[phenixbb] MSE gap

[Pavel Afonine]

If you just do what I suggested in my previous email, then I presume you 
will get what you want: a new PDB file with fixed gap and accordingly 
updated statistics in its header (statistics in REMARK 3 is what is 
supposed to go for PDB deposition).

I don't see why this may not work... Am I missing something?

Pavel.


On 1/16/2008 2:12 PM, Troy E Messick wrote:
> That's what I've used to bring them back together in previous rounds
> of refinement.  The only problem is that I want to finalize the pdb so
> I can deposit it.  If I'm making modifications to the pdb file (by
> regularizing), then I think the stats in the log file aren't accurate.
>
> Troy
>
> On Jan 16, 2008 5:02 PM, Rife, Christopher L <crife at slac.stanford.edu> wrote:
>   
>> If it's close together, just open the file in coot and use the regularize command to put them where they should be. Or, better yet, use real-space-refine to optimize it (note, this needs a map).
>>
>> Regards,
>> Chris
>>
>>
>> -----Original Message-----
>> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Troy E Messick
>> Sent: Wednesday, January 16, 2008 1:32 PM
>> To: phenixbb at phenix-online.org
>> Subject: [phenixbb] MSE gap
>>
>> Hello,
>>
>> I seem to be having a problem with phenix.refine and the
>> seleno-methionine residue (resname MSE).
>>
>> It seems that I have a gap in the peptide bond between the C atoms and
>> the N atom of the subsequent residue.  Is there something I could add
>> to the restraints_edits.params file to get it to click together?  What
>> is the distance_ideal and sigma for a peptide bond?
>>
>> Thanks for your help,
>> Troy
>>
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