Dear all,
I have a set of MS/XL restraints which I'd like to use to predict the structure of a putative homodimeric protein. Some of the XL are expected to happen within the same chain, others between the two distinct chains of the homodimer. The way I tackled the ambiguity issue so far is to explicitly generate all the possible XL/chain combinations and use this expanded list as an input for an adapted version of the human complement modeling script ( https://salilab.org/Complement) using IMP v2.9. Is there a better way to deal with ambiguity in IMP? I also found the AmbiguousCompositeRestraint https://integrativemodeling.org/2.6.1/doc/ref/classIMP_1_1pmi_1_1restraints_1_1proteomics_1_1AmbiguousCompositeRestraint.html class, but didn't yet manage to find an example script using it. I'd be grateful for any suggestions you could provide me in this respect.
Thanks so much and all the best, Francesco
Dear Francesco,
Ambiguity due to multiple copies of the same molecule is automatically taken into account. The complement example use an obsolete interface, you should look into this tutorial:
https://github.com/salilab/imp_tutorial
cheers
Riccardo
Riccardo Pellarin, PhD =================== Institut Pasteur CNRS UMR 3528 25, rue du Docteur Roux 75724 Paris Cedex 15, France riccardo.pellarin@pasteur.fr +33 (0)1 44 38 93 63
On Tue, Oct 29, 2019 at 4:13 PM Francesco RAIMONDI < francesco.raimondi@sns.it> wrote:
> Dear all, > > I have a set of MS/XL restraints which I'd like to use to predict the > structure of a putative homodimeric protein. Some of the XL are expected to > happen within the same chain, others between the two distinct chains of the > homodimer. > The way I tackled the ambiguity issue so far is to explicitly generate all > the possible XL/chain combinations and use this expanded list as an input > for an adapted version of the human complement modeling script ( > https://salilab.org/Complement) using IMP v2.9. > Is there a better way to deal with ambiguity in IMP? I also found the > AmbiguousCompositeRestraint > https://integrativemodeling.org/2.6.1/doc/ref/classIMP_1_1pmi_1_1restraints_1_1proteomics_1_1AmbiguousCompositeRestraint.html > class, but didn't yet manage to find an example script using it. > I'd be grateful for any suggestions you could provide me in this respect. > > Thanks so much and all the best, > Francesco > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >
Dear Riccardo,
many thanks for your quick and helpful reply. I managed to run the calculation using the latest IMP version (2.11) I'd like now to perform clustering and XL distance distribution analysis of the output. I'm again referring to the clustering.py and plot_cross_links.py scripts from the complement example. I managed to perform the clustering using the pmi2. However, when I try to run plot_cross_links.py using pmi2 I get error because the stat file of the clustering has changed format. Any suggestions/available example to perform such an analysis using pmi2 instead than pmi1?
Many thanks for your kind help and assistance. Best, Francesco
Il giorno mar 29 ott 2019 alle ore 16:44 Riccardo Pellarin < pellarin.riccardo@gmail.com> ha scritto:
> Dear Francesco, > > Ambiguity due to multiple copies of the same molecule is automatically > taken into account. > The complement example use an obsolete interface, you should look into > this tutorial: > > https://github.com/salilab/imp_tutorial > > cheers > > Riccardo > > > Riccardo Pellarin, PhD > =================== > Institut Pasteur > CNRS UMR 3528 > 25, rue du Docteur Roux > 75724 Paris Cedex 15, France > riccardo.pellarin@pasteur.fr > +33 (0)1 44 38 93 63 > > > On Tue, Oct 29, 2019 at 4:13 PM Francesco RAIMONDI < > francesco.raimondi@sns.it> wrote: > >> Dear all, >> >> I have a set of MS/XL restraints which I'd like to use to predict the >> structure of a putative homodimeric protein. Some of the XL are expected to >> happen within the same chain, others between the two distinct chains of the >> homodimer. >> The way I tackled the ambiguity issue so far is to explicitly generate >> all the possible XL/chain combinations and use this expanded list as an >> input for an adapted version of the human complement modeling script ( >> https://salilab.org/Complement) using IMP v2.9. >> Is there a better way to deal with ambiguity in IMP? I also found the >> AmbiguousCompositeRestraint >> https://integrativemodeling.org/2.6.1/doc/ref/classIMP_1_1pmi_1_1restraints_1_1proteomics_1_1AmbiguousCompositeRestraint.html >> class, but didn't yet manage to find an example script using it. >> I'd be grateful for any suggestions you could provide me in this respect. >> >> Thanks so much and all the best, >> Francesco >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >
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Francesco RAIMONDI -
Riccardo Pellarin