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Questions and answers => General discussions (Q&As) => Topic started by: Charu on July 24, 2012, 10:04:16 am

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Title: mutate_bases error
Post by: Charu on July 24, 2012, 10:04:16 am

Hi as I try to mutate bases in 3DFV using the command mutate_bases 'c=Y, s=14, m=DC' 3DFV.pdb 3DFV_mut.pdb, it shows a message:
"Out of 3 qualified entries

Y: 214783647_: [@@@] ===> [@@@.@] identical residue for mutation
@:..14_: [@@@] ===> identical residue for mutation
@:214783647_: [@@@] ===> [DC.@] required chainID/resnm/mutation not specified"

But I had mutated bases earlier using the same command. Could you please help me out?

Title: Re: mutate_bases error
Post by: xiangjun on July 24, 2012, 02:35:49 pm

Quote

mutate_bases 'c=Y, s=14, m=DC' 3DFV.pdb 3DFV_mut.pdb

Change comma to space, as below:

Code: [Select]

mutate_bases 'c=Y s=14 m=DC' 3DFV.pdb 3DFV_mut.pdb
Comma or semicolon is used to separate multiple mutations. I am updating command line help message to make this point clearer.

Xiang-Jun
 

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University