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This can happen if symmetrical side chains like
tyrosine or phe have the ring rotated 180* one relative
to the other. Superposition looks perfect, but Cd1 and
Ce1 are superimposed on Cd2 and Ce2, and the program
measures Cd1 to Cd1, etc, which is large.
Ed
OnLineHelpForm wrote:
I am using ccp4 version release-5_0.
I am using ccp4i.
I am using the redhat80 operating system.
My compiler is: native
I installed using compilesource
The problem is as follows:
Dear List,
A question about LSQKAB. When I superpose two structures including all of their residues in the fitting, the resulting chart shows a high rmsd for the side chain of some aminoacids. When I open the fixed structure and the output (moved) structure in spdbv, most of the indicated side chains show in fact high positional differences. However, the side chain of one residue, whose rmsd is 1.62 A according to LSQKAB, seems instead to be perfectly overlapped in spdbv (and, in fact: rmsd of side chains calculated by spdbv=0.32).
Any suggestions, please? Where am I wrong, please?
Thanks,
Claudia
I have done the following patches:
None
Thanks in advance,
Claudia, [EMAIL PROTECTED]
