I think your best bet is a perl-script filter.
On Sat, Jan 15, 2011 at 2:02 PM, Eric Martz <[email protected]>wrote:
> At 1/13/11, Rolf Huehne wrote:
> >But apparently taking only CA atoms is sometimes not sufficient for Eric
> >and his approach of using only some of the CA atoms currently does not
> >seem to be possible with the FILTER option.
>
> Dear Rolf,
>
> You are correct. I expect that for the largest biomolecules, in order
> to fit an alpha carbon filtered model into the default java memory, I
> shall need to remove some alpha carbons using the Jmol application
> (with e.g. 512 megs of memory), reconnect over the larger
> inter-atomic distances, then save the reduced-size file, then use it
> for display in e.g. Proteopedia. I have not tried it yet.
>
> You may find it useful to look at some examples of filtering large PDB
> files:
> http://www.proteopedia.org/wiki/index.php/Jmol/Visualizing_large_molecules
>
> I did succeed at connecting non-bonded atoms over arbitrary distances:
> http://www.proteopedia.org/wiki/index.php/SV40_Capsid_Simplified
> (see "See Also" for the connect command employed)
>
> -Eric
>
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Eric Martz, Professor Emeritus, Dept Microbiology
> U Mass, Amherst -- http://Martz.MolviZ.Org
>
> Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
> FirstGlance, used by Nature - http://firstglance.jmol.org
> 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org
> Biochem 3D Education Resources http://MolviZ.org
> ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
> Atlas of Macromolecules: http://atlas.molviz.org
> Workshops: http://workshops.molviz.org
> World Index of Molecular Visualization Resources: http://molvisindex.org
> PDB Lite Macromolecule Finder: http://pdblite.org
> Molecular Visualization EMail List (molvis-list): http://list.molviz.org
> Protein Explorer - 3D Visualization: http://proteinexplorer.org
> - - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
>
>
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand
> malware threats, the impact they can have on your business, and how you
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Protect Your Site and Customers from Malware Attacks
Learn about various malware tactics and how to avoid them. Understand
malware threats, the impact they can have on your business, and how you
can protect your company and customers by using code signing.
http://p.sf.net/sfu/oracle-sfdevnl
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
