3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: auffinger on October 08, 2014, 09:46:17 am

Title: Frame_mol issue with DG
Post by: auffinger 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
Title: Re: Frame_mol issue with DG
Post by: xiangjun 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
Title: Re: Frame_mol issue with DG
Post by: auffinger 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
Title: Re: Frame_mol issue with DG
Post by: xiangjun 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
Title: Re: Frame_mol issue with DG
Post by: auffinger 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