Re: [IMP-users] question about PMI included.None.xl.db file

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: [] on behalf of Riccardo Pellarin []
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)

Riccardo Pellarin, PhD

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Institut Pasteur

25, rue du Docteur Roux
75724 Paris Cedex 15, France

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+33 1 40 61 34 75

On Mon, Nov 2, 2015 at 6:18 AM, Jason Schmidberger <" target="_blank">> 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

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