[phenixbb] (no subject)

Pavel Afonine pafonine at lbl.gov
Wed Aug 20 09:17:14 PDT 2008


Hi Sid,

I'm not sure I understand what the problem is... Every time you run 
phenix.refine it produces the PDB file with refined model that has all 
the refinement details reported under "REMARK 3"; and those details are 
meant for the deposition to PDB. You are not assumed to do anything 
manually, except one thing: you need manually remove the first lines 
where the file names and some statistics step-by-step is reported (till 
the line that you mention below).

Note that nothing is changed in formating the PDB header between the few 
recent versions of PHENIX.

Pavel.


On 8/20/2008 6:57 AM, Sudharsan Sridharan wrote:
> Hi all,
>
> A quick question about extracting info/preparing pdb file for
> deposition..........
>
> I've got a pdb file after refinement using phenix 1.3b. I was
> wondering if there is a way to prepare this file / format this the
> same way as in 1.3 final where we get "REMARK IF THIS FILE IS FOR PDB
> DEPOSITION: REMOVE ALL FROM THIS LINE UP" and REMARK 3. i'm already
> running refinement 1.3 final with the same parameters just to quickly
> compare the resulting refined files/numbers. I guess I could do it
> manually but curious if there is an easier way using 1.3 final.
>
> thanks,
> Sid.
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