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Author Topic: Frame_mol issue with DG  (Read 7690 times)

Offline auffinger

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Frame_mol issue with DG
« on: October 08, 2014, 09:46:17 am »
Hi Xiang-Jun,

I don't know if we did something wrong but I got the impression that Frame_mol is handling in a weird manner DG nucleotides.
This means that although all other DNA or RNA nucleotides align well, DG does not.

Here are some files for checking.
and the command line

frame_mol -$numan ref_frames.dat $nucleo_filepath.base.pdb $nucleo_filepath.base.pdb

I checked the variables.

Can you check on your side ?

Best,

Pascal
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
http://www-ibmc.u-

Offline xiangjun

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Re: Frame_mol issue with DG
« Reply #1 on: October 08, 2014, 11:51:44 am »
Hi Pascal,

I did not notice anything special with regard to DG as far as frame_mol is concerned. Instead of the following general command,
Quote
frame_mol -$numan ref_frames.dat $nucleo_filepath.base.pdb $nucleo_filepath.base.pdb
could you show a specific example where you believe that frame_mol is not working as expected?

Xiang-Jun

Offline auffinger

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Re: Frame_mol issue with DG
« Reply #2 on: October 08, 2014, 12:27:40 pm »
Hi Xiang-Jun, will do that tomorrow.
I added 8 files to the mail.
did you get all of them ?

Best,

Pascal
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
http://www-ibmc.u-

Offline xiangjun

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Re: Frame_mol issue with DG
« Reply #3 on: October 08, 2014, 12:47:34 pm »
I saw the files, downloaded the first one and ref_frames.dat. However, I did not understand how the PDB data files are related to the ref_frames.dat. Please be specific.

Xiang-Jun

Offline auffinger

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Re: Frame_mol issue with DG
« Reply #4 on: October 09, 2014, 12:00:19 pm »
Hi Xiang-Jun,

Sorry to have taken your time with this.
The bug was obviously on my side.
During editing, one line got corrupted in my scripts.

Best,

Pascal
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
http://www-ibmc.u-

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.