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
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
> 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] Ray Tracing Crash
Package: pymol Version: 0.93-2 On Thu, Jan 22, 2004 at 08:53:37AM -0800, Morri Feldman wrote: > 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 Indeed, I can reproduce this here. Thanks for the bug report. I'll try to debug this during the weekend (won't have time tomorrow I guess), please nag me if you don't here back next week. thanks, Michael
RE: [PyMOL] c-alpha traces
Yes, PyMOL can visualize CA-only models, perform CA-based alignments on CA models, visualize all-atom models, perform CA-based alignments on all atom models, and perform all-atom alignments on all-atom models. Cheers, Warren -- 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 Michal Kurowski > Sent: Wednesday, January 21, 2004 5:37 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] c-alpha traces > > Hi, > > Some structure comparison software is only able to generate alignments > built of c-alpha atoms of both structures compared. > > Is Pymol able to visualize such alignment with (faked) backbone > shown ? > > If not what could possibly show it ? > > Regards, > > > -- > Michal Kurowski > > > > > > --- > 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] Re: c-alpha traces
Warren L. DeLano [war...@delanoscientific.com] wrote: > Yes, > > PyMOL can visualize CA-only models, perform CA-based alignments on CA > models, visualize all-atom models, perform CA-based alignments on all > atom models, and perform all-atom alignments on all-atom models. Thats great ! To make sure we both speak of the same thing: I specifically meant visualization of pdb files with c-alpha - only structure subsets from rcsb without *any* action on already centered molecules. Moreover, showing beautiful backbones ;-). Is it right ? Regards, -- Michal Kurowski
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] Help for user-defined functions
Thanks for the suggestion, and the solution.
In Versions >= 0.95, cmd.extend will will adds new commands into the
help dictionary.
In the meantime
cmd.help_sc.append('func_name')
will work...
Cheers,
Warren
--
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 Michael George Lerner
> Sent: Thursday, January 22, 2004 1:51 PM
> To: Gareth Stockwell
> Cc: pymol-users
> Subject: 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
> > 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
> >
>
>
> ---
> 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
>
RE: [PyMOL] translucent proteins
Lesley, set cartoon_transparency, 0.6 should do the trick. Note that you may need to ray-trace the image to avoid transparency artifacts. Cheers, Warren -- 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 Lesley Debono > Sent: Wednesday, January 21, 2004 10:56 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] translucent proteins > > I would like to be able to make the backbone protein in a structure > translucent so that the active site is clearly visible through the > protein. Any ideas on how to do this? > > Lesley > > > > --- > 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] RE: c-alpha traces
Michal, Unfortunately, beautiful backbones require N and C coordinates as well, because PYMOL uses AA geometry to determine orientation vectors. The best you can do with CA only is a tube. Cheers, Warren -- 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: Michal Kurowski [mailto:mic...@genesilico.pl] > Sent: Thursday, January 22, 2004 3:19 PM > To: Warren L. DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: Re: c-alpha traces > > Warren L. DeLano [war...@delanoscientific.com] wrote: > > Yes, > > > > PyMOL can visualize CA-only models, perform CA-based alignments on CA > > models, visualize all-atom models, perform CA-based alignments on all > > atom models, and perform all-atom alignments on all-atom models. > > Thats great ! > > To make sure we both speak of the same thing: > > I specifically meant visualization of pdb files with c-alpha > - only structure subsets from rcsb without *any* action on > already centered molecules. Moreover, showing beautiful > backbones ;-). > > Is it right ? > > Regards, > > -- > Michal Kurowski > > >
