Question about adding hydrogrens with reduce -- parameters for phenix.refine
Hi I am trying to generate a model with all hydrogens placed using reduce. To my surprise it only applies hydrogens to a selected few residues. How do I coax reduce to add ALL hydrogens to my model, according to the Richardson Lab paper this should be possible? The help from reduce was not helpful in that regard. Or is adding all hydrogens a bad idea? Along those lines. If I would use another tool to generate the hydrogens, like CNS(X) or Maeastro, how compatible are the parameter files? Thanks for any input Carsten
Hi Carsten, there was a bug in phenix.reduce that is fixed already (I'm not sure if this fix is in the latest PHENIX rc6). Meanwhile you can still use the online version of Reduce to add H atoms: http://molprobity.biochem.duke.edu/ Adding all hydrogens is a good idea. Pavel. On 12/6/2007 10:34 AM, Schubert, Carsten [PRDUS] wrote:
Hi
I am trying to generate a model with all hydrogens placed using reduce. To my surprise it only applies hydrogens to a selected few residues. How do I coax reduce to add ALL hydrogens to my model, according to the Richardson Lab paper this should be possible? The help from reduce was not helpful in that regard. Or is adding all hydrogens a bad idea?
Along those lines. If I would use another tool to generate the hydrogens, like CNS(X) or Maeastro, how compatible are the parameter files?
Thanks for any input
Carsten
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To my surprise it only applies hydrogens to a selected few residues. That sounds like a bug. It should add almost all hydrogens, with the few exceptions indicated in the -help output. Which version of phenix is this? -- In newer versions you can run
Hi Carsten, phenix.version to find out. The version information shown at the beginning of the phenix.reduce output would also be useful to know. Are you adding the hydrogens to protein or rna/dna?
If I would use another tool to generate the hydrogens, like CNS(X) or Maeastro, how compatible are the parameter files?
As of Sep this year phenix.refine should deal with any of the hydrogen naming conventions (old pdb, new pdb, refmac, cns). This is for standard protein and rna/dna. Ligands may require special attention, e.g. a special parameter file (use phenix.elbow). Ralf
Ralf, I am using phenix rc5 and reduce in that version. Funny, it appears I just upgraded, tough to keep up with you guys. I'll upgrade to rc6 and see if this problem still persists Thanks Carsten
-----Original Message----- From: [email protected] [mailto:[email protected]]On Behalf Of Ralf W. Grosse-Kunstleve Sent: Thursday, December 06, 2007 2:15 PM To: [email protected] Subject: Re: [phenixbb] Question about adding hydrogrens with reduce -- parameters for phenix.refine
To my surprise it only applies hydrogens to a selected few residues. That sounds like a bug. It should add almost all hydrogens, with the few exceptions indicated in the -help output. Which version of phenix is this? -- In newer versions you can run
Hi Carsten, phenix.version to find out. The version information shown at the beginning of the phenix.reduce output would also be useful to know. Are you adding the hydrogens to protein or rna/dna?
If I would use another tool to generate the hydrogens, like CNS(X) or Maeastro, how compatible are the parameter files?
As of Sep this year phenix.refine should deal with any of the hydrogen naming conventions (old pdb, new pdb, refmac, cns). This is for standard protein and rna/dna. Ligands may require special attention, e.g. a special parameter file (use phenix.elbow).
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Upgrading to rc6 fixed the reduce issue. Thanks
-----Original Message----- From: [email protected] [mailto:[email protected]]On Behalf Of Schubert, Carsten [PRDUS] Sent: Thursday, December 06, 2007 2:27 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Question about adding hydrogrens with reduce --parameters for phenix.refine
Ralf,
I am using phenix rc5 and reduce in that version. Funny, it appears I just upgraded, tough to keep up with you guys. I'll upgrade to rc6 and see if this problem still persists
Thanks
Carsten
-----Original Message----- From: [email protected] [mailto:[email protected]]On Behalf Of Ralf W. Grosse-Kunstleve Sent: Thursday, December 06, 2007 2:15 PM To: [email protected] Subject: Re: [phenixbb] Question about adding hydrogrens with reduce -- parameters for phenix.refine
To my surprise it only applies hydrogens to a selected few residues. That sounds like a bug. It should add almost all hydrogens, with the few exceptions indicated in the -help output. Which version of phenix is this? -- In newer versions you can run
Hi Carsten, phenix.version to find out. The version information shown at the beginning of the phenix.reduce output would also be useful to know. Are you adding the hydrogens to protein or rna/dna?
If I would use another tool to generate the hydrogens, like CNS(X) or Maeastro, how compatible are the parameter files?
As of Sep this year phenix.refine should deal with any of the hydrogen naming conventions (old pdb, new pdb, refmac, cns). This is for standard protein and rna/dna. Ligands may require special attention, e.g. a special parameter file (use phenix.elbow).
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
Schubert, Carsten [PRDUS]