[phenixbb] large ASU: problem with upper/lower case chain IDs

Cherepanov, Peter P p.cherepanov at imperial.ac.uk
Tue Mar 25 16:30:52 PDT 2008

Dear phenix developers, 

I am new to this list and apologize in advance if the following has been discussed before. Although, I must say, the problem is rather unusual... well, we are trying to refine a structure with 36 protein chains per asu (not much fun, but it is our best crystal form for this protein). The chains are labeled (by phaser) with UPPER and lower case characters. THE TROUBLE IS, phenix.refine confuses upper and lower case chain IDs. Now, although default refinement (no restraint_group definitions) works, it is very important for us to define groups of residues, in particular, for NCS. I tried defining chains using quotes (e.g chain "i"; or chain 'i', or "chain i", etc,etc), which did not help. Phenix chokes on our pdb file also after automatic NCS search (although it finds and defines ncs groups correctly). It is funny, because, the program does discriminate between upper and lower case characters when referring to an element (e.g. it does not accept "element Se" when coordinate file has got "SE" and vice versa). 

Analogous refinement (and NCS definitions) works great in Refmac; but would like to compare results and also take advantage of simulated annealing in phenix.refine. 

Is there a quick fix, without tedious relabeling the chains? In principle, we could use upper case characters, followed by digits 0-9 [that works], but this would make the whole process very difficult for a number of reasons; I hope there is way around it, 

thank you, 


PS: we are using v1.3b

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