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Problem in using "loopmodel" application to add missing residues

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Problem in using "loopmodel" application to add missing residues

My problem is with flags -max_helix_melt and -max_strand_melt while creating the loopfile. If I take the default values (-1), it is creating the loopfile with no LOOP information. I have tried with other values which did not give me the correct LOOP information. How should I determine the correct values for these flags to get the correct loopfile. Please suggest.

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Wed, 2014-08-27 12:43

Quick clarification, the -max_helix_melt and -max_strand_melt settings shouldn't be applicable to the regular loopmodel application - instead they're specific to the loops_from_density application, which will determine the loops based on missing electron density regions. (See ) The documentation says "Generally '-frac_loop 0.3 -max_strand_melt 1 -max_helix_melt -1 -edensity:sliding_window 9' provides good results."

The -max_helix_melt and -max_strand_melt settings are to "chew back" strands and helices to add too the loop length. The default values of -1 are supposed to allow unlimited rebuilding into secondary structural regions. One possibility for your issue is that whatever input you're using doesn't have any "missing density" by the criteria it's using, so doesn't output any loops. You may want to try increasing the -frac_loop value to do more aggressive loop remodeling.

If you're still having issues, what, exactly, are you expecting to see, and what are you actually seeing? (You can copy/paste the loopfile in the text box, or rename it with a .txt extension and then attach it to your post.)

Thu, 2014-08-28 09:42