Buz, You must fix the bond valences manually...
Mouse menu -> 3 button editing mode Ctrl-right click on bond Ctrl-W to cycle valence (repeat as necessary to get correct valences) Then optinally remove hydrogens when done (use the action [A] menu on the object -> remove hydrogens) Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Buz Barstow > Sent: Wednesday, March 23, 2005 7:54 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Adding Hydrogens to GFP Chromophore > > Hi all, > > I'm trying to use PyMol to add hydrogen atoms to this small > fragment of a PDB file, the chromophore from the GFP structure 1EMA; > > REMARK S65T Chromophore from Ormo's coordintes (1EMB). > HETATM 466 N1 CRO 66 24.077 27.513 36.610 1.00 > 11.86 N > HETATM 467 CA1 CRO 66 25.011 26.478 37.078 1.00 > 7.34 C > HETATM 468 CB1 CRO 66 25.931 26.035 35.930 1.00 > 10.77 C > HETATM 469 CG1 CRO 66 25.155 25.422 34.796 1.00 > 16.67 C > HETATM 470 OG1 CRO 66 26.679 27.129 35.461 1.00 > 14.22 O > HETATM 471 C1 CRO 66 25.730 27.106 38.245 1.00 > 18.38 C > HETATM 472 N2 CRO 66 26.975 27.732 38.216 1.00 > 9.21 N > HETATM 473 N3 CRO 66 25.274 27.124 39.509 1.00 > 17.10 N > HETATM 474 C2 CRO 66 26.043 27.875 40.370 1.00 > 5.46 C > HETATM 475 O2 CRO 66 26.022 27.962 41.566 1.00 > 13.20 O > HETATM 476 CA2 CRO 66 27.197 28.245 39.512 1.00 > 16.08 C > HETATM 477 CA3 CRO 66 23.919 26.721 39.842 1.00 > 10.87 C > HETATM 478 C3 CRO 66 23.745 25.326 40.360 1.00 > 19.28 C > HETATM 479 O3 CRO 66 22.885 25.116 41.193 1.00 > 15.72 O > HETATM 480 CB2 CRO 66 28.329 28.822 39.960 1.00 > 10.75 C > HETATM 481 CG2 CRO 66 29.437 29.370 39.124 1.00 > 7.67 C > HETATM 482 CD1 CRO 66 29.541 29.103 37.742 1.00 > 11.31 C > HETATM 483 CD2 CRO 66 30.487 30.110 39.805 1.00 > 10.79 C > HETATM 484 CE1 CRO 66 30.707 29.546 37.033 1.00 > 17.44 C > HETATM 485 CE2 CRO 66 31.614 30.563 39.085 1.00 > 10.01 C > HETATM 486 CZ CRO 66 31.718 30.300 37.721 1.00 > 9.48 C > HETATM 487 OH CRO 66 32.894 30.804 36.971 1.00 > 13.84 O > > CONECT 466 457 467 > CONECT 467 466 468 471 > CONECT 468 467 469 470 > CONECT 469 468 > CONECT 470 468 > CONECT 471 467 472 473 > CONECT 472 471 476 > CONECT 473 471 474 477 > CONECT 474 473 475 476 > CONECT 475 474 > CONECT 476 472 474 480 > CONECT 477 473 478 > CONECT 478 477 479 488 > CONECT 479 478 > CONECT 480 476 481 > CONECT 481 480 482 483 > CONECT 482 481 484 > CONECT 483 481 485 > CONECT 484 482 486 > CONECT 485 483 486 > CONECT 486 484 485 487 > CONECT 487 486 > > END > > Unfortunately, PyMol adds too many hydrogens to each carbon > in the tyrosine ring in the center of the chromophore. It > doesn't recognize that some of the carbons can have double bonds. > > Does anyone know the best way to get PyMol to recognize the > double bonds? > > All the best, > > --Buz > > > |---------------------------------------------------------| > Buz Barstow > 192 Clark Hall > Cornell University > Ithaca, NY 14853, USA > Email: b...@cornell.edu > Phone: 607 255 8678 > Fax: 607 255 8751 > |---------------------------------------------------------| > > > > > ------------------------------------------------------- > This SF.net email is sponsored by Microsoft Mobile & Embedded > DevCon 2005 Attend MEDC 2005 May 9-12 in Vegas. Learn more > about the latest Windows > Embedded(r) & Windows Mobile(tm) platforms, applications & > content. Register by 3/29 & save $300 > http://ads.osdn.com/?ad_id=6883&alloc_id=15149&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
