[PyMOL] set sphere_transparency?

2004-04-13 Thread Jason Vertrees
ideas? Thanks! -- Jason -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http://www.bscb.utmb.edu

[PyMOL] Selections

2004-04-14 Thread Jason Vertrees
? Thanks. -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http://www.bscb.utmb.edu

[PyMOL] Questions

2004-04-22 Thread Jason Vertrees
-- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http://www.bscb.utmb.edu

[PyMOL] Does (PDB) size really matter? (Help!)

2004-04-24 Thread Jason Vertrees
(max) atoms out. Much TIA, -- Jason -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http://www.bscb.utmb.edu

[PyMOL] Does (PDB) size really matter?

2004-04-25 Thread Jason Vertrees
script is as in the previous message. As of now, I'll try smaller hash_max's and also if that's not good, reduce the size of my circular lipid bilayer. Many thanks for the quick response! Regards, -- Jason -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http

[PyMOL] Rendering artifacts?

2004-04-26 Thread Jason Vertrees
In the sample png above, I would like the light grey regions to be transparent. It also seems as if the quality of the render has gotten much poorer. Any ideas? -- Jason -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http://www.bscb.utmb.edu

[PyMOL] Re: PyMOL-users digest, Vol 1 #584 - 4 msgs

2004-04-27 Thread Jason Vertrees
tangible 3-5 years ago. Thanks for the suggestion! Regards, -- Jason -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http://www.bscb.utmb.edu

[PyMOL] Re: Recommendation for MPEG encoder?

2004-05-04 Thread Jason Vertrees
short: if you haven't check out 'mplayer/mencoder' with the DiVX codec, I think it can do what you want. -- Jason -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http://www.bscb.utmb.edu

[PyMOL] Re: PyMOL-users digest, Vol 1 #633 - 2 msgs

2004-07-02 Thread Jason Vertrees
Gabriel, I've managed to render scenes for a movie that had well over 100,000 atoms. For stills, I've rendered a nucleocapsid of over 292,000 atoms. So, I'm sure it can be done. I think the real large render only took a few minutes as well. -- Jason On Wed, 2004-06-30 at 22:47,

Subject: Re: [PyMOL] Producing publication quality images

2006-03-23 Thread Jason Vertrees
PyMol hints or tips to the wiki if you have one. -- Jason -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http://www.bscb.utmb.edu PyMol Wiki:: http://www.pymolwiki.org Vertrees dot Org :: http://www.vertrees.org

[PyMOL] PyMol AMD64

2006-04-11 Thread Jason Vertrees
, praedor -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http://www.bscb.utmb.edu PyMol Wiki:: http://www.pymolwiki.org Vertrees dot Org :: http://www.vertrees.org

[PyMOL] RFC: PyMolWiki

2006-09-27 Thread Jason Vertrees
improvement page and leave a comment (http://www.pymolwiki.org/index.php/Improvements). Cheers, -- Jason -- Jason Vertrees javer...@utmb.edu

[PyMOL] Kabsch CE Align

2007-01-03 Thread Jason Vertrees
or whenever I get the C/C++ code properly plugged into PyMol. (The C++ code on my machine aligns two 400+ residue proteins in about 0.250 seconds; the Python code for 167 residue proteins, 35 seconds!) Please forward bugs/comments to me, address below. Cheers, -- Jason -- Jason Vertrees javer

[PyMOL] CE Align v0,1

2007-01-11 Thread Jason Vertrees
). Cheers, -- J -- Jason Vertrees http://vertrees.org/ http://pymolwiki.org/ http://best.utmb.edu/

[PyMOL] CE Align Wiki

2007-01-16 Thread Jason Vertrees
, -- Jason Vertrees (javer...@utmb.edu) http://vertrees.org/ -- HOME http://pymolwiki.org/ -- PyMol Wiki http://best.utmb.edu/ -- Protein Science http://www.andeanimporters.com/ -- Biz.

[PyMOL] How to superimpose two ligands?

2007-01-17 Thread Jason Vertrees
ligands from different PDBs? Thanks in advance. Feng. -- Jason Vertrees (javer...@utmb.edu) http://vertrees.org/ -- HOME http://pymolwiki.org/ -- PyMol Wiki http://best.utmb.edu/ -- Protein Science http://www.andeanimporters.com/ -- Biz.

[PyMOL] PyMolWiki Update

2007-01-18 Thread Jason Vertrees
installed the captcha image for automated spam protection. I will leave the wiki open like this until spammers prove the change unwise. -- Jason -- Jason Vertrees http://vertrees.org/ http://pymolwiki.org/ http://best.utmb.edu/

[PyMOL] How to superimpose two ligands? (GAO FENG) -- Followup

2007-01-18 Thread Jason Vertrees
could solve the problem entirely, but would need some modification to do so. Sorry if I confused anyone. References if needed: http://www.pymolwiki.org/index.php/Kabsch http://www.pymolwiki.org/index.php/Cealign Regards, -- Jason -- Jason Vertrees http://vertrees.org/ http://pymolwiki.org

[PyMOL] CE Align v0.2 Request for Help (need Windows package).

2007-01-25 Thread Jason Vertrees
reports that it does indeed work. Details are also on the Wiki. Thanks, -- Jason -- Jason Vertrees (javer...@utmb.edu) Doctoral Student Biophysical, Structural Computational Biology Program University of Texas Medical Branch Galveston, Texas http://www.best.utmb.edu/ http

[PyMOL] Important Bug Fix in Kabsch

2007-02-20 Thread Jason Vertrees
freely given away for many prying eyes, this bug may have never been caught. Thanks again, Dan. Regards, -- Jason -- Jason Vertrees (javer...@utmb.edu) http://vertrees.org/ -- HOME http://pymolwiki.org/ -- PyMol Wiki http://best.utmb.edu/ -- Protein Science http://www.andeanimporters.com

Re: [PyMOL] Electrostatic surface visualization

2007-03-08 Thread Jason Vertrees
from Robert Campbell. A lot of useful scripts are posted on his website: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Cheers, Greg -- Jason Vertrees (javer...@utmb.edu) Doctoral Student Biophysical, Structural Computational Biology Program University of Texas Medical Branch

[PyMOL] CEAlign Updated to v0.6

2007-03-27 Thread Jason Vertrees
://www.pymolwiki.org/index.php/Cealign#Version_0.6 As usual, please forward bugs/issues to me, or if it interests the list, here. Cheers, -- Jason -- Jason Vertrees (javer...@utmb.edu) Doctoral Student Biophysical, Structural Computational Biology Program University of Texas Medical Branch

[PyMOL] Subject: Transparency in cartoons

2008-01-22 Thread Jason Vertrees
/Cartoon_transparency -- Jason -- Jason Vertrees (javer...@utmb.edu) Doctoral Candidate Biophysical, Structural Computational Biology Program University of Texas Medical Branch Galveston, Texas http://www.best.utmb.edu/ http://www.pymolwiki.org/

Re: [PyMOL] Algorithm to Rotate One Set of Vectors onto Another

2008-01-29 Thread Jason Vertrees
of orthogonal vectors. Thanks! and all the best, --Buz -- Jason Vertrees (javer...@utmb.edu) Doctoral Candidate Biophysical, Structural Computational Biology Program University of Texas Medical Branch Galveston, Texas http://www.best.utmb.edu/ http://www.pymolwiki.org/

[PyMOL] PyMOLWiki Updates

2008-03-11 Thread Jason Vertrees
, please let us know how we can improve the wiki to better serve the community. Each wiki page has its own discussion page for comments. Just add your comments or feel free to update the content as you see appropriate. -- Jason -- Jason Vertrees (javer...@{utmb,cs.dartmouth}.edu) Doctoral

[PyMOL] Cool New Ways to Use PyMOL

2008-03-11 Thread Jason Vertrees
you. That's cool! They even have a video. The PyMOLWiki link is -- http://www.pymolwiki.org/index.php/ImmersiveViz I also hear that the code will be available soon. -- Jason -- Jason Vertrees (javer...@{utmb,cs.dartmouth}.edu) Doctoral Candidate Biophysical, Structural Computational

[PyMOL] Head Tracking: ImmerseViz

2008-04-25 Thread Jason Vertrees
cool idea, with lots of potential for cool extensions. -- Jason -- Jason Vertrees (javer...@{utmb,cs.dartmouth}.edu) Doctoral Candidate Biophysical, Structural Computational Biology Program University of Texas Medical Branch Galveston, Texas http://www.best.utmb.edu/ http://www.pymolwiki.org/

[PyMOL] Subject: Displaying multiple models from 1 pdb file

2008-05-20 Thread Jason Vertrees
split_states: # (1) load the CE result file load /path/to/ceResults.txt # (2) call split_states to show the other molecule split_states ceResults HTH, -- Jason -- Jason Vertrees, PhD (javer...@{utmb,cs.dartmouth}.edu) http://www.best.utmb.edu/ http://www.pymolwiki.org/

[PyMOL] NMR Chemical shift perturbation data to surface representation

2008-06-23 Thread Jason Vertrees
things such as trying to get it to b-factor like position but haven't been successful. Is there any way I can get the data to be shown in pdb with various colors representing low/high perturbation in chemical shifts? Ankit -- Jason Vertrees, PhD Dartmouth: j...@cs.dartmouth.edu (new) UTMB

Re: [PyMOL] Script for iterated `align`ment API for CEalign

2008-09-04 Thread Jason Vertrees
/Cealign Super -- http://www.pymolwiki.org/index.php/Super optAlign-- http://www.pymolwiki.org/index.php/Kabsch HTH, -- Jason -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu Boston University : jas...@bu.edu PyMOLWiki : http://www.pymolwiki.org/

[PyMOL] PyMOL Wiki Update

2008-10-02 Thread Jason Vertrees
* 115 settings documented * 155 commands documented Last week alone we had about 1000 (non-bot) visitors that checked out about 6,000 pages. (**) == statistics with bots (*) == statistics w/o bots Cheers, -- Jason Vertrees -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu

[PyMOL] Possible Useful Script: loadDir

2008-10-20 Thread Jason Vertrees
# these two commands do the same thing, in this example loadDir nonBinders/*, *.pdb, group=nonBind loadDir nonBinders/classC, *.pdb, group=nonBind Cheers! -- Jason -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu Boston University : jas...@bu.edu PyMOLWiki

[PyMOL] Secondary structure elements

2008-12-02 Thread Jason Vertrees
) ) cmd.as(cartoon) -- Jason -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu Boston University : jas...@bu.edu PyMOLWiki : http://www.pymolwiki.org/ Jason Vertrees, PhD Boston U. -- jas...@bu.edu Dartmouth -- j...@cs.dartmouth.edu

[PyMOL] Subject: weighted alignment

2009-01-20 Thread Jason Vertrees
? Best regards Magnus Franzmann -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu Boston University : jas...@bu.edu PyMOLWiki : http://www.pymolwiki.org/

[PyMOL] PyMOLWIki Survey

2009-04-10 Thread Jason Vertrees
make the wiki a better place for us all. Follow the link to take the survey: http://www.surveymonkey.com/s.aspx?sm=NPHgdFVCWobsztKtjr5s5g_3d_3d You can also access the survey from the PyMOLWiki Main Page. Cheers, -- Jason -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu

[PyMOL] PyMOLWiki: Survey Results Searching

2009-04-21 Thread Jason Vertrees
). Cheers thanks again, -- Jason -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu Boston University : jas...@bu.edu PyMOLWiki : http://www.pymolwiki.org/

[PyMOL] GIT'r Done

2009-05-02 Thread Jason Vertrees
: +49 2461 61 5385 -- Jason Vertrees, PhD Boston U. -- jas...@bu.edu Dartmouth -- j...@cs.dartmouth.edu -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features

Re: [PyMOL] Error: unknown type

2009-05-14 Thread Jason Vertrees
part before this'll become widely used for the wiki. Thanks, -- Jason -- Jason Vertrees, PhD Boston U. -- jas...@bu.edu Dartmouth -- j...@cs.dartmouth.edu -- The NEW KODAK i700 Series Scanners deliver under ANY

[PyMOL] Distinct labels on white background (ray tracing)? (Jim Remington)

2009-06-08 Thread Jason Vertrees
, but this should get you going. HTH, -- Jason -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu Boston University : jas...@bu.edu PyMOLWiki : http://www.pymolwiki.org/ -- OpenSolaris 2009.06 is a cutting edge

Re: [PyMOL] PyMOL-users Digest, Vol 37, Issue 7

2009-06-09 Thread Jason Vertrees
() exposed.sort() print Solvent exposed residues (chain,residue): for res in exposed: print res select exposed, query in tmp dele tmp # visual confirmation color white color red, byres exposed set sphere_solvent as spheres orient Cheers, Warren -- Jason

[PyMOL] Subject: Re: Hi all...

2009-06-09 Thread Jason Vertrees
() exposed.sort() print Solvent exposed residues (chain,residue): for res in exposed: print res select exposed, query in tmp dele tmp # visual confirmation color white color red, byres exposed set sphere_solvent as spheres orient Cheers, Warren -- Jason

Re: [PyMOL] Select Residus on Surface

2009-06-22 Thread Jason Vertrees
have all the information you need. Cheers, -- Jason -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu Boston University : jas...@bu.edu PyMOLWiki : http://www.pymolwiki.org/ -- Are you an open source

Re: [PyMOL] disappearing data

2009-06-22 Thread Jason Vertrees
-stealing or slow GUI updates, but it did fix the blanking data. HTH, -- Jason -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu Boston University : jas...@bu.edu PyMOLWiki : http://www.pymolwiki.org

[PyMOL] Cool Script -- Interface Residues

2009-06-29 Thread Jason Vertrees
://www.pymolwiki.org/index.php/InterfaceResidues I hope someone finds this useful. Cheers, -- Jason -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu Boston University : jas...@bu.edu PyMOLWiki : http://www.pymolwiki.org

[PyMOL] PyMOLWiki RSS Useful Performance Setting

2009-07-02 Thread Jason Vertrees
/Texture_fonts Cheers, -- Jason -- Jason Vertrees, PhD Boston U. -- jas...@bu.edu Dartmouth -- j...@cs.dartmouth.edu -- ___ PyMOL-users mailing list (PyMOL-users

[PyMOL] CGO Circles

2009-07-31 Thread Jason Vertrees
and the script does the math for you. You can find the code on the PyMOLWiki: http://www.pymolwiki.org/index.php/CgoCircle Hope someone finds this useful, -- Jason -- Jason Vertrees, PhD Boston U. -- jas...@bu.edu Dartmouth -- j...@cs.dartmouth.edu

Re: [PyMOL] undisplaying residues

2009-09-01 Thread Jason Vertrees
the cartoon of the backbone also which i dnt want. Regards, Bala -- Jason Vertrees, PhD PyMOL -- http://www.pymol.org/ PyMOLWiki -- http://www.pymolwiki.org/ -- Let Crystal Reports handle the reporting - Free Crystal

Re: [PyMOL] Inexplicable exception raised by cmd.color()

2009-09-01 Thread Jason Vertrees
): raise QuietException return r Any explanation of the bug, or an effective workaround would be greatly appreciated. Thanks, Stuart Ballard Dept. of Biochemistry UW-Madison -- Jason Vertrees, PhD PyMOL -- http://www.pymol.org/ PyMOLWiki -- http://www.pymolwiki.org

[PyMOL] PyMOL on Mac OS X 10.6 (Snow Leopard)

2009-09-02 Thread Jason Vertrees
/bin/gcc-4.2 before installing or it will fail. But, make sure you reset it to gcc-4.2 after installing PyMOL or other installs might complain. If you had problems with the Tk window and openGL window fighting for focus, this has finally been fixed! Cheers, -- Jason -- Jason Vertrees, PhD

Re: [PyMOL] Getting ranges from selections

2009-09-02 Thread Jason Vertrees
. This could be just the loops, or interface residues defined with the script from Jason Vertrees. I use iterate for this and it works well enough, however I would like to be able to make: 1. a non-redundant list (e.g. residue 12 will only appear once) 2. adjacent numbers into ranges (e.g

[PyMOL] Bond command not functioning in script

2009-09-22 Thread Jason Vertrees
. of Biochemistry University of Wisconsin-Madison -- Jason -- Jason Vertrees, PhD (e) jason.vertr...@gmail.com http://www.pymol.org/ -- PyMOL http://www.pymolwiki.org/ -- PyMOLWiki -- Come build with us! The BlackBerryreg

[PyMOL] PyMOLWiki Update

2009-10-09 Thread Jason Vertrees
to the wiki. Cheers, Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your

Re: [PyMOL] how to get RMSD from CEalign command

2009-10-30 Thread Jason Vertrees
(query) cmd.delete(template) Hope this helps, -- Jason Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event

Re: [PyMOL] how to get RMSD from CEalign command

2009-10-31 Thread Jason Vertrees
know if it works for you. -- J Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org 2009/10/31 Thomas Evangelidis te8...@mbg.duth.gr: Thomas, The PyMOL UI runs asynchronously. I think you are deleting your PDB files before they can be aligned. I made a couple changes in your script

Re: [PyMOL] setting zoom level for objects

2009-11-04 Thread Jason Vertrees
Electrostatics, for 1cbs util.protein_vacuum_esp(1cbs) util.protein_vacuum_esp(1hmt) # turn on grid mode set grid_mode, 1 # put all 1cbs stuff into slot 1 set grid_slot, 1, 1cbs* # put all 1hmt stuff into slot 2 set grid_slot, 2, 1hmt* Hope that helps, Jason Vertrees, PhD PyMOLWiki -- http

[PyMOL] To all PyMOL supporters, a message from DeLano Scientific

2009-11-05 Thread Jason Vertrees
, and ask you to please bear with us while we plan for PyMOL's future. Thanks, Elizabeth Pehrson (Warren's wife) -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org -- Let Crystal Reports handle the reporting - Free

[PyMOL] A Page for Warren on the PyMOLWiki

2009-11-10 Thread Jason Vertrees
and will continue to grow, there is no doubt about that. HTH, -- Jason Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial

Re: [PyMOL] opening multiple files

2009-11-10 Thread Jason Vertrees
) cmd.load(pdbDir + loadName, loadName) Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Tue, Nov 10, 2009 at 1:08 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Matt, Well, then you're in for some nasty debugging. That will probably end with you slapping yourself

[PyMOL] Support Future of PyMOL (passing on a message from DeLano Scientific)

2009-11-10 Thread Jason Vertrees
to the mailing list and PyMOLWiki. While there will be hiccups along the way, we again wanted to reassure you that we are here, we are working, and we look forward to PyMOL growing into the software that Warren knew it could be. Sincerely, Beth Pehrson (Warren’s wife) DeLano Scientific LLC -- Jason Vertrees

[PyMOL] Helping DelSci PyMOL

2009-11-16 Thread Jason Vertrees
it forward as long as I can. Warren was peerless, but I will do my best to keep the ball rolling. -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org -- Let Crystal Reports handle the reporting - Free Crystal

[PyMOL] Journal Covers and Wiki Update

2009-11-18 Thread Jason Vertrees
widget to find things on the wiki The main complaint on the wiki is searching. Please let me know if these changes are helping or not. Thanks, -- Jason Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org -- Let

Re: [PyMOL] Journal Covers and Wiki Update

2009-11-18 Thread Jason Vertrees
A quick note on sending covers. When sending me a cover, please: * send me a scanned copy (please do not just copy the image from the journal's website, we don't want to break copyright laws); * send me the title and any other information/links you want posted. Thanks, -- J Jason Vertrees

Re: [PyMOL] make morph with rigimol

2009-11-20 Thread Jason Vertrees
object as a multistate object. Save the output to a mutli-state PDB with: save myConf.pdb, m_out, 0 then use that in your movies. HTH, -- Jason Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Nov 20, 2009 at 2:08 PM, Michael Zimmermann micha...@iastate.edu wrote: one

Re: [PyMOL] Problem Compiling Pymol 1.2.x

2009-11-20 Thread Jason Vertrees
Stephen, openSuse Linux does not come with Pmw installed by default. Please re-download and install Pmw. Let me know if it's something else. -- Jason Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Nov 20, 2009 at 4:54 PM, Justin Lecher j.lec...@fz-juelich.de wrote

Re: [PyMOL] make morph with rigimol

2009-11-20 Thread Jason Vertrees
I realized I made a mistake. The proper import statement is: from epymol import rigimol This is shipped in the incentive build of 1.1r2. -- Jaso Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Nov 20, 2009 at 2:50 PM, Huang, Xin h...@amgen.com wrote: Thanks Jason

Re: [PyMOL] why losing information about simulation box size in pdb file after edit it?

2009-11-26 Thread Jason Vertrees
160 commands documented. Most PyMOL API commands directly mirror their UI counterparts. For example, save fileName.pdb, objName, state=0 would simply translate to cmd.save( fileName.pdb, objName, state=0 ); Finally, welcome to PyMOL. -- Jason Jason Vertrees, PhD PyMOLWiki -- http

Re: [PyMOL] The CNT pdb file with the information about simulation box size

2009-11-28 Thread Jason Vertrees
this helps, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Thu, Nov 26, 2009 at 6:00 PM, Cun Zhang apzc2...@gmail.com wrote: hi, Jason. Thank you for your advice.  I  attach the pdb file at the end. Cun Zhang The script which is to delete the water molecules

Re: [PyMOL] Show hydrogen bonds in current object only

2009-11-29 Thread Jason Vertrees
) or a multi-state object. Nice attention to detail, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Sun, Nov 29, 2009 at 9:50 PM, Robert Campbell robert.campb...@queensu.ca wrote: Hi Jason, On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees jason.vertr...@gmail.com wrote

Re: [PyMOL] APBS plugin woes

2009-11-30 Thread Jason Vertrees
FYI, that worked for me. I just copied the binary to /usr/local/lib. -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Mon, Nov 30, 2009 at 2:56 PM, Michael Lerner mgler...@gmail.com wrote: Can you go to the Program Locations tab and find out which version of APBS

Re: [PyMOL] superimpose option

2009-12-08 Thread Jason Vertrees
Hope this helps, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Tue, Dec 8, 2009 at 2:07 AM, saeid mirzaei smirzae...@yahoo.com wrote: Hi everyone, could some one tell me I can use Pymol for superimposing two protein or not if so how can I use it? Thanks

Re: [PyMOL] superimpose option

2009-12-08 Thread Jason Vertrees
are shown in PyMOL. This extension does require either a matching Python distribution that which ships with PyMOL or that you compile PyMOL from source. Thanks for the note, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Tue, Dec 8, 2009 at 11:12 AM, Michael

Re: [PyMOL] Help Needed

2009-12-11 Thread Jason Vertrees
may have more biologically meaningful results with a server made especially for this task. Hope this helps, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Wed, Dec 9, 2009 at 5:57 PM, Kousik Kundu kou...@informatik.uni-freiburg.de wrote: Dear Sir,         I, Kousik

Re: [PyMOL] dynamic bonding

2009-12-14 Thread Jason Vertrees
structure they retain the bonding topology of the first structure. If you change any intermediate state, then they all change. Anyone else? -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Mon, Dec 14, 2009 at 11:30 AM, Nicolas Bock nicolasb...@gmail.com wrote: Hello

Re: [PyMOL] Read state number of an object

2009-12-15 Thread Jason Vertrees
JW, To get the state of a multi-state system, do: get state or get state, objectName See http://pymolwiki.org/index.php/State for a starting portal to other state-based info. You can similarly set a state: set state, stateNumber, object Hope this helps, -- Jason -- Jason Vertrees, PhD

Re: [PyMOL] List of Groups

2009-12-21 Thread Jason Vertrees
will be returned, too. So, if you don't use special naming for your groups, they will run together with other objects. -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Mon, Dec 21, 2009 at 6:45 PM, David Hall dwash59_2...@yahoo.com wrote: How would someone get the list

Re: [PyMOL] RMSD produced by align command

2010-01-01 Thread Jason Vertrees
helpful link: http://www.pymolwiki.org/index.php/Category:Structure_Alignment See: fit, optAlign, intra_fit_rms. Hope this helps, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Tue, Dec 29, 2009 at 1:27 PM, Thomas Evangelidis te8...@mbg.duth.gr wrote: Dear pymol users

Re: [PyMOL] ConnectedCloud tool_syntax problems

2010-01-07 Thread Jason Vertrees
this helps, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Thu, Jan 7, 2010 at 7:16 AM, ilaria carlone ilariacarl...@hotmail.com wrote: Hi everyone! I am using PyMOL for creating molecular surfaces (SAS), starting form a pdb file. I have some problems with large proteins

Re: [PyMOL] unable to initialize plugin

2010-01-08 Thread Jason Vertrees
Ilaria, Which plugin are you trying to use? Also, please beware that scripts and plugins are different and have different methods of install. Lastly are you using PyMOL 0.99, 1.x? -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Jan 8, 2010 at 9:21 AM, ilaria

[PyMOL] PyMOL Schrodinger

2010-01-08 Thread Jason Vertrees
will now point to pymol.org. If your favorite link is lost, please let me know ASAP, but please give us some time to arrange this I'm very excited for PyMOL and look forward to working with you all. Regards, -- Jason -- Jason Vertrees, PhD jason.vertr...@schrodinger.com PyMOL Product Manager

Re: [PyMOL] acquisition of PyMOL by Schrodinger

2010-01-08 Thread Jason Vertrees
the open-source community of PyMOL. Warren really enjoyed working with the folks at Schrödinger, said Ms. Beth Pehrson, the late Dr. DeLano's wife, I know this is what Warren wanted for PyMOL's future. -- Jason -- Jason Vertrees, PhD jason.vertr...@schrodinger.com PyMOL Product Manager Schrodinger

Re: [PyMOL] select atoms near electron density

2010-01-09 Thread Jason Vertrees
Michael, I don't think this is possible with PyMOL. Distance measures are calculated from objects. -- Jason -- Jason Vertrees, PhD jason.vertr...@schrodinger.com PyMOL Product Manager Schrodinger, Inc. On Fri, Jan 8, 2010 at 7:05 PM, Michael Zimmermann micha...@iastate.edu wrote: Dear

[PyMOL] Search?

2010-01-12 Thread Jason Vertrees
Hey all, Searching on the wiki should be fixed now. There were two errors that our awesome BitGnome admin fixed. I did some simple testing and it seemed to work just fine. Please let me know if you encounter any problems. Thanks, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager

Re: [PyMOL] PyMOL-users Digest, Vol 44, Issue 4

2010-01-12 Thread Jason Vertrees
of PyMOL by Schrodinger (Thomas Stout)   2. PyMOL Schrodinger (Jason Vertrees)   3. Re: acquisition of PyMOL by Schrodinger (Jason Vertrees)   4. select atoms near electron density (Michael Zimmermann)   5. Re: select atoms near electron density (Jason Vertrees)   6. Re: select atoms near

Re: [PyMOL] Display 'outer' surface only

2010-01-13 Thread Jason Vertrees
-- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best

Re: [PyMOL] Display 'outer' surface only

2010-01-13 Thread Jason Vertrees
- Quick question regarding this - I would like to do the inverse - that is, show only the surface of interior pockets. So: fetch 2hi4 run findSurfaceResidues.py findSurfaceResidues (1phv), 0.5 flag ignore, exposed_RESULT as surface, 2hi4 Yes? Jed Jason Vertrees wrote: Hugues, Here's

Re: [PyMOL] PyMol-Schrodinger: future on the Mac

2010-01-15 Thread Jason Vertrees
(and should work on 10.5). In the meantime if you're on 10.4, please use 1.2r2. I have to reconfigure the build environment to go back to 10.4. Thanks! -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Pymol Mobile viewer?

2010-01-17 Thread Jason Vertrees
mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1

Re: [PyMOL] get translation / rotation matrix from super

2010-01-19 Thread Jason Vertrees
-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts

[PyMOL] New Feature Ideas

2010-01-19 Thread Jason Vertrees
for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] get translation / rotation matrix from super

2010-01-20 Thread Jason Vertrees
___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger

Re: [PyMOL] Getting information fron selected objects

2010-01-20 Thread Jason Vertrees
@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts

Re: [PyMOL] Feature Requests/Ideas (Sean Law)

2010-01-20 Thread Jason Vertrees
object name, to make it a multistate object. -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA

Re: [PyMOL] New Feature Ideas

2010-01-20 Thread Jason Vertrees
to be honest but the benefits could be huge. A couple of problems could be solved at once, such as integration into web pages or documents, mobile devices, etc. without any plugins or Java stuff. Interesting. -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e

Re: [PyMOL] New Feature Ideas

2010-01-20 Thread Jason Vertrees
feature enhancement at some point in the recent past. Cheers. On 1/19/2010 11:26 PM, Jason Vertrees wrote: PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page

Re: [PyMOL] new ideas

2010-01-20 Thread Jason Vertrees
structure into another or superpose 2 structures manually. Is it possible? Or I want to move a fragment of the molecule relative to the rest of the molecule. Is it possible? Maia -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603

[PyMOL] PyMOL on the Mac

2010-01-20 Thread Jason Vertrees
PyMOLers, I just want to quickly reiterate: PyMOL will still be supported on the Mac--no need to worry. Even though other Schrodinger software doesn't run on the Mac, PyMOL will. MacPyMOL will live on. Best, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e

Re: [PyMOL] New Feature Ideas

2010-01-20 Thread Jason Vertrees
level of undo. I predict this will be around after we do some major refactoring--possibly in PyMOL 2.0. :-) Thanks for your suggestions. -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] new ideas

2010-01-20 Thread Jason Vertrees
/pymol/__init__.py:                if freemol_libpy not in sys.path: modules/pymol/__init__.py:                    sys.path.append(freemol_libpy) Hopefully this all helps. -David - Original Message From: Maia Cherney ch...@ualberta.ca To: Jason Vertrees jason.vertr

[PyMOL] Feature Requests Hint

2010-01-20 Thread Jason Vertrees
PyMOLers, Just a quick note: if you're on the list and see a feature you like, please reply to that email with a quick yea vote. It's even better if you let us know why you like it. Silence regarding a feature only down-weights its perceived importance. Thanks, -- Jason -- Jason Vertrees

Re: [PyMOL] Feature Requests Hint

2010-01-21 Thread Jason Vertrees
. # ray trace the png imageName.png ,22.5cm, 10cm, dpi=300 Food for thought, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

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