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
On 9/24/21 8:37 AM, Andrea Graziadei wrote: > 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?
The authors of that paper (cc'd here) will know for sure, but all the scripts they used should be in the GitHub repository at https://github.com/integrativemodeling/CSN2019
Ben
Hi Andrea,
Here is an example of how to get the contact maps using PMI_Analysis:
https://github.com/salilab/PMI_analysis/blob/main/example/get_CMs.py
Let me know if you have any questions. Best, Ignacia
On Mon, Sep 27, 2021 at 5:43 PM Ben Webb ben@salilab.org wrote:
> On 9/24/21 8:37 AM, Andrea Graziadei wrote: > > 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? > > The authors of that paper (cc'd here) will know for sure, but all the > scripts they used should be in the GitHub repository at > https://github.com/integrativemodeling/CSN2019 > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle >
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Andrea Graziadei -
Ben Webb -
Ignacia Echeverria