Dear Xplor-NIH users
I have been using the Python interface to calculate initial structures of my protein. I have used a slightly modified version of the anneal.py scripts given on the Xplor-NIH website and in the tutorials. However, I have made no significant changes to the loop that calculates one structure (structLoopAction or calcOneStructure). While the script appears to run fine, I've noticed that the '.sa' and '.viols' files are written before the final minimisation step in Cartesian space. As a result, there are discrepancies between the final energy and violations and those which are written to file. To troubleshoot, I've put in a line of code that writes a pdb file in the appropriate place and again, it writes the structure before completion of the energy minimisation. Is there something I have done wrong, or is this a problem others have noticed? I can provide the relevant code if necessary, but it is very similar to that in template script. I've been using Xplor-NIH version 2.24 on Ubuntu 9.10. Many thanks David Yadin PhD student, Department of Biochemistry, University of Oxford -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20100617/4fe62651/attachment.html
