Messages

1

RNA structures (DSSR) / Re: Problem using --pair-list options

« on: February 14, 2020, 05:08:31 am »

It finally worked thanks to the change of the input name. Thanks Xiangjun for the fast and precise response, im going to share you via e-mail the pdb file of our structure so you can check the base pair recognision, but it works fine with the --pair-list option.

Best regards,
Ángel.

2

RNA structures (DSSR) / Problem using --pair-list options

« on: February 12, 2020, 11:28:54 am »

Dear Dr. Xiangjun,

First of all thank you for developing this software, but we are having some troubles using the --pair-list options. We have tried the examples presented on the manual but doesn't work neither (using last version of X3DNA). We have a non-canonical RNA structure with some mismatches U-U that aren't recognised automatically, so we are using the --pair-list to generate and modify it. The generation works well, the problem is at the moment to introduce through:
       x3dna -dssr -i=1msy.pdb  --pair-list -inpfile=dssr-pairs.txt
It says:
       open_file <dssr-pairs.txt> failed: No such file or directory

And deletes the dssr-pairs.txt file. We would be so gratefull if you know why is giving this problem and not working correctly.

The commands used are:
x3dna-dssr -i=1msy.pdb -o=prueba.out --pair-list (to generate the pair-list)
x3dna -dssr -i=1msy.pdb  --pair-list -inpfile=dssr-pairs.txt  (to analyse it)