[phenixbb] Loop fitting question

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Dec 13 18:09:31 PST 2010

Hi Luke,
Just reporting to the list what we found out...

There were two problems that your case helped me fix:

1. Resolve was reading sequences only up to 132 characters on a line. 
That is now changed to be unlimited. (The other sequence interpretation
tools always read any number of characters on a line, including
autobuild/autosol/automr etc).

2. At the end of loop fitting, a check was done to make sure that the new
loop does not overlap with anything in the rest of the model.  That check
was done by reassembling the chains in the model with resolve. It had the
side-effect of losing the sequence assignment if the density was poor. 
The default is now to skip that check (skip_trim=True) in fit_loops, but
to carry out the check in autobuilding, reasoning that a user is not
likely to try to build a loop where something is already present.

These changes are now checked in so versions starting with tomorrow should
have the behavior that you were looking for.

Thanks for letting me know of the problems!
All the best,
Tom T

>> 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
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb

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