Hi Jose,

I used a Chimera extension called "Xlink Analyzer" which takes XL copies into account. See the fig. 4 of their paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359615/

But I am not sure how you can do it in ChimeraX and if it is different from Chimera.

Regards, Atefeh ________________________________ From: IMP-users imp-users-bounces@salilab.org on behalf of Gorbea, Jose gorbea@pennmedicine.upenn.edu Sent: Monday, March 8, 2021 3:22 PM To: imp-users@salilab.org imp-users@salilab.org Subject: [IMP-users] Plotting XL restrains histograms from a symmetric complex on ChimeraX

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Hi all,

I was wondering if somebody has experience plotting crosslink distance histograms for symmetric complexes. Specifically, since the complex I'm currently working with is symmetric, I obtain many copies of the same pseudobond for displaying on ChimeraX, each based on different atom sets.

For example:

Chain A, residue 160 - Chain A, residue 240; Chain A, residue 160 - Chain B, residue 240; Chain A, residue 160 - Chain C, residue 240; ... Chain G, residue 160 - Chain H, residue 240; Chain H, residue 160 - Chain H, residue 240;

Some of these result in exceedingly long distances that are simply not correct. I know I can set an upper threshold through the "select maximumDistance xx" command, but I am looking for a way to obtain the set of shortest crosslinks for each residue pair combination in this assembly, even though some pairs may exceed an expected distance maximum (like a 30Å cutoff for a Ca-Ca distance) for other purposes. Any help with this would be much appreciated!

Best,

Jose Gorbea