Hi Engin,

I created the file as you mentioned earlier, but I am having some problems with it. If I keep the "./sc_radii.lib" portion, I get the following error message: 

File: "./sc_radii.lib"

Cannot be opened for reading

>>>>>> CCP4 library signal ccp4_general:Cannot find input file (Error)

raised in ccp4setenv <<<<<<

Last system error message: No such file or directory

 sc:  Cannot find input file

 sc:  Cannot find input file

Times: User:       0.0s System:    0.0s Elapsed:     0:00


I also tried removing the sc_radii.lib section, and I got the following error message: 


>>>>>> CCP4 library signal ccp4_general:Use: <logical name> <file name> (Error)

raised in ccp4fyp <<<<<<

 sc:  Use: <logical name> <file name>

 sc:  Use: <logical name> <file name>

Times: User:       0.0s System:    0.0s Elapsed:     0:00  

./sc.sh: line 5: MOLECULE: command not found

./sc.sh: line 6: CHAIN: command not found

./sc.sh: line 7: CHAIN: command not found

./sc.sh: line 10: END: command not found

./sc.sh: line 11: eof: command not found



I am not sure what I am doing wrong with this script, so can you please give me some pointers? I attached the script I'm using for your convenience.


Thank you,

Nishant Kumar Singh


On Tue, Sep 29, 2015 at 11:53 AM, Engin Özkan <[log in to unmask]> wrote:
You run it in the Terminal (if you've never used it, search for it in Spotlight).

Create a file like this (below), make sure it is executable (chmod +x filename_here), and run it (./filename_here).

#!/bin/sh -e
sc XYZIN your.pdb SCRADII ./sc_radii.lib <<eof
MOLECULE 1
CHAIN A
MOLECULE 2
CHAIN B
END
eof

The "SCRADII ./sc_radii.lib" part is unnecessary if you only have amino acid residues in your structure. Disclaimer: Haven't run sc and tested this code in a while, but should at least help you get started. The CCP4 webpage should also have examples.

Engin


On 9/29/15 9:38 AM, NISHANT SINGH wrote:

Hi Everyone,


I am using CCP4i 6.5.017 on an imac. I want to us the shape complementarity (sc) for my complex. I looked on line and on the CCP4 website, it says that sc is a CCP4 supported program, but I can't find it anywhere. I have looked through the entire program  list. Am i missing something? Please help. 


Sincerely,

Nishant Kumar Singh

-- 
Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu