Feature Requests item #1032448, was opened at 2004-09-22 04:00 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1032448&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: None Group: None Status: Open Priority: 5 Submitted By: Christoph Steinbeck (steinbeck) Assigned to: Nobody/Anonymous (nobody) Summary: Calculation and display of various surface types Initial Comment: In order to establish Jmol as a Chime replacement, the calculation and display of various surface types would be needed. The attached graphics have been take from teaching module of the german project "Networked chemistry studies" which is currently based on Chime but where at least some people would love to get rid of it. The file names "Chime Gasteiger charges" shows a model calculated by the following chime command: script="surface molsurface white 0.45; list molsurface transparent; set mep distance 99.0; set charge function gasteiger; calculate charges refresh; list molsurface color potential" The other one named "Gaussian cubs" has been created from a so-called cubs file produces by the ab-inito-program Gaussian. The cubs file is also attached. ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2006-06-15 10:05 Message: Logged In: YES user_id=1082841 >From http://bioweb.pasteur.fr/docs/doc-gensoft/naccess/README I see what you are talking about, namely: 1) An atomic accessibility file (.asa file) containing the calculated accessible surface for each atom in a PDB file, as well as the assigned van der Waal radii. 2) A residue accessibility (.rsa) file containing summed atomic accessible surface areas over each protein or nucleic acid residue, as well as the relative accessibility of each residue calculated as the %accessiblity compared to the accessibility of that residue type in an extended ALA-x-ALA tripeptide (for amino acids). See Hubbard, Campbell & Thornton (1991) J.Mol.Biol.220,507-530. You can prevent this file from being calculated if you don't need it. Several questions come to mind: Q: How is this done in light of the fact that the H atoms are not generally present for biomolecules? Q: The surfaces I'm setting up probably are too expensive computationally for proteins. What shortcuts do people use? Q: I took a relatively close look at the cdk code. It's basically the first part of what we implement in the Dots.java routine, where we use geodesic tesselation as done here. It is only calculating the "single-atom-contact" surfaces, so it would not be appropriate for actually visualizing the surface, but I can see how it gives a nice (very rough) calculation of the solvent-accessible surface area and atomic "volume". Since we already do all these calculations as part of dots rendering, I don't see why we couldn't provide this sort of analysis as well. To see the "dots" associated with this tesselation calculation, just http://www.stolaf.edu/people/hansonr/jmol/test/proto/dots.htm load 1crn.pdb set solvent 1.2 dots on color dotsconcave black color dotssaddle black As you can see, there are a lot missing! I guess I'm quite surprised that people settle for such a gross approximation. But I guess if all you are doing is getting a number and not actually drawing the surface, you might be satisfied with this. Is this all people want in terms of calculation? Q: Something I'm VERY surprised to see here is that the "surface" for which the area is being determined is not the one I've associated with the term "solvent-accessible" surface. At least not the one I've ever seen rendered. I do hope we are doing this right in Jmol! The area and volume calculated are for the surface defined by the travels of the CENTER of the solvent probe. Is that really the surface people are talking about when they refer to "solvent-accessible surface"? Not the CONTACT surface? oy. I see: http://www.netsci.org/Science/Compchem/feature14e.html yup, that's what it is. OK, I see. We are depicting not the "solvent-accessible" surface but rather the "molecular surface". The true "solvent-accessible surface" is (almost) trivial compared to the molecular surface. I think we need to discuss this on the jmol-developer list. Bob Hanson ---------------------------------------------------------------------- Comment By: dcaffrey (dcaffrey) Date: 2006-05-18 22:21 Message: Logged In: YES user_id=1040751 It would be nice if user could retrieve numbers from the console that are similar to the .rsa and .asa files produced by naccess. Questions: 1) Do you intend to use the cdk implementation? http://cdk.cvs.sourceforge.net/cdk/cdk/src/org/openscience/cdk/geometry/surface/NumericalSurface.java?revision=1.13&view=markup 2) Any updates on when this might be available? ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-09-22 08:22 Message: Logged In: YES user_id=1050060 Adding surfaces is certainly a priority. However, support for surfaces will come after the official v10 release ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2004-09-22 06:05 Message: Logged In: YES user_id=1082841 I would like to see this a priority. Descriptions of the functions can be found at http://bip.weizmann.ac.il/course/prog2/graphics/chimescript2.html#set_mep_mlp_function At the very least we should have something like: surface molsurface white 0.1; set mep distance 100.0; set charge function gasteiger; calculate charges refresh; list molsurface color potential red orange yellow green blue darkblue; list molsurface transparent; "mep" here stands for "molecular Electrostatic Potential" These are very useful. But I have found that Chime does a poor job of rendering the colors. We could do much better. Bob Hanson ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1032448&group_id=23629 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
