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Dear Deepak,
the only atom type present in DNA and not in Proteins would be the
Phosphorus. You can probably add this to sc_radii.lib yourself with the line
***P* 1.80
the radius stems from http://en.wikipedia.org/wiki/Phosphorus and the
Hello,
After following the discussion on
[ccp4bb] shape complementarity between protein and DNA surface,
is there someone here able to explain simply what the SC software
of CCP4 is calculating?
I mean, is there some intuitive/easy to understand explanation of what
SC is calculating?
I know
,
After following the discussion on
[ccp4bb] shape complementarity between protein and DNA surface,
is there someone here able to explain simply what the SC software
of CCP4 is calculating?
I mean, is there some intuitive/easy to understand explanation of what SC is
calculating?
I know I
On 02/08/2012 12:47 PM, Mike Lawrence wrote:
Hi Francois
Here's a one-liner. The major concept behind the Sc coefficient is that it measures the
extent to which, on average, the normal vectors between closest-neighbour
opposing points within the molecular interface are antiparallel.
Sc=1
Dear All
For calculation of the shape complementarity index using the Sc
program between a protein and DNA surface, does anybody have a
modified radii.lib file that includes information about DNA atoms?
Also, is there any reference that has information regarding the atomic
radii of DNA atoms?
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
Deepak Thankappan Nair wrote:
~~~
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
I think SC is THE way to calculate it.
If not working in the current release, we should get it fixed.
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
MOLECULE1 CHAIN A to define the first surface
but i get the following error:
MOLECULE1 CHAIN A
No molecule number given
BFONT
Hello Everyone,
I am trying to calculate shape complementarity of NMR structure (1U89) using
CCP4 Sc.
I get following error
$WARNING: NO CRYST CARDS READ$
BFONT COLOR=#FF!--SUMMARY_BEGIN--
$TEXT:Warning: $$ comment $$
WARNING: NO CRYST CARDS READ FROM XYZIN
$$
@JISCMAIL.AC.UK
Subject: [ccp4bb] shape complementarity using NMR structures
Hello Everyone,
I am trying to calculate shape complementarity of NMR structure (1U89) using
CCP4 Sc.
I get following error
$WARNING: NO CRYST CARDS READ$
BFONT COLOR=#FF!--SUMMARY_BEGIN--
$TEXT:Warning: $$ comment
Hi!
I am trying to calculate shape complementarity using SC in CCP4 for nucleic
acids.
SC stopped with an error no radius found for atoms of nucleic acid residues.
I can edit in the radii for those atoms in sc_radii.lib, but am wondering what
would the recommended radii be, especially for
Hello everybody,
I recently tried to feed the shape complementarity program (sc) with GRASP
surface files for visualisation. Sc is supposed to output modified surface
files, again, in GRASP format. However, the program terminated without
producing a file, or, sometimes, writing truncated ones.
Hi Reiner
I haven't seen this problem before; if you send me all the relevant files
I will try to check it out. It may relate to the fact that the GRASP files
were made with Chimera.
sincerely
Mike Lawrence
Hello everybody,
I recently tried to feed the shape complementarity program (sc)
Dear All,
Could someone please suggest me program(s) to get the shape complementarity
index for a protein complex structure of mine?
Many thanks
--
Amit Sharma, Ph.D. Research Associate, Department of Biology,
University of York, YO10 5DD UK
amit sharma wrote:
Dear All,
Could someone please suggest me program(s) to get the shape
complementarity index for a protein complex structure of mine?
Many thanks
sc, by Michael Lawrence:
http://www.ccp4.ac.uk/dist/html/sc.html
(included in ccp4 distro)
Hi Vaheh,
Below is a reply I made to the BB in 2007 after a similar enquiry. I expect the
program should still
work the same, although I haven't used it in recent releases. You have to run
it from line command,
as there is no interface for it in CCP4i. If you are running under Windows, as
I
Colleagues,
Would some one kindly suggest software that calculates shape
complementarity of two interacting proteins based on co-crystal
structure?
I've seen number of reports with sc parameter included but none of
those mention how it was done.
Among non-runnable programs in CCP4 there is the sc
Actually sc is part of the ccp4 package.
(more $CDOC/sc.doc)
The reference describing the procedure is:
1. Michael C. Lawrence and Peter M. Colman J. Mol. Biol., 234, p946 -
p950 (1993)
As you say, it calculates shape complimentarity of the surfaces as they
are docked in the
Oganesyan, Vaheh wrote:
Among non-runnable programs in CCP4 there is the sc program that indeed
does not run.
Sorry, I didn't see the rest of your post.
I had sc running and producing meaningful results back in 2006-2007,
I can check which version etc.
Ed
Hi Vaheh
I have not had anyone report problems with sc of late. If you send me
the relevant files or output I can check it out for you.
sincerely
Mike Lawrence, PhD
WEHI Principal Research Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal
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