Dear Bob, > Maybe: > REMARK 1 P2N format created by .... version:....... date:........
ok > Did you say *I* decide? Please, *you* decide! I just did not want to be pushy ;-) > What about columns 67-76? They are available in the PDB spec. just perfect If I understand you, adding chemical elements is the best approach to avoid ambiguities in Jmol. If you do need chemical elements, adding them _after_ the second column of atom names is just perfect for us (because they will not be considered by R.E.D.). If we look at the PDB format http://www.wwpdb.org/documentation/format32/sect9.html 1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 ATOM 1 N ALA A 1 11.104 6.134 -6.504 1.00 0.00 N Consequently, if you agree we could use: 13 - 16 XXXX Atom name. 70 - 73 YYYY alternative name. 77 - 78 2 letters Element symbol, right-justified (to correctly display both atom name types in Jmol) 1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 ATOM 1 XXXX ALA 1 11.104 6.134 -6.504 YYYY N > So, back to the real question: Could Jmol read a second atom name? > > Answer is yes. Would you like to have the option to read just that second > atom name, or do you need both atom names as available data? If the former, > we'll use a FILTER on the load command for this: > > load xxx.pdb FILTER "altName" > If the latter, we'll read it in as property_name. Excellent... nothing else to say. If we take as example: http://cluster.q4md-forcefieldtools.org/~ucpublic1/javaappletpdb-1.html We will be able to display: - Atom names (as usual) & - altName We already have corrected the PDB format generated by R.E.D. IV/R.E.D. Server; we will update Ante_R.E.D. 2.0/R.E.D. Server concerning the P2N file format very quickly. thanks for all Bob, regards, Francois ------------------------------------------------------------------------------ Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
