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

Jeff Headd jjheadd at lbl.gov
Sat Aug 21 20:08:21 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:

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


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