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

To: "" <>

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

From: Atefeh Rafiei <>

Date: Mon, 8 Mar 2021 22:48:36 +0000

Accept-language: en-US

Arc-authentication-results: i=1; mx.microsoft.com 1; spf=pass smtp.mailfrom=ucalgary.ca; dmarc=pass action=none header.from=ucalgary.ca; dkim=pass header.d=ucalgary.ca; arc=none

Arc-message-signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=microsoft.com; s=arcselector9901; h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-SenderADCheck; bh=GdyRSV85f2SneQahS+2JRhNT1YuRysXUkuZSzMQN/IM=; b=PAuFuIynVMRHoJ0uowKDDGwbftS4qVnJ+MmkpYGlMXvVPaP6eO5cDLD1SIl3AdVahN8A1FuJaV93Y51QqsyanszmKKhWf9d41ZWGruGYbRBm5pit1NkjPot5nrrqJCGd/vS7NWLN8qvJhVfCrPEQ6ERUVVRARO+GKCupl+zvPLCJJJjBzvyycGT5Hg0HZyZml5Q9aLvQZXcwuIFyzg7+CMrX5X8p/Q5VClW1aXuSslKsBhghShT6E4NJS5tGIDjHasZg+j+ii8UCc81530ubh2U+SM8oMK7tkJww2yqMB75WiS6Ba5Kkd3hfkUi5Dd+CvqnVIifRqej8Pcj8hCljJw==

Arc-seal: i=1; a=rsa-sha256; s=arcselector9901; d=microsoft.com; cv=none; b=mHQYqcr5neKKKOTFfvCT2TFQk99vyxT6MR5ssSuVr6UM/NqwxZokW7xG9x0hC65RDi/g+gy6TnInfyvp5QqneG9fvkB+hdHM+LmvTPnwJLFYZ0wccffE1QDOIFv+R83IB4RJEXZJLKawKU4Kz+fezNvBaIbJgg6paiLPhdNrUEPgQ+osDJU4pBYryJ0TlSFA3tdTPDVwtjJwHChsjbJiZfJNrgl0kA8WslDXeit1jqfr+cU58Gc9A1rpQz8BhTp30WF+4a64R7ptE7R2sEbqICYmGIygvaUWQDy8FQDFprqTGBJO5l3TH0gvDVhX3jSbf2zGnJMyo8Zo1PsHoFyXhQ==

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