US Align - superimposition of all proteins

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antonia.feilden
Posts: 3
Joined: Wed Feb 21, 2024 10:12 am

US Align - superimposition of all proteins

Post by antonia.feilden »

Is there a way to output the superimposition of all proteins as seen in TM Align? Is this the equivalent of the align command in pymol?
zcx@umich.edu
Posts: 69
Joined: Wed Nov 03, 2021 5:59 pm

Re: US Align - superimposition of all proteins

Post by zcx@umich.edu »

I guess that is two different questions.

.1. To have US-align output superimposed structure as seen in TM-align, use either the -o option (for superimposed structure and PyMOL scripts) and the -rasmol option (for RasMol scripts).

2. The equivalent of the "align" command in PyMOL is called "usalign", which needs to be installed by yourself. First, at the bottom of https://zhanggroup.org/US-align/, download the zip or tar.gz archive. DO NOT decompress the file. Launch PyMOL. In Plugin - Plugin manager - Install New Plugin - Install from local file, choose the zip or tar.gz archive you just download. This will install the "usalign" command that you can use as a drop in replacement of "align."
antonia.feilden
Posts: 3
Joined: Wed Feb 21, 2024 10:12 am

Re: US Align - superimposition of all proteins

Post by antonia.feilden »

Thank you for the reply.

To be explicit, is there a way the output the superimpositions when multiple proteins are aligned to one target? This corresponds to the command:

Code: Select all

usalign/USalign -dir1 [DIRECTORY]/ [LIST] [QUERY] -outfmt 2 
In TM-Align, the simultaneous superimposition of all proteins in the list against the query was possible. Is this possible in US-Align?

Best wishes,
Antonia
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