Feature Requests item #1656702, was opened at 2007-02-10 14:19 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1656702&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: Open Priority: 5 Private: No Submitted By: Angel Herraez (aherraez) Assigned to: Nobody/Anonymous (nobody) Summary: molecule name shown for PDB Initial Comment: A proposal to retrieve and use some molecule name from PDB files to be shown in Jmol title and menu. Current state: ** With MOL files: - Jmol app window title: shows the filename + extension, followed by a dash and the contents of line 1 (which usually is the molecule name or description). - Both app and applet: show the molecule name (line 1) as the topmost entry in the popup menu. - Applet: shows the filename as the bottommost sub-entry inside the former. If line 1 is empty, defaults to filename. ** With PDB files, the same degree of information would be desirable. However, currently only the filename is used: - Jmol app window title: shows the filename + extension, followed by a dash and (again) the filename without extension. - Both app and applet: show the filename (without extension) as the topmost menu entry in the popup menu. - Applet: shows the filename + extension as the bottommost sub-entry inside the former. Proposal: interpret the molecule name or description in the PDB file and use it similarly to what is done for MOLfiles' 1st line. Current use of the filename is redundant. I'm not an expert on PDB format, and the structure of PDB entries is varied, so this is open to discussion and likely to need quite a parsing. There are candidate fields: COMPND, TITLE, HEADER; if one is missing, another could take its place. HEADER is the easiest and seems logical, but it tends to contain a generic name or cathegory often not specific to the molecule (e.g. "Hydrolase(O-Glycosyl)" for lysozyme 123L.pdb); I'd prefer COMPND. 1) If "COMPND 2 MOLECULE:" field is present, use it; extract portion after MOLECULE: up to semicolon. 2) Else, use first line with "COMPND" field. 3) Else, use HEADER (trimming the deposition date and pdbcode). 4) Else, use TITLE (maybe trimmed, tends to be too long). 5) Use filename if the others fail. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1656702&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
