Dear Phenix developers, I am solving a protein-dna complex and Autobuild is able to build both the protein as well as DNA chain (one at a time). However, when I try to do the refinement, I get an error saying "Phenix could not find the geometry restraints in the standard monomer library for one or more residues in the pdb file... DG: 6 copies, DA: 3 copies, DT: 43 copies". It seems like Autobuid uses the nomenclature DA, DC, DG and DT for the DNA bases while Phenix.Refine either doesn't like the nomenclature or the restraint files uses a different one. It still however lets me do the refinement...although I don't know if it just ignores the DNA part. Can someone enlighten me on this. Also, the nomenclature Coot seems to like is Ad, Cd, Gd, Td for the DNA and doesn't like the above phenix style. In order to manipulate in coot, I had to rename all the bases...is it possible to have a format that is compatible both in Phenix and Coot or am I missing something obvious here. Thanks and Have a great weekend! Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
On Fri, May 14, 2010 at 2:41 PM, Rajagopalan, Senapathy < [email protected]> wrote:
I am solving a protein-dna complex and Autobuild is able to build both the protein as well as DNA chain (one at a time). However, when I try to do the refinement, I get an error saying “Phenix could not find the geometry restraints in the standard monomer library for one or more residues in the pdb file... DG: 6 copies, DA: 3 copies, DT: 43 copies”. It seems like Autobuid uses the nomenclature DA, DC, DG and DT for the DNA bases while Phenix.Refine either doesn’t like the nomenclature or the restraint files uses a different one. It still however lets me do the refinement...although I don’t know if it just ignores the DNA part. Can someone enlighten me on this.
This is just the GUI giving you the error, right? I think this is just a stupid case-sensitivity error I made - should be an easy fix. Could you please send me (not the list!) a relevant part of the PDB file (doesn't need to be the entire thing, just enough to give this error) so I can debug the problem? If phenix.refine itself has any problem finding the appropriate restraints, it will quit with an error almost immediately after you start it - if this doesn't happen, you should be okay. Also, the nomenclature Coot seems to like is Ad, Cd, Gd, Td for the DNA and
doesn’t like the above phenix style. In order to manipulate in coot, I had to rename all the bases...is it possible to have a format that is compatible both in Phenix and Coot or am I missing something obvious here.
I really hope this isn't necessary - we should be using a similar monomer library. What happens when you try to refine the file that was okay in Coot? Could you send me that too (or an appropriate excerpt)? thanks, Nat
Just a few quick comments for clarification:
It seems like Autobuid uses the nomenclature DA, DC, DG and DT for the DNA bases while Phenix.Refine either doesn't like the nomenclature or the restraint files uses a different one. It still however lets me do the refinement...although I don't know if it just ignores the DNA part. Can someone enlighten me on this.
phenix.refine understands the whole variety RNA/DNA names. The DA, DC, DG, DT names have been the standard PDB names as of summer 2007.
Also, the nomenclature Coot seems to like is Ad, Cd, Gd, Td for the DNA
These are older monomer library names; they've never been a standard.
and doesn't like the above phenix style.
Paul Emsley knows best, but I believe current Coot versions understand the 2007 standard PDB names, too. Ralf
Ralf W. Grosse-Kunstleve wrote:
Just a few quick comments for clarification:
It seems like Autobuid uses the nomenclature DA, DC, DG and DT for the DNA bases while Phenix.Refine either doesn't like the nomenclature or the restraint files uses a different one. It still however lets me do the refinement...although I don't know if it just ignores the DNA part. Can someone enlighten me on this.
phenix.refine understands the whole variety RNA/DNA names. The DA, DC, DG, DT names have been the standard PDB names as of summer 2007.
Coot understands these too (and converts the atom and residue names from the model to match the dictionary) - except (I should add) the C7 of DT which currently remains C5M.
Also, the nomenclature Coot seems to like is Ad, Cd, Gd, Td for the DNA
These are older monomer library names; they've never been a standard.
Not PDB standard, no. Those name are what is in the refmac dictionary.
and doesn't like the above phenix style.
Paul Emsley knows best, but I believe current Coot versions understand the 2007 standard PDB names, too.
Paul Emsley knows that this is a failing - it is a matter of finding the time to fix it. What is needed, I believe, is what Phenix does, and that is an on-the-fly conversion of old PDB atom and residue dictionary names to PDB version 3.0 names.
participants (4)
-
Nathaniel Echols -
Paul Emsley -
Rajagopalan, Senapathy -
Ralf W. Grosse-Kunstleve