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: [EMAIL PROTECTED] html: http://www.srs.ac.uk/px/pjr/ -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Rosemary Harrison Sent: 07 August 2007 09:43 To: [email protected] 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
