IMP-users September 2021

imp-users@salilab.org

4 participants
4 discussions

contact plots
by Andrea Graziadei 27 Sep '21

27 Sep '21

Hello, I have seen in some manuscripts (e.g. the cop9 signalosome paper by Gutierrez et al. https://www.pnas.org/content/117/8/4088 ) the analysis of average contact maps from clusters coming out of imp-sampcon or similar analysis of PMI modeling runs. In that manuscript for example it's in Fig. S7, panel G. I was wondering if you could tell me what is the tool used for this type of analysis, and whether it works on pdb or rmf files? How does it handle beads? I have used similar tools in the past, but those function only with PDB files, and for the system I am currently working with I am especially interested in contacts between coarse grained regions... Many thanks in advance, Andrea

3 2

REX score
by Altair Hernández 20 Sep '21

20 Sep '21

Hi, I'm running the Monte Carlo Replica Exchange sampling algorithm with IMP.pmi, which allows me to save the best N models. I'm interested in getting the rex score (IMP score) of the best N models after the sampling. So my question is: - Can the file *best.scores.rex.py <http://best.scores.rex.py>* be redirected to a desired folder from the function IMP.pmi.macros.ReplicaExchange0, I mean, before it is generated? The thing is that I'm running in parallel the same script, so I need to redirect this file to avoid it being replaced by another one. Or, is there any way to retrieve the IMP score from a ReplicaExchange object? Thanks in advance! Altair

2 1

IMP Silencing output
by Altair Hernández 20 Sep '21

20 Sep '21

Hi everyone, How can I silence warnings and output in IMP? I am using IMP.set_log_level(IMP.SILENT) but it is not working, and I have no clue about which argument I should put there (IMP.set_log_level(l = ?)). I would like it to work for both output (silencing verbose mode) and warnings. Thanks! Best, Altair

2 1

Paralellizing REX
by Altair Hernández 20 Sep '21

20 Sep '21

Hi, When sampling with IMP.pmi.macros.ReplicaExchange() in a cluster that uses slurm, an error comes out: [image: image.png] My question here is, can this function be parallelized with openmp (OMP) or/and with MPI? If so, which would be the more optimized combination between the two? Notice that in my case, I'm not running a long Replica Exchange simulation (with a high number of frames), but instead I'm iterating the whole process thousands of times with a few number of frames per modeling (50-100 frames/iteration). Finally, I'm interested in redirecting the scores output (best.scores.rex.py) to the same output folder that is created in the rex, since I want to rank all the final models according to the IMP score. Thanks in advance, Altair

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IMP-users September 2021