> How does the system handle the state ambiguity? If a crosslink is
satisfied  at a particular frame only in state1, it should count
overall as satisfied (given crosslinks are measured on in solution
ensembles),

Yes, precisely.

> but imp-sampcon and pmi_analysis are not yet equipped
to deal with this (slicing on %ge over length does not report
crosslinks as satisfied if they are under maximum distance in one of
the states only). 

I think that most of the standard analysis tools are not adapted to deal with
multistate sampling. 

Riccardo Pellarin, PhD
===================
Institut Pasteur
CNRS UMR 3528
25, rue du Docteur Roux
75724 Paris Cedex 15, France
+33 (0)1 44 38 93 63


On Tue, Feb 23, 2021 at 2:30 PM Andrea Graziadei <graziadei.a@gmail.com> wrote:
Hello,

I am building a system using topolgyReader in PMI in imp-2.13.
I have built a 2-state system by

bm = IMP.pmi.macros.BuildSystem(m, force_create_gmm_files=False)
bm.add_state(topology)
bm.add_state(topology2)

I then add crosslinks to the system with
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint

How does the system handle the state ambiguity? If a crosslink is
satisfied  at a particular frame only in state1, it should count
overall as satisfied (given crosslinks are measured on in solution
ensembles), also when for example analysing %ge violations with
imp-sampcon or similar modules...
>From what I understand, It looks to me like this is handled correctly
in the sampling, but imp-sampcon and pmi_analysis are not yet equipped
to deal with this (slicing on %ge over length does not report
crosslinks as satisfied if they are under maximum distance in one of
the states only). Is this correct?

Many thanks,

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