Re: [PyMOL] pymol licensing questions

It is *not* the GPL. It is the Python license http://sourceforge.net/projects/pymol/ see also: http://www.python.org/doc/Copyright.html I hit the send too quickly, anyways there is a fundamental difference in that derivative works of pymol AFAIK can be made proprietary, not that this would be an

[PyMOL] ANNOUNCE: apropos command to lookup commands matching a keyword.

/Apropos [2] http://www.pymolwiki.org/index.php/Grepset Comments are welcome. Have fun, Zac # # apropos.py # Author: Ezequiel Panepucci # Date: 2006-07-20 # from pymol import cmd import re def apropos(regexp=''): ''' DESCRIPTION "apropos" search

[PyMOL] ANNOUNCE: apropos command to lookup commands matching a keyword.

/Apropos [2] http://www.pymolwiki.org/index.php/Grepset Comments are welcome. Have fun, Zac # # apropos.py # Author: Ezequiel Panepucci # Date: 2006-07-20 # from pymol import cmd import re def apropos(regexp=''): ''' DESCRIPTION "apropos" search

[PyMOL] Question: general purpose "get_prompt" function

Hello People, Anyone would know how to go about generating text messages on the viewer window like the ones you get when using the Wizard's get_prompt method, without having to resort to a wizard? reason: I have a little script to deal with a trackball and I use the buttons and scrollwheel to ch

Re: [PyMOL] loading electrostatic maps generated with apbs

Michael, | If really do have an up-to-date version of my code, we should probably | figure out what's wrong off-list. I have merged your extensions into PyMOL 0.95. Terrific work. I would like to suggest, although it may be added work for you, that you keep a set of files for the curren

[PyMOL] giving back to the list: summaries on questions posted

summaries were sent back to the list with the word "SUMMARY" on the subject line making it very easy to find answers. Of course this is not enforceable but I think suggesting it to posters would help getting it done. Cheers, Zac -- Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Bru

Re: [PyMOL] Powermate dial with Pymol on OS X

ucent use to deliver | higher performing products faster, at low TCO. | http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3 | ___ | PyMOL-users mailing list | PyMOL-users@lists.sourceforge.net | https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] nvidia quadro 700xgl opengl error

some feed back is always nice. Is there a good combination of the feedback args that will only disable the opengl messages? Many thanks, Zac -- Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414

Re: [PyMOL] graphics boards

Mark, You can get an Nvidia Quadro4 380 XGL which has a stereo connector. Nvidia keeps their drivers on almost the same (if not the same) release schedule as their MS Windows drivers, they are very stable and easy to install and maintain. Zac | I know this has been discussed before on this l

Re: [PyMOL] adding residues

c_id=3638&op=click | ___ | PyMOL-users mailing list | PyMOL-users@lists.sourceforge.net | https://lists.sourceforge.net/lists/listinfo/pymol-users | Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414

[PyMOL] grep settings

Hi There, Below is a little function (also attached) that gives you the command 'grepset' so you can grep settings using a regexp. Use it like this: ### example ### PyMOL>grepset dot|line auto_show_lineson cgo_dot_radius -1.0 cg

[PyMOL] detecting focus on the graphics window

Hello There, Anyone knows of a way of detecting if the graphics window has input focus? Thanks much, Zac -- Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414

[PyMOL] powermate in linux

Hello There, I've written a very little piece of python code that uses William R Sowerbutts's rudimentary (his own words) python interface to the powermate device. BE WARNED!! This hack will crash your pymol session when you type "quit" to terminate your pymol session. this wouldn't be a problem

Re: [PyMOL] Need advice on graphic card

> What does "merged mode" mean? i'm curious about this mode too. > As far as I know, nVidia claims, that their driver can do that though > (but I haven't tested it, due to lack of a second screen and a dual-head > graphics-card. it is true. I've tried it on a Quadro 700XGL under RH9 and it is

Re: [PyMOL] force cartoons through ca

> PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414

Re: [PyMOL] Get rid of border around my images !!

antialiasing does different things to the rendering than doubling the image size can fix/make better. I would keep antialiasing and go through the added work of cropping the image. > This is a known bug when using antialiasing. You can either remove the > border in Photoshop or equivalent

Re: [PyMOL] redhat 9.0/pymol - missing something

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Re: [PyMOL] knobs on spheres

__ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414

Re: [PyMOL] Loss of resolution when printing or converting to PDF

when I said "big" I meant using the pymol command "ray" with arguments specifying the width and heigth: ray 3000,3000 this works on all platforms/OSes zac > Are we talking Windows here? What would be a good way to enhance this > resolution within linux? How does one make a "big" png? Is

Re: [PyMOL] Loss of resolution when printing or converting to PDF

Fred, Make sure you create images which are "big" enough for the size of the print you want to make, e.g. images 3000x3000 print really well on an area of about 5in x 5in (600 dpi printing resolution). Also, you should use some application in which you can properly resize the image to print the a

RE: [PyMOL] lines same color as background

ICR, nVidia > uses a unified driver architecture which is both backwards and forwards > compatible. If you do find a robust solution, please pass it along! > > Cheers, > Warren > > -- > mailto:war...@sunesis.com > Warren L. DeLano, Ph.D. > > >

[PyMOL] lines same color as background

to do with the z-buffer/fog thingy. I did run a program drawing (GL_LINES) with GL_DEPTH_TEST enabled and that worked fine. any clues? Zac -- Ezequiel Panepucci - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-926-5127 Cell: 650-714-9414

Re: [PyMOL] RE: Resolution increase

d you like me to reference the program in the > > publication? > > > > > > Thanks, > > > > > > Jason > > > > > > > > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Ezequiel Panepucci - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-926-5127 Cell: 650-714-9414

[PyMOL] label wizard

mol/wizard/label.py and from within pymol type "wizard label" Comments? Have fun, Zac file: label.py #### # # Author: Ezequiel Panepucci # Last revision: 2001-11-14 # from pymol.wizard import Wizard from pymol import cmd impor

[PyMOL] molecule name from PK* selections

Hello, Is there a way to get the corresponding molecule (or model) name for a given PK1 selection? Thanks, Zac

RE: [PyMOL] pymol sys.argv, winnt, barks

Sounds good to me and besides the syntax is consistent with a few UNIX apps. On Thu, 8 Nov 2001, DeLano, Warren wrote: > > pymol -c myscript.py -- -pymol -will -ignore -these -arguments > pymol -c myscript.py -- -your -script -interpret -them -instead > > Any objections?

[PyMOL] NMR models

Hi There, How would I go about selecting a specific model from a PDB file which includes several NMR conformations? Thanks, Zac