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Re: [IMP-users] Plotting XL restrains histograms from a symmetric complex on ChimeraX



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 <> on behalf of Gorbea, Jose <>
Sent: Monday, March 8, 2021 3:22 PM
To: <>
Subject: [IMP-users] Plotting XL restrains histograms from a symmetric complex on ChimeraX
 
[△EXTERNAL]


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