Re: [ccp4bb] Visualize symmetry operations

[chemocev marker]

Hi Aaron
may be this tool can be helpful
https://symd.nci.nih.gov/
or
in the pymol there is script


https://pymolwiki.org/index.php/Symmetry_Axis

Visualizing the transformation between two selections/objects

https://pymolwiki.org/index.php/RotationAxis

PDB has a symmetry browser

http://www.rcsb.org/pdb/staticHelp.do?p=help/advancedsearch/proteinSymmetryBrowser.html

may be it will be helpful

best

Jiri



On Wed, Jan 4, 2017 at 5:20 PM, Aaron Finke  wrote:

> Dear CCP4-keteers,
>
> Is there a program that can visualize symmetry operation positions (e.g.
> twofold screws, fourfolds) in protein structures, like CCDC Mercury does
> for small molecules?
>
> Thanks in advance,
> Aaron
>
> --
> Aaron Finke
> Staff Scientist, MacCHESS
> Cornell University
> e-mail: af...@cornell.edu
>
>

Re: [ccp4bb] Visualize symmetry operations

[Pavel Afonine]

Explore this:

http://cci.lbl.gov/cctbx/

Pavel

On Wed, Jan 4, 2017 at 8:20 AM, Aaron Finke  wrote:

> Dear CCP4-keteers,
>
> Is there a program that can visualize symmetry operation positions (e.g.
> twofold screws, fourfolds) in protein structures, like CCDC Mercury does
> for small molecules?
>
> Thanks in advance,
> Aaron
>
> --
> Aaron Finke
> Staff Scientist, MacCHESS
> Cornell University
> e-mail: af...@cornell.edu
>
>

Re: [ccp4bb] Visualize symmetry operations

[Robert Campbell]

Hi Aaron,

I have a PyMOL plugin based on cctbx (i.e. it requires the installation of 
cctbx) that will do this.  This allows one to make images like this:

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/pymol_symmetry.png


The script is called draw_symops_cctbx.py and is available here:

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

(this may site may already be listed in the repositories of the PyMOL plugin 
manager).


Cheers,
Rob


On Wed, 2017-01-04 12:38  -0800,  Pavel Afonine  wrote:

> Explore this:
> 
> http://cci.lbl.gov/cctbx/
> 
> Pavel
> 
> On Wed, Jan 4, 2017 at 8:20 AM, Aaron Finke  wrote:
> 
> > Dear CCP4-keteers,
> >
> > Is there a program that can visualize symmetry operation positions
> > (e.g. twofold screws, fourfolds) in protein structures, like CCDC
> > Mercury does for small molecules?
> >
> > Thanks in advance,
> > Aaron
> >
> > --
> > Aaron Finke
> > Staff Scientist, MacCHESS
> > Cornell University
> > e-mail: af...@cornell.edu
> >
> >  




-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc