I see in that header: REMARK 350 BIOMT1 9 0.948276 0.167716 -0.269526 -150.63600 REMARK 350 BIOMT2 9 -0.219118 0.960156 -0.173456 74.51200 REMARK 350 BIOMT3 9 0.229696 0.223542 0.947242 45.65100 REMARK 350 BIOMT1 10 0.923206 0.307479 -0.230536 -118.37800 REMARK 350 BIOMT2 10 -0.365257 0.888553 -0.277596 157.93300 REMARK 350 BIOMT3 10 0.119489 0.340484 0.932627 -27.52900 ... REMARK 350 BIOMT2 999 -0.649645 0.730202 0.211582 93.85119 REMARK 350 BIOMT3 999 -0.760086 -0.618285 -0.199983 65.48146 REMARK 350 BIOMT1 1000 -0.050280 -0.354537 0.933689 11.07467 REMARK 350 BIOMT2 1000 -0.582320 0.769924 0.260995 174.76486 REMARK 350 BIOMT3 1000 -0.811403 -0.530585 -0.245166 93.60781
but at http://www.wwpdb.org/documentation/format23/remarks2.html I see: REMARK 350 APPLY THE FOLLOWING TO CHAINS: ?, ?... REMARK 350 BIOMT1 N N.NNNNNN N.NNNNNN N.NNNNNN N.NNNNN REMARK 350 BIOMT2 N N.NNNNNN N.NNNNNN N.NNNNNN N.NNNNN REMARK 350 BIOMT3 N N.NNNNNN N.NNNNNN N.NNNNNN N.NNNNN I had assumed that the PDB file was using column-based formatting, and I'm sure on that one I'm misreading the columns. I'll change it back to reading white-space separated data. Bob [EMAIL PROTECTED] wrote: >Bob Hanson wrote: > >>biomolecule oriented Jmol users: >> >>OK, I'm convinced by my colleagues here at St. Olaf and Carleton that >>this is HUGE. Just playing with it a bit, I'm totally excited. You can >>now load a subset of the atoms in a PDB file into Jmol (a limited SELECT >>sort of filter to the LOAD command that works at the file-reading level >>for PDB files) and then also select one of the BIOMOLECULE >>specifications in the "REMARK 350" biological unit section of the header >>and apply the symmetry described in that header. >> > >Bob, this is really great. When it works correctly it will help to >reduce one major problem with large biological units: java memory. >And it will also reduce the transfer volume from several megabytes to a >few kilobytes. > >I tried revision 9339 from SVN with a few smaller examples (4otb, 1a34, >1sva) and they looked fine. At least they looked identical to the >biological units provided by the wwPDB FTP site. In the case of '1a34' >there are overlapping RNA chains but I guess this is because the >symmetry operations are not defined properly. > >I also tried the currently most challenging entry '1m4x' (compressed >file size: ~300 MB, uncompressed file size: ~1.3 GB). I was not able to >automatically generate a picture of the biological unit with Jmol yet. >(It hung up after several hours and using up about 30 GB of memory using >Java 1.4.2_13, as far as I remember. Loading it interactively without >creating an image did work.) >So I used the "*.CA; BIOMOLECULE 1; APPLY SYMMETRY" filter to load the >asymmetric unit file into the application and after ~5 minutes the >structure appeared (using ~4GB memory for the whole JavaVM). But it >looked quite strange, see the snapshot at >http://www.fli-leibniz.de/~rhuehne/jmol/1m4x-biounit1-jmol-2008_04_29.png >(colored by chain, not everything is visible) >It should rather look as is shown at the RCSB page for '1m4x' >(http://www.rcsb.org/pdb/explore/explore.do?structureId=1M4X). > >The file info in the menu showed the following: > >atoms : 2,081,520 >bonds : 47,093 >groups : 2,081,520 >chains : 3 >polymers: 1,950,530 > >The bond count seems to be wrong because some limit was reached >according to the following message(s): > >BSPT tree depth too great:150 >maximum auto bond count reached > >The polymer count is also wrong. Since there are 3 chains and 1680 units >I think it should be 5,040. > > >>I suspect as people play with this more, they will want me to expand on >>that load filter select option. What else? >> > >Since we are automatically generating images of the biological units for >all PDB entries with Jmol it would be very helpful if the filter would >also be available as command-line option. > >I noticed that all generated copies are integrated into the same >model. This prevents any easy way to select and display only specific >copies (see also Mauricios answer). We have integrated the biological >unit files available from the PDB now for about 2 years into the >"JenaLib Jmol Viewer". In these files each copy is placed into its own >model. This proved to be very useful, because it allows very easily >individual selection and manipulation. Our viewer offers for example >coloring each copy individually or coloring each chain individually >(instead of by chain identifier). > >Regards, >Rolf > >---------------------------------------------------------------- >This message was sent using IMP, the Internet Messaging Program. > > >------------------------------------------------------------------------- >This SF.net email is sponsored by the 2008 JavaOne(SM) Conference >Don't miss this year's exciting event. There's still time to save $100. >Use priority code J8TL2D2. >http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone >_______________________________________________ >Jmol-users mailing list >[email protected] >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 the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
