[phenixbb] Loop fitting question

xaravich ivan xaravich.ivan at gmail.com
Sat Dec 11 13:44:42 PST 2010

Hi Luke,
How big is your loop. I normally try to built it one molecule at a time from
both ends of the loop in COOT, refine and re-try loop building. Some times,
if the electron density is ok you can build the whole loop one amino-acid at
a time by iterative COOT, refinement and loop building.

On Fri, Dec 10, 2010 at 11:40 AM, Luke Rice <luke.rice at utsouthwestern.edu>wrote:

> Hi All,
> I am trying to see if I can save myself some time by using the loop fitting
> tools in Phenix. I think I am stalling out because of a trivial problem, but
> cursory googling, etc, has not helped. Sorry if I should have tried harder.
> I appreciate any help.
> I am using the gui, dev-601. My fasta sequence gets read fine because the
> output reports the sequence of the missing residues. Whether I use the loop
> library or not, I get the following error:
> Unable to find suitable gap to fill
> Then it appears to try to build the loop using sequence from a different
> chain (I have three chains in my structure).
> What am I doing wrong?
> Luke
> --
> Luke M. Rice
> Assistant Professor and
> Thomas O. Hicks Scholar in Medical Research
> Department of Biochemistry, ND10.300
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Dallas, TX 75390-8816
> phone: (214) 645-5931
> email: Luke.Rice at UTSouthwestern.edu
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