Re: [Jmol-users] Color structural alignment by deviation "RMSD"?

[Theis, K. W. <kt...@we...>]

Sorry, I have been using the words alignment and superposition interchangeably, but I should be more precise:

Structural alignment is a sequence alignment based on stretches of aligned sequences having the same structure.

Superposition is rotating and translating one molecule such that equivalent atoms come closer together. You have to define pairs of equivalent atoms up front, or have some quality criterion by which the pairing can be done for you.

RMSD is the root mean square of the distance of atom pairs in the two structures, after superposition. As such, the RMSD depends on the choice of atom pairs to use in the superposition (which minimizes the RMSD of the distances within that subset of atoms), and it depends on which atoms you pair up to measure distances. For example, you could superimpose molecules based on C-alpha atoms, but then calculate the RMSD of all main chain atoms (or all side chain atoms, if paired C-alpha atoms belong to residues containing the same set of atoms).

Karsten

--
Karsten Theis
Chemical & Physical Sciences Department
Westfield State College

________________________________
From: Theis, Karsten W. <kt...@we...>
Sent: Sunday, February 28, 2021 11:35 AM
To: jmo...@li... <jmo...@li...>
Subject: Re: [Jmol-users] Color structural alignment by deviation "RMSD"?

Angel asked whether Jmol tells you the paired atoms in an alignment.

You specify the residue mapping explicitly: You make two selections, and atoms are paired in order. If there are gaps in the alignment, you give a list of selections, and atoms are paired in order with each matched selection in the list.

Here is an example <https://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities> I posted in Proteopedia:


define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~actnagal and *.CA}{~actgal and *.CA} ROTATE TRANSLATE


This works because the order of paired-up atoms is the same in the two files. If it weren't, I would have to make a longer list of paired atoms, such as in the Jmol documentation:

For example, compare {2.1} {1.1} SUBSET {*.CA} ATOMS {10-20} {50-60} {30-40} {20-30} ROTATE TRANSLATE will correlate the positions of alpha carbon atoms in groups 10-20 and 30-40 of model 2.1 with corresponding atoms in groups 50-60 and 20-30 of model 1.1 and move all atoms in model 2.1 in the process. The result of this atom-atom pairing comparison is essentially the same as the PyMol pair_fit command, though easier to implement and using an exact form of the structure-structure correlation rather than an iterative process.

I wrote a tutorial on Proteopedia <https://proteopedia.org/wiki/index.php/Jmol/superposition> as well.

Karsten
--
Karsten Theis
Chemical & Physical Sciences Department
Westfield State College

________________________________
From: Angel Herráez <ang...@ua...>
Sent: Sunday, February 28, 2021 9:47 AM
To: jmo...@li... <jmo...@li...>
Subject: Re: [Jmol-users] Color structural alignment by deviation "RMSD"?

Caution External Email: This email originated outside of WSU. Do not click links, open attachments, or respond if it appears to be suspicious.

>> is there a residue to residue mapping as a result?
>>
>>
>Yes
>
And how can thay be retrieved?
I could use it for checking distances and color accordingly



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