Re: [ccp4bb] shape complementarity calculations
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.
[ccp4bb] shape complementarity calculations
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.
Re: [ccp4bb] shape complementarity calculations
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 structure. So before you attribute changes in sc to conformational changes, be sure the surfaces haven't moved wrt each other! Cheers, Ed Oganesyan, Vaheh wrote: 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.
Re: [ccp4bb] shape complementarity calculations - oops!
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
Re: [ccp4bb] shape complementarity calculations
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 Parade, Parkville Victoria 3052, AUSTRALIA Tel. 61-3-9345-2693 Fax 61-3-9345-2686 Email: lawre...@wehi.edu.au On 04/03/2009, at 9:17 AM, Oganesyan, Vaheh wrote: 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. Mike Lawrence, PhD WEHI Principal Research Fellow Division of Structural Biology Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville Victoria 3052, AUSTRALIA Tel. 61-3-9345-2693 Fax 61-3-9345-2686 Email: lawre...@wehi.edu.au
