that will not work in ptraj for the reasons I explained before. the
atoms must match. when you fit 43-86, it is using different atoms for
the fit. changing the numbering in the pdb file won't matter (as far
as I know). perhaps you can use a program that builds the missing
parts (the structure doesn't matter, but they ened to be present).
then you can use it as a reference. perhaps others can suggest good
ways of doing this.
On Thu, Jan 14, 2010 at 7:57 AM, qiaoyan <qiaoyan.dicp.ac.cn> wrote:
> Dear professor:
> I want to use the crystall structure as reference, but the structure is not complete, it has a loop lost corresponding to resi 15-42, so its structure is from 1-14 and 43-104, when I fit to resi 1-14, it seems normal, but when I fit to resi 43-86, the rmsd is very high, I have adjusted the residue number. what is the problem?
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Received on Thu Jan 14 2010 - 05:30:02 PST
