To the CCP4 community,
I have been trying to run PHASER to phase a nucleic acid structure by MR
using a partial template model. The problem is that symmetry-related molecules
generated from the output .pdb file coordinates spatially overlap with
extensive clashes. I understand from the PHASER FAQ page that this is commonly
due to a misalignment of the nucleic acid residue name in the .pdb file. I
have tried the suggested solutions by changing to either single-letter nucleic
acid nomenclature alinged to column 20 in the .pdb file or 3-letter
nomenclature. Unfortunately, these suggestions have failed to correct the
problem.
The FAQ also indicated that this issue can be caused by an incorrect
nomenclature for the "trace" atoms. I assume this is my problem since the
aforementioned solutions did not work. I would like to confirm that my atom
names are correct in terms of what PHASER expects, but I have not been able to
find relevant documentation for atom naming in any of the PHASER documentation
websites (i.e. linked from PHENIX, CCP4 or the PHASER homepage) or the CCP4bb
archives. Could anyone indicate where I could find information regarding the
nomenclature that PHASER expects for nucleic acid trace atoms (i.e. the
phosphate and ribose carbon atoms)? I'm sure it's a standard nomenclature, but
nothing I've tried has corrected the clashing problem, which makes me think I
may have some incorrect nomenclature (e.g. 'O1P' vs. 'OP1' if the non-bridging
phosphate oxygens are included). Alternatively, are there any other
suggestions of possible causes or solutions to this clashing problem?
Thank you very much for your time,
-Andy Torelli
