[PyMOL] label wizard

2001-11-14 Thread Ezequiel Panepucci
/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 import pymol class Label(Wizard

[PyMOL] lines same color as background

2002-05-30 Thread Ezequiel Panepucci
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] lines same color as background

2002-05-30 Thread Ezequiel Panepucci
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. -Original Message- From: Ezequiel Panepucci [mailto:z...@slac.stanford.edu] Sent: Thursday, May

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

2003-03-07 Thread Ezequiel Panepucci
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

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

2003-03-07 Thread Ezequiel Panepucci
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 it a

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

2003-08-12 Thread Ezequiel Panepucci
___ 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 !!

2003-09-12 Thread Ezequiel Panepucci
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] Need advice on graphic card

2003-11-11 Thread Ezequiel Panepucci
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

[PyMOL] powermate in linux

2004-02-17 Thread Ezequiel Panepucci
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

[PyMOL] grep settings

2004-03-08 Thread Ezequiel Panepucci
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 ### PyMOLgrepset dot|line auto_show_lineson cgo_dot_radius -1.0

Re: [PyMOL] adding residues

2004-03-26 Thread Ezequiel Panepucci
| ___ | 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] graphics boards

2004-04-20 Thread Ezequiel Panepucci
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

[PyMOL] nvidia quadro 700xgl opengl error

2004-05-06 Thread Ezequiel Panepucci
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] Powermate dial with Pymol on OS X

2004-05-07 Thread Ezequiel Panepucci
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 | Ezequiel Panepucci, Ph.D

Re: [PyMOL] loading electrostatic maps generated with apbs

2004-05-14 Thread Ezequiel Panepucci
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

[PyMOL] Question: general purpose get_prompt function

2004-11-04 Thread Ezequiel Panepucci
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

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

2006-07-20 Thread Ezequiel Panepucci
/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 searches through the documentation of all

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

2006-07-20 Thread Ezequiel Panepucci
/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 searches through the documentation of all

Re: [PyMOL] pymol licensing questions

2006-11-09 Thread Ezequiel Panepucci
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