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Questions and answers => General discussions (Q&As) => Topic started by: jhmin on February 05, 2014, 06:19:17 pm

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Title: Frame_mol options do not seem to function.
Post by: jhmin on February 05, 2014, 06:19:17 pm

Dear X3dna users,

I am trying to use frame_mol to view two different DNA molecules (22 bp) from same viewpoint but any option other than numbers do not seem to work.

e.g. frame_mol –5 ref_frames.dat xc149_dna_1.alc  xc149_dna_1_fm.alc

But even in this case the option "-5" or "-1" doesn't make any difference. -r, -a or -g all do not run when added to the command.

I would appreciate if you have any advice. Thank you so much for your help.

JH

PS. I have installed x3dna in Mac OS X 10.7. Thank you.

Title: Re: Frame_mol options do not seem to function.
Post by: xiangjun on February 05, 2014, 07:03:08 pm

I cannot see any problem from your sample usage of the frame_mol program. Could you provide a reproducible example to illustrate your goal and the problems you experienced?

Have a look of worked examples in directories $X3DNA/examples/calladine_drew and $X3DNA/np_recipes/R2_roll_bending distributed with 3DNA.

HTH,

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