Rolf and Angel, The problem is this:
1) Jmol maps the number in the CONECT record with the most recent ATOM or HETATM record with that number. It's a simple lookup table. 2) Rolf, you are doing a most interesting thing -- pulling out the the biomolecule transform information and using that to create a new PDF file: REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 69.40000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, R REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMOLECULE: 2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 106.40000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 69.40000 But what you can see there is that biomolecule 1 and biomolecule 2 do not contain the same atoms, apparently, since the second does not seem to involve chains A, B, C, or R. 3) You add the final CONECT sequence at the end, which includes atom references that are unique to MODEL 1 and bonds them to atoms in MODEL 2. I think it's reasonable to reset the lookup table when a MODEL command is given, so I will do that, and that should solve your immediate problem. But another problem is the waters, which are part of chain " " (blank). These remarks fail to specify what to do with those. That's a flaw, I think, in the format of this specification. Bob [EMAIL PROTECTED] wrote: >Quoting Angel Herraez <[EMAIL PROTECTED]>: > > > >>Hi Bob and Rolf >> >>I was interested by this, so I wrote a small test file >>MODEL 1 >>ATOM 1 C1 2.000 0.000 0.000 >>ATOM 2 O1 -2.000 0.000 0.000 >>ATOM 3 N1 0.000 2.000 0.000 >>ENDMDL >>MODEL 2 >>ATOM 1 C1 2.000 0.600 0.000 >>ATOM 2 O1 -2.000 0.600 0.000 >>ATOM 3 N1 0.000 2.600 0.000 >>ENDMDL >>CONECT 1 2 >>CONECT 2 1 3 >>CONECT 3 2 >> >> >> > > >Maybe it is done only under specific conditions. In my example there >is for example a hetero atom involved. (But there was no difference >when I exchanged atom 3 by a hetero atom in Angel's example.) > >Angel's example at least demonstrates that the "CONECT" record is only >used for the preceeding model: only the atoms of model 2 are connected >if I load it into the applet (11.3.47). > >Regards, >Rolf > > > >---------------------------------------------------------------- >This message was sent using IMP, the Internet Messaging Program. > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2005. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >_______________________________________________ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
