On Sun, Mar 31, 2013 at 10:09 AM, Bishwa Subedi
The bigger problem is with the refinement even after fitting the ligand. As suggested I have figured out with fitting the ligand. I performed real space refinement to the ligand and it fits well. I used the merge function in coot to merge ligands with molecules (I have two molecules in asymmetric unit ). Now the problem is with the phenix.refine. The CIF file is not accepted.
I don't know what "not accepted" means - what happened when you tried to load it? The files you sent me loaded and ran without any problems in both version 1.8.2 and the current code. The problem with the structure you fed to ReadySet is probably that the residue name is changed to LIG, which is a generic residue code that we strongly discourage using. Because you didn't supply any other CIFs and LIG doesn't uniquely identify the chemical component, ReadySet has to guess the molecular topology, which is very difficult to do from heavy-atom coordinates alone. I'm not at all surprised that this crashes. (It also screws up the chirality, but if you use the original CIF and residue name this shouldn't happen.) A general plea to the list (repeating what Pavel has said many times): when reporting problems with any part of Phenix, send us the *exact* error message you receive, along with any Python traceback (this may not always be shown). Generic descriptions like "it crashed" or "it didn't work" tell us nothing and lead to endless email exchanges. I know from experience that many users worry about filling up our inboxes with irrelevant details, but for the record: the more information you send, the better, and we would much rather hear when our code doesn't work properly than have you give up in frustration (or switch to another program). The only thing you should avoid is sending massive attachments to the entire list (although the server will block these anyway). -Nat