shape complementarity

From: Deepak Thankappan Nair
Date: 6 February 2012 03:14


Dear All,
Greetings!
Can anybody tell me a method to quantitate shape complementarity
between two surfaces? Sc program in CCP4 is not running properly.
thanks and regards
Deepak

----------
From: Edward A. Berry


Deepak Thankappan Nair wrote:
~~~ I think SC is THE way to calculate it.
If not working in the current release, we should get it fixed.
Can you be more specific?


For me using ccp4-6.2.0 it runs and gives apparently reasonable output:

 Mean normal product:    surface 2 to surface 1 =  0.419
 Median normal product:  surface 2 to surface 1 =  0.411


 Summary of results:
________________________________________________________
          D(A->B)      D(B->A)     D(A->B)+D(B->A)/2
 Mean       1.168        1.057            1.113
 Median     1.116        1.000            1.058

          S(A->B)      S(B->A)     S(A->B)+S(B->A)/2
 Mean       0.389        0.419            0.404
 Median     0.355        0.411            0.383

 Shape complementarity statistic Sc =    0.383
_

----------
From: Edward A. Berry


Deepak Thankappan Nair wrote:

Dear Dr. Berry
thanks for the mail. maybe the syntax that I provide is not correct.
i assume you have to write
MOLECULE<1>  CHAIN A to define the first surface
but i get the following error:

MOLECULE<1>  CHAIN A
  No molecule number given
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 SC:   Syntax: MOLECULE<n>
 SC:   Syntax: MOLECULE<n>

I think you don't put the "<>" in "<n>" - just the number.
here is an example that runs:

sc xyzin temp.pdb <<eof
MOLecule 1
zone C 20 C 379
MOLecule 2
zone R 74 R 196
eof

Good luck!
eab

there are no examples on the ccp4 website
any light on this would be very valuable,
regards
deepak