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: Bob Hanson (hansonr) 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: 2006-08-22 18:43 Message: Logged In: YES user_id=1082841 keep this for reference to Chime command method. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2006-07-13 00:21 Message: Logged In: YES user_id=1082841 This feature request got mixed together -- surfaces and charges. Surfaces are just about done. I want to add surface fragments still, but that is all. Charges: I would like this as well. We are all set for surfaces, so if we can add charges, it will be excellent. I will try to take a look at J.Gasteiger and M.Marsili: Tetrahedron Vol. 36. , pp. 3219-3288 (1980) and see if there is any chance we can do this. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2006-07-04 18:04 Message: Logged In: YES user_id=1082841 Recent advances in Jmol functionality may make this less of an issue. These comments refer to Jmol 10.x.19, in http://www.stolaf.edu/people/hansonr/jmol/test/proto and demonstrated and discussed at http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm and http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.txt 1) You can now render proper solvent-excluded surfaces (molecular surfaces) using the SOLVENT keyword. select (atoms-to-include) isosurface solvent <radius> 2) You can now render proper solvent-accessible surfaces using the SASURFACE keyword. select (atoms-to-include) isosurface sasurface <radius> 3) You can set the resolution in grid points per Angstrom using the RESOLUTION keyword. For a large system, 0.5 might be appropriate. isosurface resolution 0.5 sasurface 1.2 4) You can, of course, render these as dots, mesh, or solid (fill/nofill) and either translucent, or opaque using those keywords. isosurface s1 resolution 0.5 sasurface 1.2 mesh translucent and you can change these properties later using another isosurface or color command isosurface s1 opaque dots nomesh color $s1 translucent red 5) You can capture a JVXL equivalent (see http://www.stolaf.edu/people/hansonr/jmol/docs/JVXL-format.pdf) in order to deliver this surface over the web in a very compact manner that renders quickly. (Using "show isosurface" or just by looking in the Java console.) isosurface "savedfile.jvxl" 6) You can map these isosurfaces (either the original or the JVXL equivalent) using CUBE data. isosurface solvent 1.2 color "mydata.cube" 7) You can set the mapping range using the ABSOLUTE keyword. isosurface solvent 1.2 color absolute 0.1 1.0 "mydata.cube" You can save this color-mapped object as a JVXL file as well, so you only need to use the CUBE file once. 8) You can apply a variety of color schemes using the COLORSCHEME keyword. isosurface colorscheme "roygb" solvent color "mydata.cub" Other schemes include "rwb" (red-white-blue), "low" (red-green), and "high" (green-blue). 9) You can reverse the color using the REVERSECOLOR keyword: isosurface reversecolor solvent color "mydata.cub" So, in a nutshell, we've come a long way since this thread began. Still to do: fake esp surfaces along the lines of Chime, real esp surfaces using Jmol's newly built in molecular orbital quantum mechanical calculation capability using ab initio basis sets. What else? Advice is requested as to priority and direction at this point. Bob Hanson ---------------------------------------------------------------------- Comment By: dcaffrey (dcaffrey) Date: 2006-07-04 01:25 Message: Logged In: YES user_id=1040751 Sorry for the delay in responding. Yes, the naccess links and references you provide are useful. It may also be useful to look at the original paper describing the method. Lee and Richards J Mol Biol 1971 55:379-400. It provides useful details on "sectioning" the structure and computing the area for each atom slice (equations 1,2,3) Q1 Hydrogens are usually ignored. Q2 The zslice == 0.05 but I'm not aware of any shortcuts for this aproach. Q3 The Lee and Richards approximation is generally accepted and still commonly cited. While there are more sophisticated approaches it has prevailed for some reason or another. Q4 Agreed. The network science link is correct. ---------------------------------------------------------------------- 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 ------------------------------------------------------------------------- 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
