[PyMOL] (no subject)

2019-03-16 Thread Len Banaszak
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[PyMOL] (no subject)

2018-10-16 Thread Jose Arturo Sanchez Paz
Please unsubscribe me. -- *Dr. Arturo Sánchez* Full member of the American Society for Virology Full Member of the World Society for Virology Miembro de la Red Mexicana de Virología Miembro del Consejo Consultivo Científico de la CIBIOGEM *Centro de Investigaciones Biológicas del Noroeste

[PyMOL] (no subject)

2018-10-11 Thread P Divya
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[PyMOL] (no subject)

2018-10-07 Thread ragini sinha
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Re: [PyMOL] (no subject)

2017-07-31 Thread David Hall
For some reason, the people doing brew have decided to stop supporting compiling tcl-tk with X11 support. Not 100% sure, but I'm pretty certain pymol cannot use tcl-tk with aqua. If you already had pymol installed, this seems to eliminate the external gui. If you didn't, new installations of pymol

[PyMOL] (no subject)

2017-07-29 Thread jacky zhao
Hi, pymol external gui menus missing, I have compiled pymol in mac os by using brew. Anyone can provide some suggestions? Jacky -- Lei Zhao, Ph.D. & M.D. Associate Professor National Clinical Research Center for Normal Aging and Geriatric National Engineering Research Center for Antibody Medici

Re: [PyMOL] (no subject)

2017-04-04 Thread Vivien Schoonenberg
This worked! Thank you Leandro and Jed! From: jedg...@gmail.com [mailto:jedg...@gmail.com] On Behalf Of Jed Goldstone Sent: Tuesday, April 4, 2017 11:35 To: Vivien Schoonenberg Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] (no subject) Try using remove not alt +A to remove

Re: [PyMOL] (no subject)

2017-04-04 Thread Jed Goldstone
Try using remove not alt +A to remove alternative conformations. Jed On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg < vivienschoonenb...@gmail.com> wrote: > Hi there, > > > > I’m saving the sequences from each chain of the PDB via pymol with > > >>save something.fasta, chain A > > > > Th

Re: [PyMOL] (no subject)

2017-04-04 Thread Leandro Bortot
Hi, You probably have a pdb file which has multiple possible conformations for some residues. You can check this by visual inspection of such residues. They have two side chains coming from the same CA. In the text file you can see the conformations marked as A and B in the residue name field

[PyMOL] (no subject)

2017-04-03 Thread Vivien Schoonenberg
Hi there, I'm saving the sequences from each chain of the PDB via pymol with >>save something.fasta, chain A This is the same sequence that is shown in pymol and seems to correspond to the structure I am looking at. However, when I loaded new B-factors in my structure, I noticed somethin

[PyMOL] (no subject)

2015-12-10 Thread Dan Lin
Dear all: It appears that pymol only interpolates motions that include rotations by moving the object along an arc. I would like to make a movie that does not do this, but rather, moves the object along a straight line while rotating the object. Unfortunately, I'm absolutely at a loss about how I

[PyMOL] (no subject)

2015-10-09 Thread Raag Saluja
Hi! What is the command for superimposing a .gro file and a .pdb file in PyMOL? I tried opening the .gro file and then loading the .pdb file. Consequently, I could only see the latter and not the former. Thank you in advance! -- Regards, Raag

[PyMOL] (no subject)

2015-08-04 Thread Dak Aboah Monrovia
daka...@yahoo.com-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-

Re: [PyMOL] (no subject)

2015-04-20 Thread Edward A. Berry
On 04/19/2015 02:08 AM, leila karami wrote: > Dear Marcelo > > Thanks for your quick answer. > > Unfortunately, I can't open the link (https://www.pymol.org/citing) you > suggested me. perhaps your firewall or browser is blocking the https: connection or rejecting the certificate? Try http: in

Re: [PyMOL] (no subject)

2015-04-18 Thread Marcelo Marcet
Hi Leila, No problem, here is the content of the site. If you need the reference manager files (BibTex or EndNote files), I am happy to email them to you as well. Cheers, Marcelo Citation Format Please cite PyMOL, AxPyMOL and JyMOL as shown below. Be sure to edit the version number in acco

Re: [PyMOL] (no subject)

2015-04-18 Thread Jordan Willis
PyMOL The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC. JyMOL The JyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC. AxPyMOL The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 1.7.4 Schrödinger, LLC. > On Apr 18, 2015, at 11:08 PM, leila karami

[PyMOL] (no subject)

2015-04-18 Thread leila karami
Dear Marcelo Thanks for your quick answer. Unfortunately, I can't open the link (https://www.pymol.org/citing) you suggested me. Thanks in advance. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop

Re: [PyMOL] (no subject)

2015-04-18 Thread Marcelo Marcet
Hi Leila, Take a look at the link below: https://www.pymol.org/citing Cheers, Marcelo > On Apr 18, 2015, at 11:55 PM, leila karami wrote: > > Dear all > > How to cite pymol in my paper? > > Thanks. > -

[PyMOL] (no subject)

2015-04-18 Thread leila karami
Dear all How to cite pymol in my paper? Thanks. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bo

[PyMOL] (no subject)

2014-09-01 Thread Pawe? Gniewek
Hi all, I wonder if it's possible to fill the space (like in the case of nucleotide's ring) between three arbitrary/selected atoms. I'm trying to render an object which is not a biomolecule so "cartoon_ring_mode" is no use for me. Cheers, pawel ---

Re: [PyMOL] (no subject)

2014-07-02 Thread Thomas Holder
Hi Aliya, yes, likely there is a clash. But that's hard to tell without seeing your data. Cheers, Thomas On 01 Jul 2014, at 11:34, Aliya Holland wrote: > Hello, > > I just created an animation of a conformational change of a specific domain > on a molecule. During the animation the domain

[PyMOL] (no subject)

2014-07-01 Thread Aliya Holland
Hello, I just created an animation of a conformational change of a specific domain on a molecule. During the animation the domain rotates just as it should, however other parts of the molecule moves with the conformation change. I was wondering if that was part of the PyMOL programming or if ther

Re: [PyMOL] (no subject)

2013-06-17 Thread Gianluigi Caltabiano
Auto vyzdobena http://www.domarn.se/capcutgrahampatterson/?vhotmailID=gfesuzgz -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _

Re: [PyMOL] (no subject)

2013-04-26 Thread Davi de Miranda Fonseca
My PyMOL 1.5.0.5 works fine in Windows 8 (64 bits). Try the following: - Press Windows Key + Q - This should open the search apps thingy, type pymol - It should show all PyMOL shortcuts, try the "PyMOL + Tcl-Tk GUI + Console" - Does PyMOL still refuses to open? Did you get any error message? On 2

Re: [PyMOL] (no subject)

2013-03-20 Thread Thomas Holder
Hi Nina Marie, I haven't tested that thoroughly, but for me Incentive PyMOL 1.5.0.5 runs fine on Windows 8. Cheers, Thomas Wolf, Nina Marie wrote, On 03/19/13 21:11: > Hi, > > I recently upgraded my computer to windows 8. Since then, pymol will not > open. Is the latest version of pymol incom

[PyMOL] (no subject)

2013-03-19 Thread Wolf, Nina Marie
Hi, I recently upgraded my computer to windows 8. Since then, pymol will not open. Is the latest version of pymol incompatible with windows 8? Or is there something I can do to get it working on my computer? -- Everyon

Re: [PyMOL] (no subject)

2012-11-26 Thread Jason Vertrees
Hi Mary, Just a hint for any future lists you might be on: most modern email lists, including pymol-users, have footers with links to subscription options. You simply click that to get to a subscription page where you can unsubscribe. In this case, I removed you from the list to save you the hass

[PyMOL] (no subject)

2012-11-26 Thread Mary Hall
How do I remove myself from the PyMOL users list? I'd like to stop receiving emails. Thank you. M. Hall -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps

[PyMOL] (no subject)

2012-06-13 Thread Mintu Chandra
I have downloaded the pymol linux version in my kubuntu 12.4 , but while > installing, it is asking for -Kubuntu 11.04 _Natty Narwhal_ - Release i386 > (20110427.1). Please suggest me what shoul i do??? -- Live Security Vir

[PyMOL] (no subject)

2011-10-29 Thread guridis
This message was sent using IMBB - WebMail. -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App Wo

Re: [PyMOL] (no subject)

2011-09-04 Thread Thomas Holder
Hi Noloofar and Lina, >> I would like to calculate partial charges of my pdb. Is it possible to do it > > In pymol: > > Action-> compute -> partial charge sum this doesn't calculate partial charges, sorry. This does: Action -> generate -> vacuum electrostatics But better would be to use pdb2p

Re: [PyMOL] (no subject)

2011-09-04 Thread lina
On Sun, Sep 4, 2011 at 8:37 PM, niloofar niknam wrote: > > > Deal list, > I would like to calculate partial charges of my pdb. Is it possible to do it In pymol: Action-> compute -> partial charge sum > by Pymol? If not, Is anyone know any server > or  software to do it? > I have another questi

[PyMOL] (no subject)

2011-09-04 Thread niloofar niknam
  Deal list, I would like to calculate partial charges of my pdb. Is it possible to do it by Pymol? If not, Is anyone know any server or  software to do it? I have another question too, when aligning two structure in Pymol, there is a RMSD for the total structure, is there any command to cal

Re: [PyMOL] (no subject)

2010-05-28 Thread Nat Echols
On Fri, May 28, 2010 at 10:49 AM, Thomas Juettemann wrote: > Hi Chris, > > the emails are only sent to you because you subscribed to the pymol-users > list. > If you don't want them anymore you need to unsubscribe. > > Click on "Show details" at the top of this email. Click then on: > unsubscribe

Re: [PyMOL] (no subject)

2010-05-28 Thread Thomas Juettemann
Hi Chris, the emails are only sent to you because you subscribed to the pymol-users list. If you don't want them anymore you need to unsubscribe. Click on "Show details" at the top of this email. Click then on: unsubscribe Unsubscribe from this mailing-list That will do the magic. On Fri,

[PyMOL] (no subject)

2010-05-28 Thread Christian De Ford
Please stop sending me daily emails its very annoying, i would appreciate if you erase me from the list Thank you! -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourcefo

[PyMOL] (no subject)

2009-09-01 Thread Joel Tyndall
PS is it possible to run two versions at once on a PC (a quick test failed) _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand http://www.researcherid.com/rid/C-2803-2008

Re: [PyMOL] (no subject)

2009-03-24 Thread Warren DeLano
__ From: Rotem Sertchook [mailto:rotem.sertch...@weizmann.ac.il] Sent: Tuesday, March 24, 2009 12:11 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] (no subject) Hi, I'm looking for a way to calculate set of torsion angels from selected residues (for example Chi1 dihedral

Re: [PyMOL] (no subject)

2009-03-24 Thread gilleain torrance
Hi, I think that it probably is possible to do this from within pymol, and probably quite convenient for single molecules. However, there are two other possible approaches, which would be helpful for multiple molecules. Firstly, there is a program called 'dang' made by the Richardson group: htt

[PyMOL] (no subject)

2009-03-24 Thread Rotem Sertchook
Hi, I'm looking for a way to calculate set of torsion angels from selected residues (for example Chi1 dihedral of all His residues). Is it possible to write PyMOL script for such task ? Any hints to write such script will be appreciated! Thank you Rotem -

Re: [PyMOL] (no subject)

2009-02-19 Thread Warren DeLano
ursday, February 19, 2009 5:42 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] (no subject) > > Hello all especially Warren, > > What does > > "Sorry, time-sequential stereo 3D not available" > > mean. It is printed out when

[PyMOL] (no subject)

2009-02-19 Thread Justin Lecher
Hello all especially Warren, What does "Sorry, time-sequential stereo 3D not available" mean. It is printed out when I start pymol. I am using current HEAD. Thanks justin -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH,

[PyMOL] (no subject)

2008-02-26 Thread Grigoryan Hasmik
hasg...@yahoo.com - Looking for last minute shopping deals? Find them fast with Yahoo! Search.

Re: [PyMOL] (no subject)

2007-04-18 Thread DeLano Scientific
-users@lists.sourceforge.net > Subject: [PyMOL] (no subject) > > Hello, > I would like to ask about building phosphate group at Tyr > residue. Is there any posibility to do it at PyMOL programe? > Thank you for answer > Martin Sztacho > > ---

[PyMOL] (no subject)

2007-04-16 Thread Martin Sztacho
Hello, I would like to ask about building phosphate group at Tyr residue. Is there any posibility to do it at PyMOL programe? Thank you for answer Martin Sztacho

Re: [PyMOL] (no subject)

2007-02-23 Thread Tsjerk Wassenaar
Dear Bernhard, The user manual is quite informative where it comes to making selections. There is not a polar/nonpolar grouping made for you, but you can easily select the residues based on their names (resn or r.). select basic, (resn lys,his,arg) As a side note, on this as well as all other u

[PyMOL] (no subject)

2007-02-23 Thread Bernhard Kleine
Hello and good morning, being newly arrived in this list, I am a molecular biologist working recently in endocrinology and epigenetics and living in the black forest in the south west of germany. Since I am not fully content with the picture quality which I can get with Rasmol, I am trying to use

Re: [PyMOL] (no subject)

2006-11-07 Thread gilleain torrance
Hi, I don't know how simple you want it, but python lets you print just like: print cmd.distance(a, b) assuming that a and b are strings that are atom selections. See http://www.pymolwiki.org/index.php/Translate_And_Measure for a more complex example! :) gilleain On 11/7/06, Giacomo B

[PyMOL] (no subject)

2006-11-07 Thread Giacomo Bastianelli
Dear Users, I would like with a simple script to export some data regarding distances. Do any of you know how to write an output with all distances that I set up? Thanks in advance Giacomo Giacomo Bastianelli EIMID Ph.D Fellow (www.eimid.org ) Marie Curie EST gba

[PyMOL] (no subject)

2006-08-10 Thread mati
hello all pymol draw lines between near atom with no real connection between them! I wanted to know if there is a way to prevent pymol of making the bonds (lines) between atom and that pymol will connect atom only by a specific request (like a connect line in the pdb file) CONECT 416 778 (wh

Re: [PyMOL] (no subject)

2006-07-17 Thread Donglu Xie
sive, possibly because the displays aren't necessarily > sync'd on the VBL, or because the LCD context may not be stereo-capable. > > Cheers, > Warren > > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists

[PyMOL] (no subject)

2006-07-13 Thread Donglu Xie
Hi Dear Pymol-users, Sorry about this long message. I am struggling to configure X Windwo to enable stereo. Two monitors are connected with the NVIDIA GPU Quadro FX 3400 card. One monitor is ViewSonic VP2030b LCD, another is ViewSonic G225fb CRT. Try to configure X widnow to enable stereo with Xi

[PyMOL] (no subject)

2006-07-07 Thread Gabrielle Malo
Hello all, I am a new PyMOL user trying to prepare figures for publication. I'm confused about the difference between the isomesh level of the 'mesh' in PyMOL and the contour level of the electron density map that I read in from CCP4. For example, for one of my figures I created a 3sigma Fo

[PyMOL] (no subject)

2006-05-29 Thread O. J. Ganesh
Hey again PyMOL gurus, >* O. J. Ganesh [2006-05-18 16:09] wrote: >> >> Hey PyMOL gurus: >> >> I have a 'perfect' helix. Is there some way to 'loosen' all of the >> angles in the helix so instead of 3.6 residues per turn, I could >> have, say, 8 residues per turn. My goal is to make the heli

[PyMOL] (no subject)

2006-04-20 Thread Orla O'Sullivan
Hi all This probably a very stupid question but its driving me mad. I have produced two Raster 3D scences using molscript and have loaded them into pymol. What I want to do is to be able to move them on screen independent of each other. Is this possible? Regards Orla Dr.Orla O'Sulli

Re: [PyMOL] (no subject)

2006-03-26 Thread Andrea Spitaleri
Hi, for this purpose I have used caver program. You can download it free of charge from here http://loschmidt.chemi.muni.cz/caver/download.php I hope this help Regards andrea 2006/3/27, srilath...@jubilantbiosys.com : > dear sir > iam a pymol user, do we can find area & volume of a

[PyMOL] (no subject)

2006-03-26 Thread Srilatha_P
dear sir iam a pymol user, do we can find area & volume of active site in pymol if we can, just tell me how to do it thanking you srilathaThanks & Regardssrilatha potlapellyMSc Biotechnology

Re: [PyMOL] (no subject)

2006-03-06 Thread gilleain torrance
Hi, I found out how to do ... something ... like this the other day.

RE: [PyMOL] (no subject)

2006-03-04 Thread EPF (Esben Peter Friis)
half of Blanton Tolbert Sent: Sat 2006-03-04 15:01 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] (no subject) Hi pymol community I would like to recapitulate the crystal packing arrangement of a protein structure to look for neighbor interactions. Is it possible to do this in pymol?

[PyMOL] (no subject)

2006-03-04 Thread Blanton Tolbert
Hi pymol community I would like to recapitulate the crystal packing arrangement of a protein structure to look for neighbor interactions. Is it possible to do this in pymol? If so, please provide me some insight. Thanks, Blanton Tolbert Graduate Student University of Rochester Biophysic

Re: [PyMOL] (no subject)

2006-03-03 Thread Andrea Spitaleri
Hi try align or fit regards andrea 2006/3/3, srilath...@jubilantbiosys.com : > dear all > can we superimpose structures in pymol > Thanks & Regards > srilatha potlapelly > MSc Biotechnology > Drug discovery, > #450,4th D Main, 12th cross, > Mahalakshmipuram - 560086 > Bangalore > Office: +9180-2

[PyMOL] (no subject)

2006-03-03 Thread Srilatha_P
dear all can we superimpose structures in pymolThanks & Regardssrilatha potlapellyMSc BiotechnologyDrug discovery, #450,4th D Main, 12th cross, Mahalakshmipuram - 560086 Bangalore Office: +9180-23495461-64  Extn.-1029

[PyMOL] (no subject)

2005-11-02 Thread D . Bryan Prince
To all: I am new to PyMol, and to structure programs in general. I am trying to build a beta sheet from a peptide molecule in the pdb. I can't seem to load more than one molecule at a time, and I do not see any instructions related to it in the manual. I am running version 0.98 beta 32 on a M

RE: [PyMOL] (no subject)

2005-09-25 Thread Warren DeLano
sourceforge.net] On Behalf Of > Joseph Fernandez > Sent: Sunday, September 25, 2005 11:19 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] (no subject) > > There is a very useful functionality in Sybyl, whereby the > user can "merge" a residue from

[PyMOL] (no subject)

2005-09-25 Thread Joseph Fernandez
There is a very useful functionality in Sybyl, whereby the user can "merge" a residue from one molecular area, into another molecular area. The residue then becomes a part of the latter moleculear area, without deleting it. I wonder whether there is such a functionality in PyMol. As an example

RE: [PyMOL] (no subject)

2005-07-28 Thread Warren DeLano
delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of yi zhang > Sent: Sunday, July 24, 2005 8:43 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] (no subjec

Re: [PyMOL] (no subject)

2005-07-25 Thread lieven
On Sunday 24 July 2005 05:42, yi zhang wrote: > cmd.symexp('sym', 'obj', 'obj',10 ) > > of course, I can manually save each symmetry-related > molecule to *.pdb file by clicking save molecule > button, but how can I write a script to save all of > them or part of them? the symmetry-related objects

[PyMOL] (no subject)

2005-07-23 Thread yi zhang
Hi, everyone, I used symexp command in pymol to generate symmetry-related molecule, something like: cmd.symexp('sym', 'obj', 'obj',10 ) of course, I can manually save each symmetry-related molecule to *.pdb file by clicking save molecule button, but how can I write a script to save all of them

Re: [PyMOL] (no subject)

2005-07-20 Thread Joel Tyndall
Check out the post on "High end graphics". This will solve the problem. Basically you can ray-trace your molecule at a resolution bigger tahn teh screen size and then cut it down afterwards effectively generating a high resolution graphic from a 72 dpi starting point Cheers J Kolli, Madhavi

[PyMOL] (no subject)

2005-07-20 Thread Kolli, Madhavi
Hi, I've just started using PyMol for making some figures. I'm very happy that it is so easy to use. However the resolution of my pictures is very bad even after rendering them. When I print them they are very pixellated. I'm sure there is something I'm not doing right. Any help, suggestions

[PyMOL] (no subject)

2005-02-16 Thread Alexey V Paramonov
Hi, I have a problem with PyMOl 0.97 viewing pdb file with several models (MODEL 1...ENDMDL) I can upload somewhere (or attach?) the screenshot + pdb file to show it (~1.3 Mb).

[PyMOL] (no subject)

2004-06-16 Thread James Stevens
Hi, The lab I am part of now has the licensed MacPymol incentive product. In response to the brilliant crystallography on OS X website maintained by Bill Scott, he recommends using a Powermate dial (Griffin Technology). I would like to follow in his footsteps, however the instructions he provi

[PyMOL] (no subject)

2004-04-26 Thread ELHAM MOHAMMADI
Hello! I have 2 questions: 1) What is the correct/common email address to send your questions on PyMOL? 2) I have downloaded PyMOL on a PC(microsoft windows XP)using the instructions posted on the PyMOL site. But I am not able to get input files form the Internet--I simply wanted to go to the PUB

RE: [PyMOL] (no subject)

2004-04-22 Thread Warren DeLano
ril 22, 2004 2:35 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] (no subject) > > > hi ppl, > > is there a way to sort the list of objects/selections in the > panel on the right side other than loading/selecting stuff in > a specific order? >

[PyMOL] (no subject)

2004-04-22 Thread Christian Rummey
hi ppl, is there a way to sort the list of objects/selections in the panel on the right side other than loading/selecting stuff in a specific order? simple example: I compare several ligands in a specific site, and save the data as pymol sessions; after adding new ligands//site conformations I'd

[PyMOL] (no subject)

2004-04-06 Thread xiaofeng qian
Hi,everybody: Is there someway so that I can generate several asymmetry molecules from one asymmetry unit in pymol? Thank you. Xiaofeng _ Check out MSN PC Safety & Security to help ensure your PC is protected and safe. http://s

RE: [PyMOL] (no subject)

2004-04-05 Thread Warren DeLano
ers-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Mohammad Wadud Bhuiya > Sent: Monday, April 05, 2004 5:53 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] (no subject) > > Dear pymol usres > > I want to increase

[PyMOL] (no subject)

2004-04-05 Thread Mohammad Wadud Bhuiya
Dear pymol usres I want to increase the resolution of the figure but how? Save file is png and resolution is very poor and print quality is not good. I also make CA model by xfit and save file is rasted3d and it is opened by pymol and save as png but figure is not good quality for its low reso

Re: [PyMOL] (no subject)

2003-08-20 Thread Matt Stephenson
Hi Blanton, Are you running the unstable tree, or have you just copied the pymol-0.90-2 package to stable, you either have to enable the unstable tree, or copy the numeric-py22 package from the unstable to stable, it can be found at '/sw/fink/dists/unstable/main/finkinfo/sci' see here; http

[PyMOL] (no subject)

2003-08-19 Thread Tolbert, Blanton
I was attempting to install pymol 0.9 using fink and got the following error message, Failed: Can't resolve dependency "numeric-py22" for package "pymol-0.90-2" (no matching packages/versions found) Can anyone advise me on what to do to get around this? Thanks in advance. Blanton

Re: [PyMOL] (no subject)

2003-05-28 Thread Cameron Mura
Hi Martin, Visit Robert Campbell's repository of PyMOL scripts (http://adelie.biochem.queensu.ca/~rlc/work/pymol/)...where you'll find Python scripts to import into PyMOL for drawing unit cell edges (draw_cell.py), symmetry axes (draw_symops.py), and lots of other stuff... Cameron mkie

[PyMOL] (no subject)

2003-05-28 Thread mkienetz
Dear All, How do I show the unit cell using pymol? Martin Martin Kienetz 429 MSB Department of Biochemistry University of Alberta Edmonton AB T6G 2H7 (780) 492-2422

Re: [PyMOL] (no subject)

2002-11-19 Thread Kristian Rother
Fei Xu wrote: HI! Dr. Delano: Would you like to tell me how I can control the size of the ball, if I pick an atom and show it like a ball? Dear Fei Xu: 1. You select an atom 2. You display it as a ball 3. You type: set sphere_scale = 2.0 Here, the number is the size proportional to an origina

[PyMOL] (no subject)

2002-11-19 Thread Fei Xu
HI! Dr. Delano: Would you like to tell me how I can control the size of the ball, if I pick an atom and show it like a ball? Have a nice day! Fei

[PyMOL] (no subject)

2002-10-31 Thread wgscott
Hi Lieven: I don't have windows pymol or access currently to a windows machine, so I will have to tell you how I did it on the Mac version and then hope it is essentially identical with windows. I did this about 6 months ago in order to hyperlink quicktime to Powerpoint in XP. I am assuming

RE: [PyMOL] (no subject)

2002-10-11 Thread DeLano, Warren
Subject: [PyMOL] (no subject) Hello, On the advice of a friend, I recently downloaded the OSX beta version of PyMOL. So far I'm very,very impressed. I have two questions: 1. How do you display a simple CA trace. I saw the selection for a backbone trace. 2. I want to rms-fit two struc

[PyMOL] (no subject)

2002-10-09 Thread Craig Smith
Hello, On the advice of a friend, I recently downloaded the OSX beta version of PyMOL. So far I'm very,very impressed. I have two questions: 1. How do you display a simple CA trace. I saw the selection for a backbone trace. 2. I want to rms-fit two structural homologs. How is this done

[PyMOL] (no subject)

2002-06-07 Thread Sona Vasudevan
Hello All, Need your help: I would like to overlay a cartoon representation onto a surface representation and would like to color certain residues that show up on the surface representation. This is what I did and recall doing awhile ago but it isn't working now. I would appreciate knowing what

Re: [PyMOL] (no subject)

2002-02-16 Thread Warren L. DeLano
On Sun, 17 Feb 2002, Nat wrote: > From an earlier reply... > > The easiest way to use PyMOL as a module is to use PyMOL as your Python > > interpreter. It isn't trivial to launch PyMOL from within a running > > Python interpreter, but it can be done under unix (only). See pymol.com > > and modul

[PyMOL] (no subject)

2002-02-16 Thread Nat

Re: [PyMOL] (no subject)

2001-11-22 Thread Warren L. DeLano
On Thu, 22 Nov 2001, Sona Vasudevan wrote: > Hi! > > Just wondering if there is a way to save a pymol session like in Insight > and setor if I want to get back to it. PyMOL isn't quite as sophisticated as Insight II in this respect, however the logging features can achieve session-like behavior

[PyMOL] (no subject)

2001-11-22 Thread Sona Vasudevan
Hi! Just wondering if there is a way to save a pymol session like in Insight and setor if I want to get back to it. Thanks. sona Sona Vasudevan National Center for Biotechnology Information National Library of Medicine National