Many thanks rewiting the script to ensure targetSerial > sourceSerial
fixed the display (all 25 het sets) Phil Robert Hanson wrote: > Phil, you are in luck. It's a simple problem. The PDB specification > requires that you specify each connection twice. > > http://www.wwpdb.org/documentation/format32/sect10.html > > "The connectivity list given here is redundant in that each bond > indicated is given twice, once with each of the two atoms involved > specified in columns 7 - 11." > > Jmol has this in its code: > > if (targetSerial < sourceSerial) > continue; > > so as not to duplicate connections. That's your problem. You are just > missing those redundancies. > > Jmol disregards some of the other nuances of the CONECT command (such > as the required order) but does not disregard this one. > > > I think Jmol is generally ignoring your CONECT records and instead > using its autobond features -- I have to think about why that would be > the case. This can differ depending upon the protein and how many > connections there are, thus the difference between with and without > the protein. > > There could be some other issue, but I think if you fix that CONECT > problem all should be fine. At least run a test with the added lines > > CONECT 5548 5549 > CONECT 5545 5548 > CONECT 5549 5551 > CONECT 5554 5555 > CONECT 5552 5554 > CONECT 5550 5552 > CONECT 5549 5550 > > All of those bonds should be missing currently, not just the two you > mentioned. > > As far as Jmol is concerned, all you really need to make sure is that > the number in the first field is smaller than the numbers in the other > fields; but it's still an invalid PDB file if you do not duplicate the > connections, and some programs may not read it. I don't know. > > Bob > > On Tue, Oct 13, 2009 at 5:44 AM, Phil Cunningham > <[email protected] <mailto:[email protected]>> wrote: > > I have a problem with CONECT records and Jmol > > I am using Autodock (Scripts) to dock retinoic acid on a protein > and generate 25 docking positions. Autodock seems loath to recognise > connectivity! - so I add to > the docked HETATM the required CONECT records. I use a perl script. > I use the same script on the 25 HETATMs and generate a pdb file which > contains the PROTEIN as chain A and the 25 Retinoic acid positions as > HETATM + CONECT records > > Each atom is uniquely numbered(cols 1-6) > Each Retinoic Acis is identified uniquely by chain(col 6) and residue > name(cols 18-20) > The CONECT records are generated from the atom numbers > > > When I view the protein - retinoic acid 'complex' SOME of the > retinoic acids > have 'lost' their conectivity! (tho not all retinoic acids - 13/25 > display as required) > > Even more confusing to me is the observation that when I display > one of > the 'bad' retinoic acids > as a simple 'PDB' file (No protein - just the 1 Retinoic acid > molecule) > the connectivity is fine! > > > Can some one elucidate the rules Jmol uses to display the CONECT > records > in the 'correct' manner svp > > yours etc > below is a HET set that is fine alone but looses C7-C8 and C6-C7 > connectivity when viewed in the complex > of Protein and 25 Retinoic acids > HETATM 5545 C8 D03 D 4.302 -14.703 33.035 > HETATM 5546 C9 D03 D 4.962 -15.735 32.295 > HETATM 5547 C19 D03 D 4.899 -17.196 32.590 > HETATM 5548 C7 D03 D 3.747 -15.066 34.309 > HETATM 5549 C6 D03 D 2.441 -14.585 34.670 > HETATM 5550 C5 D03 D 2.207 -13.243 35.023 > HETATM 5551 C1 D03 D 1.428 -15.698 34.708 > HETATM 5552 C4 D03 D 0.828 -12.750 35.250 > HETATM 5553 C18 D03 D 3.283 -12.231 35.143 > HETATM 5554 C3 D03 D -0.096 -13.887 35.602 > HETATM 5555 C2 D03 D 0.025 -15.087 34.687 > HETATM 5556 C17 D03 D 1.678 -16.512 35.974 > HETATM 5557 C16 D03 D 1.659 -16.655 33.543 > HETATM 5558 C10 D03 D 5.750 -15.266 31.201 > HETATM 5559 C11 D03 D 5.117 -15.075 29.951 > HETATM 5560 C12 D03 D 6.060 -14.635 28.932 > HETATM 5561 C13 D03 D 6.460 -15.569 27.907 > HETATM 5562 C14 D03 D 5.882 -15.308 26.654 > HETATM 5563 C20 D03 D 7.399 -16.716 28.119 > HETATM 5564 C15 D03 D 6.175 -16.168 25.517 > HETATM 5565 O2 D03 D 7.117 -15.827 24.778 > HETATM 5566 O1 D03 D 5.454 -17.168 25.244 > CONECT 5551 5555 5549 5557 5556 > CONECT 5555 5554 > CONECT 5554 5552 > CONECT 5552 5550 > CONECT 5550 5549 5553 > CONECT 5549 5548 > CONECT 5548 5545 > CONECT 5545 5546 > CONECT 5546 5558 5547 > CONECT 5558 5559 > CONECT 5559 5560 > CONECT 5560 5561 > CONECT 5561 5562 5563 > CONECT 5562 5564 > CONECT 5564 5565 > > -- > Phil Cunningham > Senior Bioinformatics Officer > Room 3.157 Franklin Wilkins Building > Department of Biochemistry > King's College University of London > 150 Stanford Street > London SE1 9NH > > tel 020 7848 4239 > fax 020 7848 4500 > > email [email protected] <mailto:[email protected]> > > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. > Jumpstart your > developing skills, take BlackBerry mobile applications to market > and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > Jmol-users mailing list > [email protected] > <mailto:[email protected]> > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 -- Phil Cunningham Senior Bioinformatics Officer Room 3.157 Franklin Wilkins Building Department of Biochemistry King's College University of London 150 Stanford Street London SE1 9NH tel 020 7848 4239 fax 020 7848 4500 email [email protected] ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
