question about generating cif and pdb file using elbow
Hi, I am using phenix.elbow to generate pdb and cif files with the tripos format file: phenix.elbow --initial_geometry egcg.mol2 --opt --output="LIG" --pdb-ligand The input pdb file contains hydrogen atoms and the output pdb file also contains hydrogen atom. My crystal data only difftracted to 2.4A, so hydrogen atoms cannot be seen. In the refinement, my ligand should not contain hydrogen atoms. So I add one more option not to add hydrogen following the online phenix documentation: phenix.elbow --initial_geometry --write-hydrogens=False egcg.mol2 --opt --output="LIG" --pdb-ligand *However, the program failed. Does anyone know why?* Usage: phenix.elbow [options] *phenix.elbow: error: no such option: --write-hydrogens* -- Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: [email protected] lab phone: 216-368-3337
Qun Two things. I think you will find a large group of people who will disagree with your assertion that your refinement should not contain hydrogens. Secondly, can you tell me which version your are using? Is it 1.4-3? Nigel On 3/19/09 4:21 PM, crystallogrphy wrote:
Hi, I am using phenix.elbow to generate pdb and cif files with the tripos format file:
phenix.elbow --initial_geometry egcg.mol2 --opt --output="LIG" --pdb-ligand
The input pdb file contains hydrogen atoms and the output pdb file also contains hydrogen atom. My crystal data only difftracted to 2.4A, so hydrogen atoms cannot be seen. In the refinement, my ligand should not contain hydrogen atoms. So I add one more option not to add hydrogen following the online phenix documentation:
phenix.elbow --initial_geometry --write-hydrogens=False egcg.mol2 --opt --output="LIG" --pdb-ligand
*However, the program failed. Does anyone know why?* Usage: phenix.elbow [options] *phenix.elbow: error: no such option: --write-hydrogens*
-- Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: [email protected] mailto:[email protected] lab phone: 216-368-3337 ------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
As far as I recall the write-hydrogens options is an expert option, depending on the version of elbow. Check out the elbow documentation on how to become an expert. As far as hydrogens are concerned, I would second Nigel's concern. Adding hydrogens in riding mode has the very real potential of improving the geometry of your structure due to the imposed anti-bumping restraints. You could try refinement with and without and see where it takes you. As a note of caution, elbow writes (Nigel correct me if I am wrong) PDB V3 compatible hydrogen names, which may cause some graphics programs to choke. Newer versions of coot (0.5.2 or later) seem to work fine. HTH Carsten -----Original Message----- From: [email protected] [mailto:[email protected]]On Behalf Of crystallogrphy Sent: Thursday, March 19, 2009 7:22 PM To: [email protected] Subject: [phenixbb] question about generating cif and pdb file using elbow Hi, I am using phenix.elbow to generate pdb and cif files with the tripos format file: phenix.elbow --initial_geometry egcg.mol2 --opt --output="LIG" --pdb-ligand The input pdb file contains hydrogen atoms and the output pdb file also contains hydrogen atom. My crystal data only difftracted to 2.4A, so hydrogen atoms cannot be seen. In the refinement, my ligand should not contain hydrogen atoms. So I add one more option not to add hydrogen following the online phenix documentation: phenix.elbow --initial_geometry --write-hydrogens=False egcg.mol2 --opt --output="LIG" --pdb-ligand However, the program failed. Does anyone know why? Usage: phenix.elbow [options] phenix.elbow: error: no such option: --write-hydrogens -- Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: [email protected] lab phone: 216-368-3337
Hi Qun, You can remove hydrogen atoms easily using coot if you want . Anyway, hydrogen are in the structure even if the resolution for them is not high enough. So someone suggest to add them when we check or refine structures. Just as Carsten said ,you can refine your structure with hydrogen and see what is there difference or not. liu Schubert, Carsten [PRDUS] wrote:
As far as I recall the write-hydrogens options is an expert option, depending on the version of elbow. Check out the elbow documentation on how to become an expert.
As far as hydrogens are concerned, I would second Nigel's concern. Adding hydrogens in riding mode has the very real potential of improving the geometry of your structure due to the imposed anti-bumping restraints. You could try refinement with and without and see where it takes you. As a note of caution, elbow writes (Nigel correct me if I am wrong) PDB V3 compatible hydrogen names, which may cause some graphics programs to choke. Newer versions of coot (0.5.2 or later) seem to work fine.
HTH
Carsten
-----Original Message----- *From:* [email protected] [mailto:[email protected]]*On Behalf Of *crystallogrphy *Sent:* Thursday, March 19, 2009 7:22 PM *To:* [email protected] *Subject:* [phenixbb] question about generating cif and pdb file using elbow
Hi, I am using phenix.elbow to generate pdb and cif files with the tripos format file:
phenix.elbow --initial_geometry egcg.mol2 --opt --output="LIG" --pdb-ligand
The input pdb file contains hydrogen atoms and the output pdb file also contains hydrogen atom. My crystal data only difftracted to 2.4A, so hydrogen atoms cannot be seen. In the refinement, my ligand should not contain hydrogen atoms. So I add one more option not to add hydrogen following the online phenix documentation:
phenix.elbow --initial_geometry --write-hydrogens=False egcg.mol2 --opt --output="LIG" --pdb-ligand
*However, the program failed. Does anyone know why?* Usage: phenix.elbow [options] *phenix.elbow: error: no such option: --write-hydrogens*
-- Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: [email protected] mailto:[email protected] lab phone: 216-368-3337
------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Qun Wan, check out this: http://www.phenix-online.org/documentation/refinement.htm#anch28 and slide #37 here: http://www.phenix-online.org/presentations/neutron_japan_2009/ -> Structure refinement and PHENIX (morning session) (PDF) this says some things about hydrogens in refinement. Pavel.
My crystal data only difftracted to 2.4A, so hydrogen atoms cannot be seen. In the refinement, my ligand should not contain hydrogen atoms. So I add one more option not to add hydrogen following the online phenix documentation:
phenix.elbow --initial_geometry --write-hydrogens=False egcg.mol2 --opt --output="LIG" --pdb-ligand
*However, the program failed. Does anyone know why?* Usage: phenix.elbow [options] *phenix.elbow: error: no such option: --write-hydrogens*
-- Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: [email protected] mailto:[email protected] lab phone: 216-368-3337 ------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Pavel, I installed the new version of phenix as follows: I downloaded the new version to my Download folder and then untar.and cd to the phenix-installer-<version> folder. Here I run ./install. By default it installed the phenix at /usr/local. Can I now delete the phenix-installer-<version> folder from my 'Download' folder? Thanks... Raja
participants (6)
-
crystallogrphy -
junfeng liu -
Nigel W Moriarty -
Pavel Afonine -
Raja Dey -
Schubert, Carsten [PRDUS]