Re: [PyMOL] Assign secondary structure on group

2015-03-13 Thread Thomas Holder
The latest update to SVN fixes this.

Cheers,
  Thomas

Thomas Holder wrote, On 03/06/15 15:35:
> Hi Matt,
> 
> thanks for the bug report. If you use the command line instead, it
> works if you put the group name in parenthesis, which forces PyMOL to
> treat it as an atom selection:
> 
> PyMOL> dss (nameofgroup)
> 
> Cheers, Thomas
> 
> On 06 Mar 2015, at 14:53, Matthew Baumgartner 
> wrote:
> 
>> Hi, I'm using pymol 1.7.4.0. The A> assign sec. struct. command
>> doesn't seem to work when you call it on a group. It works fine on
>> the objects in the group individually, but it doesn't apply the
>> command to the objects when called from a group.
>> 
>> Thanks, Matt Baumgartner

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

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Re: [PyMOL] Assign secondary structure on group

2015-03-06 Thread Thomas Holder
Hi Matt,

thanks for the bug report. If you use the command line instead, it works if you 
put the group name in parenthesis, which forces PyMOL to treat it as an atom 
selection:

PyMOL> dss (nameofgroup)

Cheers,
  Thomas

On 06 Mar 2015, at 14:53, Matthew Baumgartner  wrote:

> Hi,
> I'm using pymol 1.7.4.0.
> The A> assign sec. struct. command doesn't seem to work when you call it 
> on a group. It works fine on the objects in the group individually, but 
> it doesn't apply the command to the objects when called from a group.
> 
> Thanks,
> Matt Baumgartner

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
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by Intel and developed in partnership with Slashdot Media, is your hub for all
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Re: [PyMOL] assign secondary structure?

2003-12-17 Thread Robert Campbell
* Michael Bovee  [2003-12-16 14:27] wrote:

> Hmm. When I try this I get a syntax error:
> __
> PyMOL>load EcHRSade.pdb
>  Executive: object "EcHRSade" created.
> PyMOL>hide
> PyMOL>show cartoon
> PyMOL>dss EcHRSade
> Traceback (most recent call last):
>   File "/sw/lib/pymol/modules/pymol/parser.py", line 251, in parse
> exec(com2[nest]+"\n",pymol_names,pymol_names)
>   File "", line 1
>  dss EcHRSade
> ^
>  SyntaxError: invalid syntax
> _
> 
> I also get the error if I type on the command line  "dss EcHRSade.pdb"
> 
> Apparently pymol's dss works for others? Maybe a problem in the fink 
> package, or on my particular system?
> I'm running the current fink package, 0.90-2, compiled from source on 
> my PBG3(Lombard/Bronze).

I think this is the problem.  The dss command was introduced in version
0.91.  I think you need to upgrade.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D. 
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6  Canada   http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2



RE: [PyMOL] assign secondary structure?

2003-12-11 Thread Warren L. DeLano
Michael,

Unfortunately PYMOL/dss doesn't generate quite enough
information to recreate PDB SHEET and HELIX records.  PyMOL (like other
programs) simplifies the secondary structure concept down to a
per-residue property.  There is no such thing as a sheet or helix in
PYMOL, but merely sets of proximal residues with a secondary structure
property (ss) of 'H' or 'S'.  

load object-name.pdb
hide
show cartoon
dss object-name

Should be sufficient to get you a secondary structure representation for
any protein.

States represent multiple conformations -- you shouldn't need to worry
about them

Cheers,
Warren


--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
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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 Bovee
> Sent: Thursday, December 11, 2003 1:38 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] assign secondary structure?
> 
> Hi,
> I have a 'raw' pdb file of atom coordinates only, and I'm hoping to
use
> the dss command in pymol to get helix and strand designations that I
> can paste back into the header space of the pdb so that I can model
> fancy helices and strands and so forth to get a nice picture in pymol.
> Then I can superpose features with homologous proteins for which this
> header info is available. I just didnt want to modify or create this
> header info 'by hand' if I didn't have to...
> 
> But, I can't get dss to work in pymol (even the refman warns that this
> algorithm has not been rigorously validated). The refman says USAGE is
> dss selection, state
> Does this mean I need to first make a selection that encompasses some
> part (or whole) of the molecule, or should this work on the entire
pdb?
>   I don't know what 'states' are so I just opted for '0' which is
> supposed to mean 'all states'.
> 
> Thanks,
> --Michael Bovee
> 
> 
> 
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