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

amadrona at uci.edu amadrona at uci.edu
Sun Aug 22 16:17:13 PDT 2010

> On Sat, Aug 21, 2010 at 5:41 PM,  <amadrona at uci.edu> wrote:
>>> 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
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> phenixbb at phenix-online.org
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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.


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