Feature Requests item #855049, was opened at 2003-12-05 15:24 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=855049&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface Improvements Group: None >Status: Closed Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Bob Hanson (hansonr) 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: Bob Hanson (hansonr) Date: 2006-09-15 22:10 Message: Logged In: YES user_id=1082841 An old, old anonymous request finally accomplished. load 1crn.pdb select surfacedistance=0 color white load 1a31.pdb color surfacedistance calculate surface +1.2 #default, but calculate surface +1.5 #customizable This uses the dots/geosurface fast-surface generator to simply count the number of dots; pretty simple! The distance value is an approximation -- just the minimum distance from an atom to a surface ATOM. So this results in all surface atoms having a value of 0, and all other atoms having a value of > 0. Note that you can say: select not solvent set dotsSelectedOnly calculate surface +1.2 and any solvent water will NOT be inside the boundary. Bob ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2006-08-22 18:34 Message: Logged In: YES user_id=1082841 we could do this relatively easily now. It just has to do with how many points are present from a dots-based rendering of the solvent-accessible surface. Atoms/Groups could be colored based on distance from the surface or selected based on some specified distance from the surface. Could be very interesting. ---------------------------------------------------------------------- Comment By: molvisions (molvisions) Date: 2004-02-26 16:25 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: Miguel (michaelthoward) Date: 2004-02-26 16:07 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 ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
