Ravi,
Do you use "pairfitting" or "align" command in PyMol? Align works well
for me even for different (but homologous) proteins.
Another popular alternative is to use Stamp (U. of Dundee) for the
alignment of the PDBs
(http://www.compbio.dundee.ac.uk/Software/Stamp/stamp.html)
Hugo
Ravi Bojja wrote:
Hi,
I have an unique problem with pairfitting, My Protein is comprised of
helices and loops,
In active and inactive forms there are no changes in helical
structures, but only loops orientation are changed
after pairfitting, one the structure is shifted about 0.5 angstroms,
Is there any command to shift the 0.5 angstroms of one structure, so I
that I can see both
PDB structures as one uniform helix with disoriented loops in active
and inactive form,
thanks
Ravi
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--
Hugo G. de Teran, PhD.
Departmento de Farmacología / Instituto de Farmacia Industrial
Universidade Santiago de Compostela
Facultad de Farmacia Phone: +34 981 563 100 ext 13040
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