PyMOL Molecular Graphics System

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 <gareth@...>
European Bioinformatics Institute

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
                       |                       / \ | mlerner@...

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 <gareth@...>
> 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@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

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:warren@...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pymol-users-admin@... [mailto:pymol-users-
> admin@...] On Behalf Of Michal Kurowski
> Sent: Wednesday, January 21, 2004 5:37 PM
> To: pymol-users@...
> 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
> <michal@...>
> 
> 
> 
> 
> -------------------------------------------------------
> 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@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Warren L. DeLano [warren@...] 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
<michal@...>

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:warren@...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pymol-users-admin@... [mailto:pymol-users-
> admin@...] 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
>                        |                       / \ | mlerner@...
> 
> 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 <gareth@...>
> > 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@...
> > 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@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

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:warren@...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: Michal Kurowski [mailto:michal@...]
> Sent: Thursday, January 22, 2004 3:19 PM
> To: Warren L. DeLano
> Cc: pymol-users@...
> Subject: Re: c-alpha traces
> 
> Warren L. DeLano [warren@...] 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
> <michal@...>
> 
>