Thanks, Pavel, for your suggestions. As far as I can tell, there isn't a gap in the input pdb file, and phenix.refine is creating the gap. I was thinking of using the refinement.geometry_restraints.edits to define the distance and angle, however, I wasn't sure what the distance_ideal and sigma is for a peptide bond. I think without specifying the restraints, phenix.refine will keep creating the gap, so I think your idea about doing a final round of refinement without the restraints will work. Troy On Jan 16, 2008 4:51 PM, Pavel Afonine wrote:

Hi Troy,

one way of going doing this is (if atoms are not too far away, although try anyway) (Ralf may have a better idea):

1) Use custom bonds between these two atoms N and C for a short and simple refinement run just to close the gap. To do this, create a file "custom_bond.param" and put the following lines there:

refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = "chain A and resid 125 and name C" atom_selection_2 = "chain A and resid 125 and name N" distance_ideal = 1.4 sigma = 0.02 } }

and run phenix.refine like this:

% phenix.refine model.pdb data.mtz custom_bond.param

In this context the precise value in "distance_ideal = 1.4" is not important: all you want at this step is to bring these two atoms close enough so next time you run phenix.refine it automatically recognizes the covalent bond. Hopefully this refinement run will bring these two atoms close enough.

2) After the gap is closed in "step 1)", run all your subsequent refinement jobs without specifying the file "custom_bond.param", so the proper value for "distance_ideal" is used (and angle as well).

Please let us know if this didn't help or you have any questions! Pavel.

On 1/16/2008 1:31 PM, Troy E Messick wrote:

...

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

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 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: [email protected] [mailto:[email protected]] On Behalf Of Troy E Messick Sent: Wednesday, January 16, 2008 1:32 PM To: [email protected] 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

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

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

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