[buster-discuss] Error running refine

[Dale Tronrud]

Hi,

    I'm not part of Global Phasing but I thought I'd give your question 
a try.  When I run your script I get more detailed output than you posted.

[dale at localhost tst]$ ./partA.sh
job failed
see log file ./partA.log tail of this:
   http://www.globalphasing.com/buster/wiki
     /usr/local/buster_snapshot_20210305/autoBUSTER/bin/linux64/refine 
-p 
/Users/bsub0002/Documents/FABP/FABP4/11462-analogues/CR_159955_02_col_1_17077f_MFP-0012310_refine_19-coot-0.pdb 
-m 
/Users/bsub0002/Documents/FABP/FABP4/11462-analogues/Refine_19/CR_159955_02_col_1_17077f_MFP-0012310_refine_19.mtz 
-L 
/Users/bsub0002/Documents/FABP/FABP4/11462-analogues/eLBOW_18/MFP-0012310.cif 
-d /Users/bsub0002/Documents/FABP/FABP4/11462-analogues/./partA -M MapOnly

  ERROR : [refine-0009] unknown argument
 
"/Users/bsub0002/Documents/FABP/FABP4/11462-analogues/eLBOW_18/MFP-0012310.cif"


real	0m2.256s
user	0m0.999s
sys	0m1.324s

The script is complaining that it doesn't know what to do with the name 
of your CIF.  I see that it introduces the CIF with "-L" and not the 
proper "-l".  Change to a lower case "l" and try again.

    When I change it to "l" and create a file with the name of the CIF I 
get different error messages.  Those messages indicate that Buster is 
starting but failing because I don't have your environment.  I think 
changing the letter will get you moving.

Dale Tronrud


On 5/24/2021 7:45 PM, Bishwa prakash subedi wrote:
> Hi there,
> 
> I am new to Buster and have just installed the 
> “BUSTER_snapshot_20210420” on my Mac. I tried to run the refinement 
> using script file but I do keep getting following error:
> 
> *[refine-0009] unknown argument “partA.sh”*
> 
> I have no idea what this error means as there is no further detail about 
> the error and attached with this email is the script file. Could you 
> please help me with fixing this?
> 
> I have not installed mogul due to the Mac version (Big Surf version 
> 11.3.1) I am currently using and license issue. Could that be the reason 
> for the error? And is there a way to use eLBOW output CIF file to be 
> used as input in BUSTER. My attempt to run refine with -d, -m and -L 
> straight into the terminal with use of CIF file from grade web server 
> too gives the same error with unknown argument pointing to the cif file 
> path.
> 
> Could someone please help me run the script with ligand ON
> 
> Thanking you in advance for the valuable time.
> 
> Cheers,
> 
> World light
> 
> 
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