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 do, you have to start a DOS prompt window and run it from there. You might even need to specify the full path of the binary executable. You also need to specify the output log file, and you can either type your input directly or put it in a text file. I hope this helps.
Pierre p.s. I echo Ed Berry's exhortation: If you have been running MD on your interacting molecules, the SC parameter is probably meaningless. But I am prepared for surprises. ***************************** Start of previous Reply *************************************** 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. ****************************** End of previous reply ******************************************* ********************************************************************** Dr. Pierre Rizkallah, Senior Lecturer in Structural Biology, School of Medicine, Academic Avenue, Heath Park, Cardiff CF14 4XN email: rizkall...@cf.ac.uk phone + 44 29 2074 2248 >>> "Oganesyan, Vaheh" <oganesy...@medimmune.com> 03/03/09 10:28 PM >>> 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 program that indeed does not run. Thanks in advance. _______ Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
