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Thanks everyone, it worked. Sorry for not seeing the obvious. This is the first time I am working from the terminal. So I am still getting used to it. Sincerely, Nishant On Tue, Sep 29, 2015 at 4:44 PM, Engin Özkan <[log in to unmask]> wrote: > 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 >>>> >>>> >>> > >