Dear Bob, I am hoping to capitalize upon Jmol's ability to filter and do symops during PDB file loading, and still be able to show the result in the applet (e.g. in Proteopedia) when the biomolecule is too big to fit in default java memory. Our assumption is that very few Proteopedia users will do the setting to increase default java applet memory. In most cases, filtering to backbone atoms plus ligand would fit.
In Proteopedia we have so far avoided having to pre-process PDB files before loading them into Jmol. Thus the question: can Jmol do what we need without the need for PDB file pre-processing outside of Jmol. It seems to be able to do everything except include ligand. At 1/11/11, you wrote: >I think you will have to do the deletion after loading. >"nonwaterhetatm" is just too specialized. Is "hetatm" too specialized? Given that I see no other way to include them by filtering? I am assuming that "hetatm" plus "![hoh]" would load only the ligands. >Are you really saying that on some large systems the presence of the >hetatm will blow memory? Or you mean the ligands don't get loaded >when you use the filter? No, I am not worried about the hetatm blowing memory. Yes, I mean I need a way to load only the backbone atoms plus the non-water hetatm. >Why not just load the ligands separately as a separate model? First, I don't know any way to load the ligands separately, short of something like load =xxxx filter "![ala],[arg], ... all 20 amino acids,[da],[a], all 10 ribo and deoxy nucleotides,[hoh]" Second, it would keep things much simpler to have everything in one model (as they were in the original PDB file before filtering and symops). To get ligand, I am willing to filter-exclude (with !) a list of all 20 amino acids and all 10 nucleotides, but it appears that the present filter syntax won't allow me to combine that with INCLUDING the backbone atoms from the very same residues. -Eric >On Tue, Jan 11, 2011 at 12:16 PM, Eric Martz ><<mailto:[email protected]>[email protected]> wrote: >I would like to be able to filter backbone atoms and non-water HETATM >(ligands and adducts). This would be useful for fitting large >biomolecules into the default java memory (applet). > >A small example is 3d6y, a 2.7A X-ray structure. Asymmetric unit: > - chains 2 (1 protein, 1 dna) > - ligands: berberine, glycerol > - HOH oxygens: 34 > >Biomolecule 1: > - chains 4 (2 protein, dna double helix) > - ligands duplicated > >load =3d6y filter "*.ca,*.p,biomolecule 1" > >gives me backbone atoms for protein and nucleic, but I have not found >any way to get the nonwater HETATM. Perhaps a new filter parameter >could be added, something like > >load =3d6y filter "*.ca,*.p,nonwaterhetatm" > >or > >load =3d6y filter "*.ca,*.p,hetatm,![hoh]" > >???? > >-Eric > > >------------------------------------------------------------------------------ >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>http://p.sf.net/sfu/oracle-sfdevnl >_______________________________________________ >Jmol-users mailing list ><mailto:[email protected]>[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>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 ------------------------------------------------------------------------------ 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
