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
