> I'm back working on my Jmol applet pages > <http://doolittle.ibls.gla.ac.uk:9006/david/ProteinMotifDB.html> and > I'm writing chimetoggle controls to turn on and off ligands > associated with protein structures. I encountered the following > problem: > > I am refering to specific ligands in the pdb file which I have in my > database. I can turn them on with commands of the type: > <param name="script" value="set hetero off; select LLP; spacefill; > color cpk; set hydrogen off">
I suggest that group names always be written 1. in upper case, as in the PDB file (which you are doing) 2. in square brackets ... to avoid parsing confusing As in ... select [LLP] > Initially I turned these off with the simple command that works in > rasmol/chime: > <param name="altscript" value="restrict protein"> > However in the particular case cited (LLP in 1a8i.pdb) there are > amino acids in the ligand and Jmol treats the ligand as protein. We worked very hard on the definitions of 'protein' and 'amino' in Jmol to try to make them more flexible. I may be mistaken, but I believe that 'protein' and 'amino' mean the same thing in RasMol/Chime ... the enumerated list of standard amino acid groups. In Jmol, 'amino' refers to the standard list of amino acid groups. The selection is done by name only (as in RasMol/Chime ... I think). Example: a PDB file contains a group called [CYS]. The [CYS] group contains contains tree atoms: C, Yb, and S. When the 'select amino' command is given then Jmol will select these atoms because the group name is a reserved group name for amino acids. The implementation of 'protein' is completely different. It looks at the structure and connectivity of the atoms within the group without even looking at the group name. Basically, if it has a N-CA-C=O backbone then it will be considered amino, independent of the sidechains. This allows it to pick up 'mutated' amino acids (I do not know the proper name). Example: Using the file from the previous example ... the atoms in the [CYS] group are not selected when I say 'select protein' because the atoms do not form an amino acid backbone. Example: I have some group in a .pdb file that has a mutated sidechain. The backbone is intact. Jmol will select this group when I say 'select protein' because it has a N-CA-C=O backbone (Note: I wrote the backbone as N-CA-C=O ... but, in fact, Jmol does not/cannot verify =O with .pdb files) > It > would be nice if I could specifically turn LLP off, but the best I > can do to get back to where I was is: > <param name="altscript" value="restrict 0;cpk off;restrict > protein;wireframe off; backbone 0.3"> > Does anyone know a more elegant way of doing this? restrict not [LLP] Miguel ------------------------------------------------------- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
