On 14/10/13 03:16, Jane wrote:
Hi all, I am refining a protein structure with phenix and COOT, and COOT worked fine for three runs. The pdb file is composed of two protein chains, two ligand chains, and a water chain. Suddenly at the last run the pdb file opened by COOT only has chain A but the mtz file still displays all the chains, while the same file opened by Pymol contains all the chains. Does anyone know how to solve the problem? I am using Mac OS 10.6.8 system, and the COOT version is 0.7. I have tried to uninstall and install it several times with two installation files (one from the CCP4 website, the other from a link on phenix documentation), and it does not help.
I believe that the problem lies not with Coot, but with your coordinates file. Coot, like other mmdb-using programs (in "standard" mode), will terminate file-reading when it encounters non-compliance in the file, and present you with the atom set that it did manage to read.
The fact that Pymol parses the file shows (to me at least) that the Pymol PDB parser is somewhat more lax about adherence to the standard.
Check the console (the window from which you started coot) - it should be sufficient to identify the problem.
I'll make a note to promote such coordinate read error notifications to a info-dialog.
Paul.
