Re: [ccp4bb] Coot and Hs
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 -0.00 -0.000.0 > SCALE2 0.00 0.005989 0.000.0 > SCALE3 0.00 0.00 0.0059810.0 > ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 A > N > ANISOU1 N THR A 2 9721 7539 9478 1186 2103297 A > N > ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 A > C > ANISOU2 CA THR A 210790 8621 9925 1145 1971285 A > C > ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 A > C > ANISOU3 CB THR A 210519 8251 9322 1244 1638409 A > C > ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 A > O > ANISOU4 OG1 THR A 210309 7971 9516 1332 1549489 A > O > ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 A > C > ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403582 A > C > ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 A > C > ANISOU6 C THR A 210101 8073 9151869 2179 63 A > C > ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 A > O > ANISOU7 O THR A 2 9210 7258 8131790 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 -0.00 -0.000.0 > SCALE2 0.00 0.005989 0.000.0 > SCALE3 0.00 0.00 0.0059810.0 > ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 A > N > ANISOU1 N THR A 2 9721 7539 9478 1186 2103297 A > N > ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 A > C > ANISOU2 CA THR A 210790 8621 9925 1145 1971285 A > C > ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 A > C > ANISOU3 CB THR A 210519 8251 9322 1244 1638409 A > C > ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 A > O > ANISOU4 OG1 THR A 210309 7971 9516 1332 1549489 A > O > ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 A > C > ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403582 A > C > ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 A > C > ANISOU6 C THR A 210101 8073 9151869 2179 63 A > C > ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 A > O > ANISOU7 O THR A 2 9210 7258 8131790 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 remov
Re: [ccp4bb] Coot and Hs
I think that we will have to 'remediate' Coot (and the whole of CCP4 for good measure). I advise all SHELXL users NEVER to deposit hydrogen atoms, it saves lots of hassle. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Thu, 19 Jun 2008, Edward Snell wrote: > It's due to PDB versions 2.3 and 3.0. It's a pain, and Paul is aware of > it. The solution you describe works and it's always nice to check with > Molprobity. I've tried using the PDB tools to change 3.0 to 2.3 but they > also have problems :-( > > > > For us poor souls who are suffering with hydrogen any fix would be > appreciated. For now, I am pulling the detector back :-) > > > > Eddie. > > > > Edward Snell Ph.D. > Assistant Prof. Department of Structural Biology, SUNY Buffalo, > Hauptman-Woodward Medical Research Institute > 700 Ellicott Street, Buffalo, NY 14203-1102 > Phone: (716) 898 8631 Fax: (716) 898 8660 > Email: [EMAIL PROTECTED] Telepathy: 42.2 GHz > > Heisenberg was probably here! > > > > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > Roberto Steiner > Sent: Thursday, June 19, 2008 10:27 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Coot and Hs > > > > 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 -0.00 -0.000.0 > > SCALE2 0.00 0.005989 0.000.0 > > SCALE3 0.00 0.00 0.0059810.0 > > ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 > AN > > ANISOU1 N THR A 2 9721 7539 9478 1186 2103297 > AN > > ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 > AC > > ANISOU2 CA THR A 210790 8621 9925 1145 1971285 > AC > > ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 > AC > > ANISOU3 CB THR A 210519 8251 9322 1244 1638409 > AC > > ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 > AO > > ANISOU4 OG1 THR A 210309 7971 9516 1332 1549489 > AO > > ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 > AC > > ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403582 > AC > > ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 > AC > > ANISOU6 C THR A 210101 8073 9151869 2179 63 > AC > > ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 > AO > > ANISOU7 O THR A 2 9210 7258 8131790 2339-23 > AO > > ATOM 8 HA THR A 2 25.639 62.015 24.900 1.00 71.84 > AH > > ATOM 9 HB THR A 2 27.009 64.232 24.226 1.00 69.26 > AH > > ATOM 10 HG1 THR A 2 28.232 62.991 26.212 1.00 67.50 > AH > > ATOM 11 HG21 THR A 2 26.275 65.055 26.303 1.00 61.19 > AH > > ATOM 12 HG22 THR A 2 25.104 64.300 25.596 1.00 61.19 > AH > > ATOM 13 HG23 THR A 2 25.894 63.607 26.753 1.00 61.19 > AH > > > > > > Written: > > CRYST1 45.460 166.970 167.200 90.00 90.00 90.00 P 21 21 21 > > SCALE1 0.021997 -0.00 -0.000.0 > > SCALE2 0.00 0.005989 0.000.0 > > SCALE3 0.00 0.00 0.0059810.0 > > ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 > AN > > ANISOU1 N THR A 2 9721 7539 9478 1186 2103297 > AN > > ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 > AC > > ANISOU2 CA THR A 210790 8621 9925 1145 1971285 > AC > > ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 > AC > > ANISOU3 CB THR A 210519 8251 9322 1244 1638409 > A
Re: [ccp4bb] Coot and Hs
Hi Paul, How can I add Hs (hydrogens) stereochemically to protein or peptide using COOT without altering the coordinates of non-hydrogen atoms. Thanks. Sam. > Date: Thu, 19 Jun 2008 15:57:46 +0100 > From: [EMAIL PROTECTED] > Subject: Re: [ccp4bb] Coot and Hs > To: CCP4BB@JISCMAIL.AC.UK > > Dear Roberto, > > Roberto Steiner wrote: >> Dear all, >> >> a problem possibly at the coot/mmdb interface... > > Indeed. > >> 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. > > Technical answer: > > The current PDB parser in Coot is from mmdb and is for PDB format > version 2.3. Phenix.refine and other modern programs use PDB format > version 3.0 [1] - released over a year ago. PDB version 3.0 > "Remediated" does not wrap the hydrogen (or other) names and so the > hydrogen name "unmangler" - which is what is tripping you up - need not > be executed. I'd like to make Coot compatible with the current PDB > standard. If CCP4 were to release a version of mmdb compatible with > Coot, I could do that right away [2]. I'm hoping that they will do so > today^H^H^H^H^H soon. > >> The only solution right now (that I know of) is to remove all Hs and >> generate them again (molprobity for example) prior to refinement. > > Bleugh. Non-optimal (no matter how fine Molprobity is). > > Paul. > > [1] or version 3.1? > [2] I imagine. _ Introducing Live Search cashback . It's search that pays you back! http://search.live.com/cashback/?&pkw=form=MIJAAF/publ=HMTGL/crea=introsrchcashback
Re: [ccp4bb] Coot and Hs
It's due to PDB versions 2.3 and 3.0. It's a pain, and Paul is aware of it. The solution you describe works and it's always nice to check with Molprobity. I've tried using the PDB tools to change 3.0 to 2.3 but they also have problems :-( For us poor souls who are suffering with hydrogen any fix would be appreciated. For now, I am pulling the detector back :-) Eddie. Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Email: [EMAIL PROTECTED] Telepathy: 42.2 GHz Heisenberg was probably here! From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Roberto Steiner Sent: Thursday, June 19, 2008 10:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot and Hs 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 -0.00 -0.000.0 SCALE2 0.00 0.005989 0.000.0 SCALE3 0.00 0.00 0.0059810.0 ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 AN ANISOU1 N THR A 2 9721 7539 9478 1186 2103297 AN ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 AC ANISOU2 CA THR A 210790 8621 9925 1145 1971285 AC ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 AC ANISOU3 CB THR A 210519 8251 9322 1244 1638409 AC ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 AO ANISOU4 OG1 THR A 210309 7971 9516 1332 1549489 AO ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 AC ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403582 AC ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 AC ANISOU6 C THR A 210101 8073 9151869 2179 63 AC ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 AO ANISOU7 O THR A 2 9210 7258 8131790 2339-23 AO ATOM 8 HA THR A 2 25.639 62.015 24.900 1.00 71.84 AH ATOM 9 HB THR A 2 27.009 64.232 24.226 1.00 69.26 AH ATOM 10 HG1 THR A 2 28.232 62.991 26.212 1.00 67.50 AH ATOM 11 HG21 THR A 2 26.275 65.055 26.303 1.00 61.19 AH ATOM 12 HG22 THR A 2 25.104 64.300 25.596 1.00 61.19 AH ATOM 13 HG23 THR A 2 25.894 63.607 26.753 1.00 61.19 AH Written: CRYST1 45.460 166.970 167.200 90.00 90.00 90.00 P 21 21 21 SCALE1 0.021997 -0.00 -0.000.0 SCALE2 0.00 0.005989 0.000.0 SCALE3 0.00 0.00 0.0059810.0 ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 AN ANISOU1 N THR A 2 9721 7539 9478 1186 2103297 AN ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 AC ANISOU2 CA THR A 210790 8621 9925 1145 1971285 AC ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 AC ANISOU3 CB THR A 210519 8251 9322 1244 1638409 AC ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 AO ANISOU4 OG1 THR A 210309 7971 9516 1332 1549489 AO ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 AC ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403582 AC ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 AC ANISOU6 C THR A 210101 8073 9151869 2179 63 AC ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 AO ANISOU7 O THR A 2 9210 7258 8131790 2339-23 AO ATOM 8 HA THR A 2 25.639 62.015 24.900 1.00 71.84 AH ATOM 9 HB THR A 2 27.009 64.232 24.226 1.00 69.26 AH ATOM 10 HG1 THR A 2 28.232 62.991 26.212 1.00 67.50 AH ATOM 11 HG2 THR A 2 26.275 65.055 26.303 1.00 61.19 AH ATOM 12 HG2 THR A 2 25.104 64.300 25.596 1.00 61.19 AH ATOM 13 HG2 THR A 2 25.894 63.607 26.753 1.00 61.19 AH Does anyone know (Paul?) the reason for the above? The only solution right now (that I know of) is to remove all
Re: [ccp4bb] Coot and Hs
Dear Roberto, Roberto Steiner wrote: Dear all, a problem possibly at the coot/mmdb interface... Indeed. 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. Technical answer: The current PDB parser in Coot is from mmdb and is for PDB format version 2.3. Phenix.refine and other modern programs use PDB format version 3.0 [1] - released over a year ago. PDB version 3.0 "Remediated" does not wrap the hydrogen (or other) names and so the hydrogen name "unmangler" - which is what is tripping you up - need not be executed. I'd like to make Coot compatible with the current PDB standard. If CCP4 were to release a version of mmdb compatible with Coot, I could do that right away [2]. I'm hoping that they will do so today^H^H^H^H^H soon. The only solution right now (that I know of) is to remove all Hs and generate them again (molprobity for example) prior to refinement. Bleugh. Non-optimal (no matter how fine Molprobity is). Paul. [1] or version 3.1? [2] I imagine.
[ccp4bb] Coot and Hs
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 -0.00 -0.000.0 SCALE2 0.00 0.005989 0.000.0 SCALE3 0.00 0.00 0.0059810.0 ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 AN ANISOU1 N THR A 2 9721 7539 9478 1186 2103 297 AN ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 AC ANISOU2 CA THR A 210790 8621 9925 1145 1971 285 AC ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 AC ANISOU3 CB THR A 210519 8251 9322 1244 1638 409 AC ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 AO ANISOU4 OG1 THR A 210309 7971 9516 1332 1549 489 AO ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 AC ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403 582 AC ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 AC ANISOU6 C THR A 210101 8073 9151869 2179 63 AC ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 AO ANISOU7 O THR A 2 9210 7258 8131790 2339 -23 AO ATOM 8 HA THR A 2 25.639 62.015 24.900 1.00 71.84 AH ATOM 9 HB THR A 2 27.009 64.232 24.226 1.00 69.26 AH ATOM 10 HG1 THR A 2 28.232 62.991 26.212 1.00 67.50 AH ATOM 11 HG21 THR A 2 26.275 65.055 26.303 1.00 61.19 AH ATOM 12 HG22 THR A 2 25.104 64.300 25.596 1.00 61.19 AH ATOM 13 HG23 THR A 2 25.894 63.607 26.753 1.00 61.19 AH Written: CRYST1 45.460 166.970 167.200 90.00 90.00 90.00 P 21 21 21 SCALE1 0.021997 -0.00 -0.000.0 SCALE2 0.00 0.005989 0.000.0 SCALE3 0.00 0.00 0.0059810.0 ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 AN ANISOU1 N THR A 2 9721 7539 9478 1186 2103 297 AN ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 AC ANISOU2 CA THR A 210790 8621 9925 1145 1971 285 AC ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 AC ANISOU3 CB THR A 210519 8251 9322 1244 1638 409 AC ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 AO ANISOU4 OG1 THR A 210309 7971 9516 1332 1549 489 AO ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 AC ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403 582 AC ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 AC ANISOU6 C THR A 210101 8073 9151869 2179 63 AC ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 AO ANISOU7 O THR A 2 9210 7258 8131790 2339 -23 AO ATOM 8 HA THR A 2 25.639 62.015 24.900 1.00 71.84 AH ATOM 9 HB THR A 2 27.009 64.232 24.226 1.00 69.26 AH ATOM 10 HG1 THR A 2 28.232 62.991 26.212 1.00 67.50 AH ATOM 11 HG2 THR A 2 26.275 65.055 26.303 1.00 61.19 AH ATOM 12 HG2 THR A 2 25.104 64.300 25.596 1.00 61.19 AH ATOM 13 HG2 THR A 2 25.894 63.607 26.753 1.00 61.19 AH 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]
