Re: [PyMOL] Ray Tracing Crash
On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote: Regarding my problems raytracing on my debian/testing machine. What is the exact version of the pymol .deb you're using? 0.93-2? What architecture are you running on? i386 or something else? Do you use pymol's internal raytracer, or povray? Does the raytracing-demo from the demo-menu work? thanks, Michael
[PyMOL] Help for user-defined functions
Does anyone know if it is possible to add 'help' documentation to my own user-defined functions? What I want is to be able to define a new PyMOL command by executing the following script: #-- def some_func: ''' Some help docs here... ''' # Python code here... cmd.extend(some_func, some_func) #-- ... and then type 'help some_func'. Gareth -- Gareth Stockwell gar...@ebi.ac.uk European Bioinformatics Institute
Re: [PyMOL] Ray Tracing Crash
On Thu, 22 Jan 2004 11:02:25 +0100 Michael Banck wrote: On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote: Regarding my problems raytracing on my debian/testing machine. What is the exact version of the pymol .deb you're using? 0.93-2? pymol_0.93-2_i386.deb What architecture are you running on? i386 or something else? i386, Pentium III Do you use pymol's internal raytracer, or povray? I invoke the raytracer by typing ray. I assume this is the internal raytracer. Does the raytracing-demo from the demo-menu work? The ray tracing demo works. But after running the raytracing-demo, pymol will crash if I type either: hide spheres show sticks ray or: hide spheres show lines ray Thanks, Morri thanks, Michael --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Morri Feldman
Re: [PyMOL] Help for user-defined functions
Hi,
I haven't seen this documented anywhere, so I have no idea if it's the
Right Way to do things, but I think all you need to do is add
cmd.help_sc.append('some_func')
after the cmd.extend('some_func',some_func) call. should this be built in
to cmd.extend()?
-michael
--
This isn't a democracy;|_ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
On Thu, 22 Jan 2004, Gareth Stockwell wrote:
Does anyone know if it is possible to add 'help' documentation to my own
user-defined functions? What I want is to be able to define a new PyMOL
command by executing the following script:
#--
def some_func:
'''
Some help docs here...
'''
# Python code here...
cmd.extend(some_func, some_func)
#--
... and then type 'help some_func'.
Gareth
--
Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics Institute
---
The SF.Net email is sponsored by EclipseCon 2004
Premiere Conference on Open Tools Development and Integration
See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
http://www.eclipsecon.org/osdn
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] crash with new version
I recently installed a new version of pymol using all-in-one archive pymol-0_93-bin-linux-libc6-i386.tgz. When I try to run pymol the program crashes and gives this error message: pymol.com: line 14: 10610 Floating point exception$PYMOL_PATH/pymol.exe $* I am trying to do this on a PC running SuSe Linux 8.2. Strangely other PCs in the lab which use SuSe 8.2 as well do not have this problem. Does anyone have an idea where this might come from? thanks, mark -- Mark Pfuhlfon: 0116 223 1544 Department of Biochemistryfax: 0116 223 1503 University of Leicester email: m...@le.ac.uk University Road www: www.le.ac.uk/biochem/mp84 Leicester LE1 7RH
RE: [PyMOL] How to send pymol command to pymol by python interpreter
Takefumi, You only need to worry about this if you're using an external Python interpreter with a modular build of PyMOL. For example, after installing a late-model linux PyMOL RPM, you run python script.py Where script.py contains the following sequence: import pymol pymol.finish_launching() which is needed to insure that PyMOL's API in the parallel thread is defined ready to receive messages. The problem is that PyMOL can't launch until import pymol completes and returns and __main__.pymol is defined. However, that means that the next command in your script will need to be executed before PYMOL has had a chance to initialize itself. So the current approach is to launch the PyMOL thread, and then call a function which blocks until PyMOL is all ready to go... Cheers, Warren [PS If there's anyone out there with a more elegant alternative for launching the PyMOL thread from a standalone Python script, I'd sure like to hear it : )]. -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Takefumi Sora Sent: Wednesday, January 21, 2004 10:57 PM To: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] How to send pymol command to pymol by python interpreter Hi. I appreciate your answer, Warren. Thank you. Please let me ask one more question. You said I need two lines first: import pymol pymol.finish_launching() As long as I use,I can't the role of pymol.finish_launching() if I don't call this, what troubles will happen ? Takefumi SORA --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] How to send pymol command to pymol by python interpreter
On Thu, 22 Jan 2004, Warren L. DeLano wrote: Where script.py contains the following sequence: import pymol pymol.finish_launching() [PS If there's anyone out there with a more elegant alternative for launching the PyMOL thread from a standalone Python script, I'd sure like to hear it : )]. I don't have anything significant to contribute to a revised interface right now, but I just wanted to say that I think it is strange that an import statement starts doing things like launching threads. The import should just make an interface available, and then the script can use the interface to create a pymol object or whatever: import pymol pymolHandle = pymol.create(options like window size, parent window to create in) pymolHandle.cmd.show(sticks, someName) The pymol.create() blocks until things are ready, so it is sort of the same as calling pymol.finish_launching(), but it seems more natural to this programmer. I don't expect import statements to do much. If I import imaplib it doesn't create an interface to an IMAP server, right? It just gives me the ability to do so. It would be up to the application to maintain or pass around pymolHandle to various modules/objects to get things done. Perhaps an app could use pymol.create() to create another instance, a second rendering window? Shared model underneath? Hmmm. . . When I delete pymolHandle or it goes out of scope, the thread should shut down and other resources should be released. It should NOT kill my application as it currently does when I call cmd.quit(). It's just a thread, it shouldn't be making decisions for my application. -Bob -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Takefumi Sora Sent: Wednesday, January 21, 2004 10:57 PM To: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] How to send pymol command to pymol by python interpreter Hi. I appreciate your answer, Warren. Thank you. Please let me ask one more question. You said I need two lines first: import pymol pymol.finish_launching() As long as I use,I can't the role of pymol.finish_launching() if I don't call this, what troubles will happen ? Takefumi SORA --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
