Roberto, An also less than optimal work around might be to take your refined .pdb from PHENIX or CCP4 and run it through the downgrade utility on MolProbity to change to PDBv2.3 format before working in Coot. I don't think it is necessary to convert back to PDBv3.0 for phenix.refine, but MolProbity will do this automatically if you upload a PDBv2.3 file.
The workhorse of the conversion is a program called the Remediator, which is available for download here: http://kinemage.biochem.duke.edu/software/remediator.php It certainly is a pain to have to be switching back and forth, but this should allow you to keep your refined hydrogen positions. Good Luck, -bob On Thu, Jun 19, 2008 at 7:26 AM, Roberto Steiner <[EMAIL PROTECTED]> wrote: > Dear all, > a problem possibly at the coot/mmdb interface... > If one uploads a pdb file (from phenix.refine in the example below) that > contains Hs into Coot and then writes it out (with or without any > modification done on it) Coot shifts the HG2n of THR on the right by one > column space. Because column 17 is kept empty > the result is three identical HG2 THR protons. > Example: > Uploaded: > CRYST1 45.460 166.970 167.200 90.00 90.00 90.00 P 21 21 21 > SCALE1 0.021997 -0.000000 -0.000000 0.00000 > SCALE2 0.000000 0.005989 0.000000 0.00000 > SCALE3 0.000000 0.000000 0.005981 0.00000 > ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 A > N > ANISOU 1 N THR A 2 9721 7539 9478 1186 2103 297 A > N > ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 A > C > ANISOU 2 CA THR A 2 10790 8621 9925 1145 1971 285 A > C > ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 A > C > ANISOU 3 CB THR A 2 10519 8251 9322 1244 1638 409 A > C > ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 A > O > ANISOU 4 OG1 THR A 2 10309 7971 9516 1332 1549 489 A > O > ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 A > C > ANISOU 5 CG2 THR A 2 9547 7174 7845 1451 1403 582 A > C > ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 A > C > ANISOU 6 C THR A 2 10101 8073 9151 869 2179 63 A > C > ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 A > O > ANISOU 7 O THR A 2 9210 7258 8131 790 2339 -23 A > O > ATOM 8 HA THR A 2 25.639 62.015 24.900 1.00 71.84 A > H > ATOM 9 HB THR A 2 27.009 64.232 24.226 1.00 69.26 A > H > ATOM 10 HG1 THR A 2 28.232 62.991 26.212 1.00 67.50 A > H > ATOM 11 HG21 THR A 2 26.275 65.055 26.303 1.00 61.19 A > H > ATOM 12 HG22 THR A 2 25.104 64.300 25.596 1.00 61.19 A > H > ATOM 13 HG23 THR A 2 25.894 63.607 26.753 1.00 61.19 A > H > > Written: > CRYST1 45.460 166.970 167.200 90.00 90.00 90.00 P 21 21 21 > SCALE1 0.021997 -0.000000 -0.000000 0.00000 > SCALE2 0.000000 0.005989 0.000000 0.00000 > SCALE3 0.000000 0.000000 0.005981 0.00000 > ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 A > N > ANISOU 1 N THR A 2 9721 7539 9478 1186 2103 297 A > N > ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 A > C > ANISOU 2 CA THR A 2 10790 8621 9925 1145 1971 285 A > C > ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 A > C > ANISOU 3 CB THR A 2 10519 8251 9322 1244 1638 409 A > C > ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 A > O > ANISOU 4 OG1 THR A 2 10309 7971 9516 1332 1549 489 A > O > ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 A > C > ANISOU 5 CG2 THR A 2 9547 7174 7845 1451 1403 582 A > C > ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 A > C > ANISOU 6 C THR A 2 10101 8073 9151 869 2179 63 A > C > ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 A > O > ANISOU 7 O THR A 2 9210 7258 8131 790 2339 -23 A > O > ATOM 8 HA THR A 2 25.639 62.015 24.900 1.00 71.84 A > H > ATOM 9 HB THR A 2 27.009 64.232 24.226 1.00 69.26 A > H > ATOM 10 HG1 THR A 2 28.232 62.991 26.212 1.00 67.50 A > H > ATOM 11 HG2 THR A 2 26.275 65.055 26.303 1.00 61.19 A > H > ATOM 12 HG2 THR A 2 25.104 64.300 25.596 1.00 61.19 A > H > ATOM 13 HG2 THR A 2 25.894 63.607 26.753 1.00 61.19 A > H > Does anyone know (Paul?) the reason for the above? > The only solution right now (that I know of) is to remove all Hs and > generate them again (molprobity for example) prior to refinement. > Cheers, > Roberto > --- > Roberto Steiner > Randall Division of Cell and Molecular Biophysics > New Hunt's House > King's College London > Guy's Campus > London, SE1 1UL > Phone +44 (0)20-7848-8216 > Fax +44 (0)20-7848-6435 > e-mail [EMAIL PROTECTED] > > > >
