Hi!,

most probably yes, some of your cross-links where excluded for some reason. There should be another file that lists the excluded cross-links. Also the log the of script execution should tell you why cross-links were excluded (i.e., missing protein or residue)

R

Riccardo Pellarin, PhD
===================
Institut Pasteur
25, rue du Docteur Roux
75724 Paris Cedex 15, France

On Mon, Nov 2, 2015 at 6:18 AM, Jason Schmidberger <jason.schmidberger@sydney.edu.au> wrote:
Hello,

I have been running IMP::pmi with a protein complex we are working on in our lab. I have managed to adapt the PMI online example (RNA pol) to work for my example. 

A series of files are output in the execution directory: included.None.xl.db, excluded.None.xl.db, missing.None.xl.db

In my "included.None.xl.db file" I only have the following two lines;

{'res2': '155', 'prot1': 'mol3', 'prot2': 'mol5', 'res1': '160'}

{'res2': '155', 'prot1': 'mol3', 'prot2': 'mol5', 'res1': '154'}


I include more than 30 x-link restraints in my set up. When I compare this to the same file as output with the worked RNA pol example, that file has many more entries. 

QUESTION: what is the meaning behind this file? Does it mean most of my x-link restraints were thrown out?

Cheers,

Jason


_______________________________________________
IMP-users mailing list
IMP-users@salilab.org
https://salilab.org/mailman/listinfo/imp-users