[PyMOL] Learning Python for PyMOL

2001-12-10 Thread DeLano, Warren
-mode-alist)) (global-font-lock-mode) -- END .emacs excerpt -- 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: DeLano, Warren

RE: [PyMOL] CSD .dat files

2001-12-14 Thread DeLano, Warren
Charles, .dat is a hopefully oversubscribed file extension, and the .dat which PyMOL currently recognizes is for Macromodel. If you are have some development skills, consider writing a Python-based CSD file parser for the Chemical Python portion of PyMOL. Any ChemPy model can be loaded

RE: [PyMOL] pymol on SGI

2001-12-18 Thread DeLano, Warren
Danny, I think your problem is one of two possibilities: either your LD_LIBRARY_PATH is not being set correctly by pymol.com, or your python1.5.so shared object isn't valid. You might try using linking against a static Python library as described in

RE: [PyMOL] ray doubts

2002-01-18 Thread DeLano, Warren
Ricardo, Yes, ray makes a huge difference in quality. You get true specular reflections (not just OpenGL interpolations), you get perfectly round spheres, you get shadows, you get clean transparent surfaces (without artifacts), and you get better depth-cue fogging (although with light

RE: [PyMOL] Installing from source on a linux box

2002-02-04 Thread DeLano, Warren
Michael, Try checking out a new copy of the source code from the current CVS repository -- the Makefiles have been simplified somewhat, so compilation under Linux may go easier. You should only need to change the Python version in one place : ) Read INSTALL.linux-rh7x Cheers, Warren --

[PyMOL] Version 0.78 Release w/ RPMs

2002-02-06 Thread DeLano, Warren
PyMOL Version 0.78 is now available for download from http://pymol.sf.net I'm pleased to announce my first release of PyMOL Linux RPMs, which were made possible with assistance from Stephen Adler (Brookhaven NL). These should greatly simplify the installation process for RedHat 7.x users. Thanks

RE: [PyMOL] using external python interpreter to control pymol ??

2002-02-19 Thread DeLano, Warren
NOTE: the following is unix-specific. This is a common problem with PyMOL. Right now it is impossible (in practice) to use PyMOL as merely an imported module within an external interpreter (i.e. without using pymol.com instead of python to invoke the interpreter). This will be fixed in a later

RE: [PyMOL] RNA and Pseudo-atom Models

2002-02-28 Thread DeLano, Warren
Busy day on the list : ) I'll take this one... From: Albion Baucom [mailto:bau...@biology.ucsc.edu] Nice to hear from you Albion, glad to see you're finally getting a chance to try the package. I want to make high resolution, smooth (high frame rate) playing movies of the Ribosome. Great

RE: [PyMOL] multiple MODEL files

2002-03-25 Thread DeLano, Warren
From: Eckhart Guthöhrlein I'm trying to use pymol for the display of pdb files containing multiple models using the MODEL card. Indeed, pymol reads in all models in the file. Currently, I'm able to switch between them using the frame command. Is there a different way to do this?

RE: [PyMOL] H-bonds too thick

2002-04-10 Thread DeLano, Warren
From: Mario Sanchez [mailto:sanc...@if.sc.usp.br] I am drawing hydrogen bonds using command dist, but the rayied image has a too thick line to these interactions. I was not able to find the command to set the thickness of it, but I hope someone (DeLano?) will be able to help me. You can

RE: [PyMOL] easy (?) question

2002-05-01 Thread DeLano, Warren
From: Byron DeLaBarre [mailto:by...@slac.stanford.edu] Anyone out there know how to prevent bonding of adjacent but chemically unconnected atoms in pymol? Two step process: 1. edit the PDB file and replace ATOM with HETATM 2. after the HETATM's add a single record CONECT following by

RE: [PyMOL] Linux install problem

2002-05-03 Thread DeLano, Warren
Gareth, That is an unusual error. I suspect it has something to do with your symbolic links, which isn't the most reliable way to solve the dependency problem. Instead, delete those symlinks, and modify Rules.make to seek out the system libraries in the usual location. Rules.linux-rh7x

RE: [PyMOL] Let's Introduce Your Company To China Government

2002-05-03 Thread DeLano, Warren
From: Marc Saric [mailto:marc.sa...@mpi-dortmund.mpg.de] 2. Let's Introduce Your Company To China Government (investcn2...@yahoo.com.cn) ^ ^ ^ ^ Shouldn't that have been filtered out? Absolutely. After digging into the settings, I found that SourceForge doesn't protect these

RE: [PyMOL] problem importing pymol.cmd module

2002-05-06 Thread DeLano, Warren
Michael, A present, you can't simply import the PyMOL program as a module. You need to use PyMOL as your Python interpreter. You can use Run from the File menu or the run command from within PyMOL. PyMOLcd c:\some_directory PyMOLrun myscript.py Since you are under windows, you can use the

RE: [PyMOL] Colors and ray-tracing

2002-05-28 Thread DeLano, Warren
My guess is that you may still be showing sticks in the original object, instead of just cartoons. If you have the same overlapping representation in two objects, it isn't predictable which will show up in the ray-tracer, and you can get exactly this behavior, where you see one color in OpenGL

RE: [PyMOL] Update to ScriptBox 0.3 for PyMOL

2002-06-20 Thread DeLano, Warren
From: Kristian Rother [mailto:kristian.rot...@berlin.de] As suggested by Warren, i have made some improvements to the ScriptBox, which should integrate better into PyMOL now, Thanks Kristian! On my page, there is also a 'quick and dirty' hack for PyMOL. FilePipe.py allows to execute

RE: [PyMOL] How to run PyMol from within Python?

2002-07-09 Thread DeLano, Warren
From: Johan Leckner [mailto:jo...@pasteur.fr] I'm having problems running PyMol from within another Python program. This is not the recommended way to run PyMOL and may lead to problems. You can run Python programs within PyMOL as follows: from the command-line: pymol example.py #

RE: [PyMOL] color gradient

2002-07-11 Thread DeLano, Warren
Jeff, It would take a little Python programming, but modules/pymol/util.py has the rainbow command which can be modified so as to give a more restricted gradient than the current rainbow. usage: load prot.pdb util.rainbow(prot) (or just select the rainbow option on the color pop-up

RE: [PyMOL] Re: movie -script - conversion from .png to .tga

2002-07-15 Thread DeLano, Warren
Trissa, I think that the line may have been wrapped in your copy of the input file. Try making sure that entire Python in the script file appears on a single line -- then it should work. Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis

RE: [PyMOL] How to run PyMol from within Python?

2002-07-16 Thread DeLano, Warren
So there is no way to run and control PyMol from within another python program? If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, then you can launch PyMOL from an external Python program as shown in examples/devel/start_pymol.py. However, this is not recommended

RE: [PyMOL] pymol without GL

2002-07-17 Thread DeLano, Warren
Not right now... In order to build PyMOL without linking to real GL libraries, you'd either need a fake copy of the GL API, or #define out all of the gl calls in PyMOL (many hours of work). Sorry! Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis

RE: [PyMOL] molecular sculpting

2002-07-18 Thread DeLano, Warren
Molecular sculpting works like a real-time energy minimizer, except that it isn't minimizing the energy. Instead, its just trying to return local atomic geometries (bonds, angles, chirality, planarity) to the configuration the molecules possess when they were first loaded into PyMOL. To

RE: [PyMOL] Problem with Seleno-Cysteine

2002-08-06 Thread DeLano, Warren
alter eys/,type='ATOM' sort The problem is that, by default, PyMOL doesn't create ribbons for HETATMs (typically ligands and solvent). With the above command, you're converting selenocysteine residues into regular atoms and sorting them into place so that they can be included in the ribbon.

RE: [PyMOL] How to ouput a PDB file with transformed coordinates?

2002-08-08 Thread DeLano, Warren
No, not a stupid question. PyMOL doesn't currently provide a means for doing this -- I'll put it on the list... Cheers, Warren -Original Message- From: Luca Jovine [mailto:lucajov...@mac.com] Sent: Thursday, August 08, 2002 4:41 PM To: Mailing List PyMol Subject: [PyMOL] How to

RE: [PyMOL] byres, around, expand etc

2002-08-13 Thread DeLano, Warren
layer4/Selector.c http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/pymol/pymol/layer3/Selector.c search for SELE_ARD_ and SELE_EXP_ in SelectorModulate1 in and SELE_BYR1 in SelectorLogic1 -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341

RE: [PyMOL] Pymol slow on a mac G4 with os 10.1

2002-08-23 Thread DeLano, Warren
Yes, the Fink and GNU/Darwin versions of PyMOL are unaccelerated. As far as I know, the only way to get access to hardware is to call Apple's platform-specific OpenGL libraries from within a platform-specific window. I am still working on the native OSX port, but with competition from all

RE: [PyMOL] Re: Amber

2002-09-09 Thread DeLano, Warren
Michael, None of the official releases have Amber trajectory support (although the mac 0.84 beta may have an early version of this code). I'm planning on another release near the end of September. If you can build from the CVS repository, then you can use the code today: (1) make

RE: [PyMOL] electron density maps

2002-09-20 Thread DeLano, Warren
Scott, isomesh msh1, map1, 1.5, myobject, carve=2.1 The postfix carve=2.1 will trim density which is more than 2.1 A from myobject. You may want to play around with the exact cutoff... Cheers, Warren -Original Message- From: Scott Classen [mailto:clas...@uclink.berkeley.edu]

RE: [PyMOL] pair_fit crashes

2002-09-26 Thread DeLano, Warren
Hi Jeremy, If the proteins have significant homology, then you can use the align command: align prot1ca,prot2 which will perform a sequence alignment of prot1 against prot2, and then an optimizing fit using the CA positions. I'm not sure if the help text for align got into 0.82, but the

[PyMOL] RE: pyMol help (Ball Sticks)

2002-09-30 Thread DeLano, Warren
From: George Nicola I've tried several settings and commands but cannot figure out how to make a simple ball-and-stick representation of a molecule. Can it be done in Pymol? George, Yes, but it is non-obvious: hide lines show sticks show spheres set stick_radius=0.1 set sphere_scale=0.25

RE: [PyMOL] moving one segment relative to the rest

2002-09-30 Thread DeLano, Warren
Shohei, The easiest way to do this is to split the objects and then use the rotate command. # save as a .pml file... load 1FJ1.pdb # split PDB file create anti=(chain F) create fab=(chain A,B) # delete original object delete 1FJ1 # color objects color green,fab color pink,anti # color

RE: [PyMOL] Stereographics CrystalEyes problem

2002-10-08 Thread DeLano, Warren
Yep, we ran into the same problem with our ESGI emitters and FireGL2 cards -- we ended up having to buy new StereoGraphics (E-2) emitters for the Linux machines (~$200). http://www.qualixdirect.com/ part # SV-008-A-PC-E2 Cheers, Warren -Original Message- From: Viktor Hornak

RE: [PyMOL] CMYK colors

2002-10-22 Thread DeLano, Warren
Thanks for the suggestion? For now, why not just redefine the existing colors? No need for a leading underscore... set_color green= [0.00 , 0.53 , 0.22] etc. Note that there are default atom colors such as carbon, nitrogen, oxygen, hydrogen, sulfur, etc. which should also be redefined.

RE: [PyMOL] distance parameters

2002-10-23 Thread DeLano, Warren
From: Jules Jacobsen [mailto:jo...@hermes.cam.ac.uk] you can change most of the parameters using set dash_n where n= length, width, gap, radius. Unfortunately dash_color doesn't exist. ...but you can change the color of a distance object color red,dist01 Warren

RE: [PyMOL] PyMol Manual

2002-10-28 Thread DeLano, Warren
Gordon, I fully agree with your assessment that PyMOL is currently unable to reach its potential due to a number of factors, including poor documentation. Nevertheless, I do have a defined plan for eliminating these deficits. It involves securing funding to hire people under contract

RE: [PyMOL] Current settings list in Pymol OSX

2002-10-30 Thread DeLano, Warren
This is undocumented: To get a list of settings: from pymol import setting print setting.get_name_list() To get the current value of a setting: print setting.get_setting_text(bg_rgb) print setting.get_setting_text(gamma) To get a list of names with values: print map(lambda

RE: [PyMOL] making a two step movie in pymol

2002-10-30 Thread DeLano, Warren
mset 1 x360 movie.roll 1,180,1,axis=y movie.roll 181,360,1,axis=x -Original Message- From: Craig Smith [mailto:boiler...@mac.com] Sent: Wednesday, October 30, 2002 11:43 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] making a two step movie in pymol How do I create a

RE: [PyMOL] help with surface parameters

2002-11-11 Thread DeLano, Warren
Scott, From: Scott Classen [mailto:clas...@uclink.berkeley.edu] Hello fellow PyMOLers, Is the surface in PyMOL a solvent accessible surface or a molecular surface? It looks like a solvent accessible surface to me. Is there any way to change the radius of the water probe that is

RE: [PyMOL] Color plotting of electron density contours?

2002-11-12 Thread DeLano, Warren
Bill, There has been some discussion of this desirable feature, but it doesn't currently exist. Cheers, Warren -Original Message- From: wgsc...@chemistry.ucsc.edu [mailto:wgsc...@chemistry.ucsc.edu] Sent: Tuesday, November 12, 2002 1:27 PM To: pymol-users@lists.sourceforge.net

RE: [PyMOL] Pymol ignores SCALE records in PDB files

2002-11-27 Thread DeLano, Warren
Keith, Thank you for bringing this issue to my attention. I can confirm that PyMOL doesn't currently read SCALE records. In order to generate correct crystal symmetry, it requires the input PDB coordinates to be properly oriented and translated with respect to the crystal

RE: [PyMOL] Zooming in animations

2002-12-02 Thread DeLano, Warren
Chris, If you are talking about a controlled zoom into a specific active site region, there isn't any automated way to do this. Peter's movie.zoom routine can help with a general zoom. Try this: fragment arg mset 1 x100 movie.zoom 1,100,1,0 mappend 1:move z,-100 rewind mplay Cheers,

RE: [PyMOL] Rolling your own functions in PyMol

2003-01-07 Thread DeLano, Warren
Stephen, You're looking for the PyMOL API function extend: from pymol import cmd cmd.extend(ramp_colors,ramp_chain.ramp_colors) Would then permit the following: ramp_colors chain A See help extend for more info... Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D.

RE: [PyMOL] measuring distances

2003-01-08 Thread DeLano, Warren
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

RE: [PyMOL] 1pit.pdb

2003-01-12 Thread DeLano, Warren
Jack, What are all those extra Q atoms in the pdb file? They look to me like compromise/placeholder coordinates for NMR-equivalent hydrogens...or something like that. To get a reasonable picture, you can get rid of the extra bonds with unbond elem q*,all or just nuke the Q atoms

RE: [PyMOL] new user

2003-01-14 Thread DeLano, Warren
From: Nukri Sanishvili [mailto:rsanishv...@anl.gov] There is a new thing (I'm pretty sure it's a bug, not a feature) in 0.86: When I Tab for command completion, the command ends with a comma when in fact = is expected. For example, set cartoon_fl(Tab)at_sheets, not set

RE: [PyMOL] Separate surfaces

2003-01-20 Thread DeLano, Warren
Jacob, It look to me like you've found a bug in PyMOL with the manual approach. What's happening is that the result of a subsequent ignore command isn't updating the surface which was created before it. The scripted behavior is correct, since all geometric objects should reflect the

RE: [PyMOL] Bug in selections

2003-01-23 Thread DeLano, Warren
Carsten, You're bumping up against a 63-character limit I currently have for any one individual argument in PyMOL's internal parser. Obviously I need to either safeguard that limitation to prevent a crash or eliminate it. You can still do this in a single selection, as follows select

RE: [PyMOL] non-related question related: electrostatics

2003-01-28 Thread DeLano, Warren
Doug, (1) I've got a hard deadline to have this capability in the program less than 1 month from now...not the pot. calc., just the import, rendition, and coloring. (2) no clue Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis

RE: [PyMOL] q: discrete colors and adjacent cartoon segments

2003-01-28 Thread DeLano, Warren
Bartholomeus, You have run into limitations in PyMOL's handling of single objects. The answer to both these questions is to split your molecule into multiple object and color/show independently. Use the create command to make copies, and then use alter to reassign secondary structure codes

RE: [PyMOL] stop an accidental or problematic ray trace

2003-01-28 Thread DeLano, Warren
Anthony, I agree that we need one, but it doesn't currently exist. The same can be said for surface calculations, especially when you've loaded a 500 frame MD trajectory and accidentally show surface (doh!). My advice: save sessions often and make liberal use of PyMOL's logging capability.

RE: [PyMOL] Pymol and Autodock

2003-02-06 Thread DeLano, Warren
. 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: Alan Wilter Sousa da Silva [mailto:a...@biof.ufrj.br] Sent: Thursday, February 06, 2003 7:41 AM To: DeLano

RE: [PyMOL] select residues 4 angstrom away from the center atom or residue

2003-03-14 Thread DeLano, Warren
Certainly, For example: to create a selection near145 consisting of all atoms within 4 A of residue 145: select near145, all within 4 of 145/ And to select complete residues: select near145, byres ( all within 4 of 145/ ) Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D.

RE: [PyMOL] different transparencies

2003-03-16 Thread DeLano, Warren
internal raytracer isn't likely to support perspective any time soon. Instead, I recommend using PovRay. Cheers, Warren Subject: Re: [PyMOL] different transparencies DeLano, Warren wrote: Because of the way settings work in PyMOL, you will need to split your spheres into different objects

[PyMOL] A New Phase for PyMOL

2003-03-16 Thread DeLano, Warren
Dear PyMOL Users and Friends, It is with great excitement and anticipation that I announce a new phase for PyMOL: Beginning April 3rd, 2003, I will be committed FULL-TIME to the development, documentation, and support of this Open-Source package through my limited liability company,

RE: [PyMOL] fink install fail: pymol-0.86-4

2003-03-18 Thread DeLano, Warren
Kevin, It looks to me like you are missing Numeric Python. Either you need to remove the _PYMOL_NUMPY option from the Rules.make, or you need Numpy installed. There is likely a Fink package which contains it, but I suspect this dependency may have been missed in the creation of the

RE: [PyMOL] Transparent cartoons?

2003-03-18 Thread DeLano, Warren
Fred, Not currently. To the rest of the list: How important is this to people? Please send me an email directly if you think it would be an important feature to add. Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc.