Feature Requests item #855049, was opened at 2003-12-05 16:24 Message generated for change (Comment added) made by molvisions You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=855049&group_id=23629
Category: None Group: None Status: Open Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: a way to detect distance from surface Initial Comment: Rasmol has predefined selection parameter of amino acids called surface and one called buried. Since so much relies on interaction at surfaces it would be nice if JMOL could select actual surface residues and buried residues. Another reason for such a request - I was looking at this paper below and naively thought it might be easy to use Chime to color/list residues based on atom depth. (It is especially interesting since in general more conserved residues usually tend to be solvent inaccessible.) I tried to come up with a script that would start color coding based on atom depth but realized the problem was that after I had calculated the water accessible surface area I couldn't figure out the command to select residues within a certain distance from the calculated surface. I looked at MDL's info on surface stuff but couldn't figure it out. Anyway it would be nice to think about for building into Jmol since in the building process. A lot of drug design and examination of interactions depends on surfaces. Here is the paper: Atom depth in protein structure and function Alessandro Pintar, Oliviero Carugo and Sandor Pongor Atom depth, originally defined as the distance between a protein atom and the nearest water molecule surrounding a protein, is a simple but valuable geometrical descriptor of the protein interior. <http://reviews.bmn.com/journals/atoz/latest? pii=S0968000403002287&node=TOC%40%40TIBS% 40028%4011%40028_11> ---------------------------------------------------------------------- Comment By: Timothy Driscoll (molvisions) Date: 2004-02-26 17:25 Message: Logged In: YES user_id=920824 the Rasmol/Chime functionality described here is *quite* simplistic. buried and surface are just pre-defined sets of residues that are generally found in one locale or the other. it does not acutally calculate these properties for each structure file! that said, I do agree that powerful surface generation and rendering would be an excellent addition to Jmol. I believe GRASP has one of the best set of surface tools around - my opinion, of course, but a good place to poke around if possible. ---------------------------------------------------------------------- Comment By: Michael T Howard (michaelthoward) Date: 2004-02-26 17:07 Message: Logged In: YES user_id=608250 Unfortunately, I cannot get to this article. I need to understand the complexity of determining the distance from the surface. To me it sounds complicated. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=855049&group_id=23629 ------------------------------------------------------- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps & Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
