Feature Requests item #1010651, was opened at 2004-08-17 05:55 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1010651&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: Closed Priority: 5 Submitted By: Miguel (migueljmol) >Assigned to: Bob Hanson (hansonr) Summary: Jan's priority list Initial Comment: ---------------------------- Original Message ---------------------------- Subject: Re: [Jmol-developers] surface From: "Jan Reichert" <[EMAIL PROTECTED]> Date: Tue, July 6, 2004 12:35 To: [email protected] -------------------------------------------------------------------------- Miguel wrote: >>>Q: Do you mean 'alone' as if the other atoms were not in the file? >>> >>> >>> >>Yes >> >> >> >>>If so, then that is not compatible with RasMol/Chime behavior. >>> >>> >>> >>but of much more use >> >> >> >>>Q: Is that what you want? >>> >>> >>> >>yes, I want to be able to visualize binding pockets (where solvent and/or a ligand is in contact with the protein under experimental conditions) >> >> > >OK > >Q: Is this high-priority or low-priority for you? > > > my priority list: -. MessageCallBack output at least compatible to RasMol echo show selected group * set picking correct PDB atom number -. access to the color scheme set helix color red (now color structure should use red for helix parts) set carbon color green (from now on color cpk should use green for carbons) -. rockets with http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1ne6 Exception in thread "AWT-EventQueue-2" java.lang.NullPointerException at javax.vecmath.Tuple3f.set(Tuple3f.java:161) -. surface rendering -. script access to distances, angles, torsions ... surface area ...*--> MessageCallBack center [0.0, 0.0, 0.0] output *--> -. color hbonds type -. general use of atom expression, e.g. bond 23:A.CA 23:A.O1 -. further operators for advanced scripting bound and count *--> -. --noscript (size should be viewer size) -. molecule -. script accessing PDB file -. stereo Regards, Jan ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2006-08-22 17:57 Message: Logged In: YES user_id=1082841 -. MessageCallBack output at least compatible to RasMol echo see much broader message reporting capability than RasMol in Jmol 11 show selected group * huh? set picking ?? correct PDB atom number ?? -. access to the color scheme possible set helix color red (now color structure should use red for helix parts) set carbon color green (from now on color cpk should use green for carbons) set carbon green implemented; helix color depends upon selected atoms -. rockets with http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1ne6 ? -. surface rendering done -. script access to distances, angles, torsions ... surface area ...*--> MessageCallBack done using getProperty measurementInfo center [0.0, 0.0, 0.0] output *--> getProperty centerInfo -. color hbonds type done, I think -. general use of atom expression, e.g. bond 23:A.CA 23:A.O1 connect -. further operators for advanced scripting bound and count *--> selected connected(4) or connected(3, (iron)) -. --noscript (size should be viewer size) ? -. molecule select within(molecule,(atomno=1)) -. script accessing PDB file getProperty fileContents -. stereo done ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1010651&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
