Re: [PyMOL] can't save pdb from within pymol

[Jason Vertrees]

Hi David (and list),

Your PyMOL sessions are fine, it's the save syntax you're using.
Please use the following syntax when saving via the command line:

save fileName.pdb, aPyMOLSelection

It's important that the filename come first, and be immediately
followed by a comma.  Please check "help save" for more information.
If you're saving a multi-state system (your PSE has two states) then
you can add the state flag as

save fileName.pdb, aPyMOLSelection, state=0

to save all states or

save fileName.pdb, aPyMOLSelection, state=2

to save state 2.

Cheers,

-- Jason

On Thu, Jan 27, 2011 at 7:59 PM, Jason Vertrees
 wrote:
> Hi David,
>
> Can you please send me the PSE?  If not, do you have multiple states?
> Are you using the save command or the GUI?
>
> Cheers,
>
> -- Jason
>
> On Thu, Jan 27, 2011 at 1:50 PM, David A.  Horita  wrote:
>> Hi,
>> I've apparently managed to create a pse of a protein that loads fine but
>> won't save the pdb coordinates (I get a file with END in it, and nothing
>> else).
>> Any ideas how to get the coordinates out?
>>
>> pymol 1.1b3 linux, windows (same pse has same result under both OS's)
>>
>> Thanks,
>> Dave
>>
>> -
>> David A. Horita, Ph.D.
>> Department of Biochemistry
>> Wake Forest University School of Medicine
>> Winston-Salem, NC 27157-1016
>> Tel: 336 713-4194
>> Fax: 336 716-7671
>> email:  dhor...@wfubmc.edu
>> web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
>>
>> --
>> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>> Finally, a world-class log management solution at an even better price-free!
>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> February 28th, so secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsight-sfd2d
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires 
February 28th, so secure your free ArcSight Logger TODAY! 
http://p.sf.net/sfu/arcsight-sfd2d
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] can't save pdb from within pymol

[Jason Vertrees]

Hi David,

Can you please send me the PSE?  If not, do you have multiple states?
Are you using the save command or the GUI?

Cheers,

-- Jason

On Thu, Jan 27, 2011 at 1:50 PM, David A.  Horita  wrote:
> Hi,
> I've apparently managed to create a pse of a protein that loads fine but
> won't save the pdb coordinates (I get a file with END in it, and nothing
> else).
> Any ideas how to get the coordinates out?
>
> pymol 1.1b3 linux, windows (same pse has same result under both OS's)
>
> Thanks,
> Dave
>
> -
> David A. Horita, Ph.D.
> Department of Biochemistry
> Wake Forest University School of Medicine
> Winston-Salem, NC 27157-1016
> Tel: 336 713-4194
> Fax: 336 716-7671
> email:  dhor...@wfubmc.edu
> web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
>
> --
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires 
February 28th, so secure your free ArcSight Logger TODAY! 
http://p.sf.net/sfu/arcsight-sfd2d
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] can't save pdb from within pymol

[David A. Horita]

Hi,
I've apparently managed to create a pse of a protein that loads fine but won't 
save the pdb coordinates (I get a file with END in it, and nothing else).
Any ideas how to get the coordinates out?

pymol 1.1b3 linux, windows (same pse has same result under both OS's)

Thanks,
Dave

-
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016
Tel: 336 713-4194
Fax: 336 716-7671
email:  dhor...@wfubmc.edu
web:  
http://www1.wfubmc.edu/biochem/faculty/Horita.htm

--
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires 
February 28th, so secure your free ArcSight Logger TODAY! 
http://p.sf.net/sfu/arcsight-sfd2d___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net