[Chimera-users] matchmaker and MSA

[arrafzaher at campus.technion.ac.il]

Hi Elaine,
In the second method I am able to open that file in Excel.

I can’t figure out Which file format I need to save into in order to be able to open the file saved from the first method?

Thanks,
Zaher


From: Elaine Meng <meng at cgl.ucsf.edu>
Reply-To: Chimera <chimera-users at cgl.ucsf.edu>
Date: Friday, 18 September 2020 at 23:07
To: Zaher Arraf <arrafzaher at campus.technion.ac.il>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] matchmaker and MSA

Hi Zaher,
First use the Multalign Viewer (sequence window) Headers menu to show the RMSD histogram(s) that you want: CA, backbone, and/or full.  Then use that same Headers menu "Save..." option to save to file with RMSD vs. alignment position.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fmultalignviewer%2Fframemav.html&data=02%7C01%7Carrafzaher%40campus.technion.ac.il%7Ce850fb26533f4dbad01108d85c0e7f8a%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637360564627492243&sdata=FebaUKmKSrsUC8Q9LtRIoALPU%2FnCaVDfuNsh5mMQbFg%3D&reserved=0>>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers>

This example image shows all three RMSD histograms:
[cid:image001.png at 01D69270.FC7E5AE0]

... or if you want the list to be RMSD vs. structure residue numbering instead of alignment numbering, start the "Render by Attribute" tool (in menu under Tools... Structure Analysis) and use that tool's File menu to save the corresponding residue attribute(s) named "mavRMSD[...]". This is possible because sequence alignment header values are automatically assigned as attributes of the associated residues.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Frender%2Frender.html%23saving&data=02%7C01%7Carrafzaher%40campus.technion.ac.il%7Ce850fb26533f4dbad01108d85c0e7f8a%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637360564627502207&sdata=6gDuDyLa49TccFfjFGvk0YgZU51NATe3EmD7aS2fdzw%3D&reserved=0>>

In ChimeraX, you can only show one RMSD header at a time but you can choose whether it is ca, backbone, or full.  The ChimeraX Sequence Viewer has its own menu including Headers to control this and also saving the header to file, but instead of on the top bar it is a context menu shown with right-click or ctrl-click, depending on your type of computer.   The attribute is also assigned but ChimeraX does not yet have saving attributes to file.

I hope this helps,
Elaine


On Sep 18, 2020, at 12:38 PM, arrafzaher at campus.technion.ac.il<mailto:arrafzaher at campus.technion.ac.il> wrote:

Thank you Elaine,
No worries.
One Last Question (Hopefully),
Is there a way to produce a datasheet of RMSD for each position aligned from the 3 structures?
Zaher


This email is from an external mail server, be judicious when opening attachments or links
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200924/a38d3349/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 166545 bytes
Desc: image001.png
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200924/a38d3349/attachment-0001.png>