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Also, I just saw your sc.sh file from your second email, and you seem to have commented out MOLECULE 2. I am not sure why you'd do that.
Use
MOLECULE 1
CHAIN A
MOLECULE 2
CHAIN B
I assume you are measuring shape complementarity between molecule 1 (which is in chain A) and molecule 2 (which is in chain B).
Engin
On 9/29/15 3:02 PM, NISHANT SINGH wrote:
Hi again,
I tried running only "sc" without any command line arguments and I the correct output (ends with Number of radii read from sc_radii file: 79).
I also gave a relative path to the sc_radii.lib file. I tried testing the script interactively, but I wasn't sure what commands to type, so I put in everything after the sc xyzin line in the attached script, which also didn't work. (Was I using the wrong commands?)
I added "env | grep CCP4" at the beginning of the script (it was uncommented previously) but I dont think the output got any better.
i am attaching a screenshot of the output and the script with this email.
Thanks for the help guys, much appreciate it.
Sincerely,
Nishant Kumar Singh
On Tue, Sep 29, 2015 at 3:20 PM, Edward A. Berry <[log in to unmask]> wrote:
For whatever it is worth, the file in question is at $CLIB/data/sc_radii.lib
I don't have the latest ccp4, but what I get just running "sc" with no
command line arguments is:
FORMATTED OLD file opened on unit 7
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: SCRADII, Filename: /sw/lnx/ccp4-6.4.0/lib/data/sc_radii.lib
<!--SUMMARY_END--></FONT></B>
Number of radii read from sc_radii file: 79
Opening PDB input file with logical name XYZIN
(which fails since XYZin is not defined)
Engin's script is for if you have copied sc_radii to the current directory,
presumably to customize it.
If you left that off and it still doesn't find sc_radii,
maybe you have not set up your environment for running
from the command line.
If you just type "sc" with no arguments and you don't get:
Number of radii read from sc_radii file: 79
then this is probably the case. Or you have found a bug in the program.
Then you need to first source one of the setup files
$CCP4/include/ccp4.setup-csh
$CCP4/include/ccp4.setup-sh
You can figure out what $CCP4 is by noticing when you start ccp4i:
Top level CCP4 directory is /sw/lnx/ccp4-6.4.0
On 09/29/2015 02:43 PM, Phil Jeffrey wrote:
One central dogma of Unix:
no matter how apparently absurd the error message, it's literally true.
> File: "./sc_radii.lib"
>
> Cannot be opened for reading
So, the file sc_radii.lib cannot be found in the current directory (i.e.
".") in whatever context you're running in. I rather strongly suggest
that the missing file is the literal truth here.
For the rest of the errors, the first clue is:
> sc: Use: <logical name> <file name>
Are you using the CCP4 standard method of:
sc xyzin my_file.pdb
or did you leave the xyzin part out ? xyzin is not a file name, it's
the logical unit name to which the file name becomes associated. It's a
*lot* easier to debug if you include the (part of the) script you're
actually using and not make us guess.
Cheers,
Phil Jeffrey
Princeton
On 9/29/15 2:30 PM, NISHANT SINGH wrote:
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