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
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 +33 1 40 61 34 75
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 > >
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.frmailto: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.aumailto: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
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Riccardo Pellarin