Re: [ccp4bb] Surface complementarity

Protein crystallography Programs for crystallography X-ray detectors
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CCP4bb <-- 2007 <-- August 2007 <-- 07 August 2007

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From: "Pauptit, Richard A" Richard {- dot -} Pauptit {- at -} ASTRAZENECA {- dot -} COM
Date: 2007-08-07

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Subject: Re: Surface complementarity
From: "Rizkallah, PJ (Pierre)" p {- dot -} j {- dot -} rizkallah {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-08-07

Hi Rosemary,

The SC manual URL http://www.ccp4.ac.uk/dist/html/sc.html does contain
all the information you need, but I agree it takes some deciphering.

The basic parameters are the selections of two 'molecules' whose
interface you want to study. For that purpose, the script or line input
is really minimal, such as:

molecule 1
zone C 3 C 5
molecule 2
chain D
chain E
end

Here molecule 1 is a number of residues in chain C (zone), and molecule
2 is all of chains D and E. You can include and exclude other atoms in
each 'molecule' selection. The instruction 'end' tells the program to
start calculating. You can modify the program defaults by adding other
instructions for 'dot density', 'probe radius' and others, but I usually
run it with all the hard wired defaults. These parameters are largely
equivalent to their counterparts in AREAIMOL to determine how accurately
you want the interfaces to be calculated.

Good Luck.

Pierre
************************************************************************
*******
Pierre Rizkallah, Daresbury Laboratory, Warrington, Cheshire WA4 4AD,
U.K.
Phone: (+)44 1925 603808 Fax: (+)44 1925 603124
e-mail: p.j.rizkallah@dl.ac.uk html: http://www.srs.ac.uk/px/pjr/
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Rosemary Harrison
Sent: 07 August 2007 09:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Surface complementarity

Hi,

I would like to use the SC program but I m having some problems.
Unfortunately the "examples" webpage is not active anymore so I am
fumbling a bit in the dark.

I can get as far as sc xyzin xxx.pdb

but then it asks for

Selection commands:

and I dont know what to type in.

Can anyone help?

Thanks in advance

Rose

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CCP4bb <-- 2007 <-- August 2007 <-- 07 August 2007

Previous message:
Subject: AstraZeneca US permanent PX position
From: "Pauptit, Richard A" Richard {- dot -} Pauptit {- at -} ASTRAZENECA {- dot -} COM
Date: 2007-08-07

Next message:
Subject: needles vs crystals
From: shivesh kumar 2shivesh {- at -} GMAIL {- dot -} COM
Date: 2007-08-07