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

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

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"?

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>> 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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