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