Re: [phenixbb] phenix.ready_set hydrogens not compatable with coot library

On Sat, Aug 21, 2010 at 5:41 PM, wrote:

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Sorry I meant to ask if there was any way to use phenix.ready_set "old".  I don't know the syntax but I read that it would output hydgrogens with a nomenclature that was compatable with coot library.

Hi Yarrow,

PHENIX uses the PDB version 3.x naming conventions, and Coot does not always conform to this standard, which is the problem you are running into. It is the hope that eventually all programs will use the PDB standard, and we do so as part of our goal to make sure files generated by PHENIX are ready for deposition to the PDB. (As an aside, if you refine your structure with H atoms attached it is good practice to deposit your final model with H atoms present.)

If you need to go back to a the PDB version 2.3 standard, there is a program called "Remediator" that converts between the two standards available here: http://kinemage.biochem.duke.edu/software/remediator.php

I recommend using the Python version (more robust), and if you run into any trouble with it please let me know.

Thanks, Jeff _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Thanks Jeff, I downloaded the python version and saved the remediator_python.py and the master_hash.txt file in /Users/yarrowmadrona/scripts/python. I then set the python environment by adding: setenv PYTHONPATH "/Users/yarrowmadrona/scripts/python" to my .tcshrc file. However, when I try to type "remediator_python.py model pdb" I get an uknown commmand error. I also changed the shebang line in python.py to read: #!sw64/lib/python2.6. (location of python2.6 fink installation) I am just learning how to use scripts so any information you can give me would be helpful. Thank you. -Yarrow