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
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