Feature Requests item #1032448, was opened at 2004-09-22 05:00 Message generated for change (Comment added) made by dcaffrey 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: dcaffrey (dcaffrey) Date: 2006-05-18 23:21 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 09:22 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 07:05 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
