10 %, or so) of the movie frame rate compared to a Geforce2MX440 running on a Pentium III (450 MHz) in my office! Here, I would really expect a huge difference in frame rate. I also don't understand this. A possible explanation would be that pymol, upon automatic detection of the graphics card, internally changes the complexity of the calculations resulting in a slower but improved image? Best regards, Dirk. On Wednesday 08 January 2003 09:40, gordon wrote: > Hi > I recently upgraded from a geforce 2 to a geforce 4 ti4200, and I don't > really notice a performance improvment (running linux). I judge this > based on how smoothly large sized proteins can be rotated with spheres > on. > Just wondering why? > > Thanks in advance > Gordon -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OSRA/007 CH-5232 Villigen PSI, Switzerland E-mail: dirk.kostr...@psi.ch Phone: +41-56-310-4722 Fax: +41-56-310-4556 WWW: http://www.sb.psi.ch
Re: [PyMOL] ScriptBox
> If anyone has any suggestions they'd be most appreciated. I like ScriptBox > a lot so do you think there's any chance of incorporating this into PyMol > either as a GUI window or as its own dropdown scripts menu that could also > list all the scripts in a given directory?? Hello, There is a very recent (6.1.) package of rTools available from http://www.rubor.de/bioinf , where ScriptBox and some other tools are contained. Most things are accessible from menus, You can also add Your own scripts to the box using the add_script command. rTools 0.5.2 is still a Beta release, although many bugs have been fixed already. Particularly, installation under Windows is still a little eXPerience. Kristian Rother
[PyMOL] graphics performance
Hi I recently upgraded from a geforce 2 to a geforce 4 ti4200, and I don't really notice a performance improvment (running linux). I judge this based on how smoothly large sized proteins can be rotated with spheres on. Just wondering why? Thanks in advance Gordon -- Gordon Wells Department of Biochemistry University of Pretoria
