Hi Riccardo, thanks for your comments. I thought it may be something like that. Strangely, my excluded cross-links file was empty. This is a strange one. I am new to IMP and trying to find my feet. I went through my execution log and could find no direct evidence of x-link rejection (I can attach this tomorrow morning when back at work). But I likely missed something. I will keep looking into it. The program runs to some conclusion (a 20000 frame trajectory is output) that makes some kind of sense, but I can't be sure which x-links are being used yet. This "included.None.xl.db" file being more or less empty got me concerned. Thanks again mate. Jason ________________________________ From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] on behalf of Riccardo Pellarin [pellarin.riccardo@gmail.com] Sent: 02 November 2015 19:37 To: Help and discussion for users of IMP Subject: Re: [IMP-users] question about PMI included.None.xl.db file 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 riccardo.pellarin@pasteur.fr<mailto:riccardo.pellarin@pasteur.fr> +33 1 40 61 34 75 On Mon, Nov 2, 2015 at 6:18 AM, Jason Schmidberger <jason.schmidberger@sydney.edu.au<mailto: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<mailto:IMP-users@salilab.org> https://salilab.org/mailman/listinfo/imp-users