Are you running refinement to cause the separation? If so, you can try the intra_chain=True option in later version to link the two residues. If that fails send me the files directly. Cheers Nigel NB. Any files sent to me will be held in strictest confidence. On Tue, Aug 20, 2013 at 12:00 PM, Dmitry Rodionov wrote:

Click Real space refine zone. Then click on your previous residue, then click on the newly added residue.

HTH, Dmitry

On 2013-08-20, at 2:53 PM, Heather L Condurso wrote:

...

Dear all,

I have been trying to add a residue to my model in coot for hours now. The add terminal residue function adds a residue far from the end of my chain and I've tried moving it manually and it keeps going back and it never makes a bond between the two amino acids. Is there a trick in coot or a better way to do this in phenix?

Thanks, Heather Condurso UF-Department of Chemistry _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

Thank you all. I do not know what solved my issue but I deleted many UNK residues that though having a lower number came after the end of my chain in the pbd file and now it is working. I had tried real space refine and moved it manually but without avail. Maybe this version of coot 0.6.2-pre-1 is unhappy with pdb from phenix autobuild/refine. On Tue, Aug 20, 2013 at 3:18 PM, Ursula Schulze-Gahmen < [email protected]> wrote:

Heather,

I am using the stand alone version of coot and I am adding terminal residues all the time. I have the same experience as you do , that the residue is usually added far away from the end of my chain. I then move it into a sensible position relative to the chain end and refine the geometry on coot. I have never seen the residue moving back to its original position. Perhaps try the stand alone version of coot and see if it works there for you.

Ursula

On Tue, Aug 20, 2013 at 11:53 AM, Heather L Condurso wrote:

...

Dear all,

I have been trying to add a residue to my model in coot for hours now. The add terminal residue function adds a residue far from the end of my chain and I've tried moving it manually and it keeps going back and it never makes a bond between the two amino acids. Is there a trick in coot or a better way to do this in phenix?

Thanks, Heather Condurso UF-Department of Chemistry

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-- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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