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Xiaoyi Deng wrote:
Dear all:
I used moleman2 to calculate the contacts between chain A and B. Can
anyone suggest a program to calculate the contacts between the
interface of dimer-dimer?
Thank you,
Xiaoyi
Graduate student
University of Nebraska
Deep-View (Swiss PDB Viewer) allows to calculate (and visualise) a
'contact surface'
between two subunits, by loading the subunits into different layers.
Residues contributing to the contact surface can be selected by CTRL-
click
on the contact surface line in the 'Cavities' menu, available
The answer to your question is called Phaser. Using Phaser, you can input
multiple search models in one search routine to look for
solutions.
You should read the online manual and tutorials, if you are not already
familiar with Phaser. You can also 'modify' or appropriately
'trim' your
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Hi,
If you checked the Ramachandran plot using PROCHECK, you may think
almost all residues belong to the most favoured, additional allowed,
or generously allowed regions of the Ramachandran plot that is the
part 1 of the PROCHECK output PostScript file.
But if you checked the part 2 of the
OK, I'm properly chastised - outlier does not equal bad.
However, residues which are not flagged as problematic or unusual
during validation should not be flagged in the final pdb file.
And I have read Gerard's paper, and the molprobity paper. Recently.
Sue
On Sep 21, 2007, at 9:57 AM,
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