Showing RMSD

[jaremko@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
When I run these commands:

mm #7,9,13,15,19 to #3/a show true
color byattribute seq_rmsd  #3 palette blue:red:yellow

Will these show the average seq_rmsd of 7,9,13,15,19? Or will I just see the seq_rmsd of 19? If the average isn't shown,  can this be implemented? This would be a nice feature for interpreting variability within a conformation.  Also,  the ability to obtain a seq_rmsd without alignment would be helpful.
Thanks,
Matt

Log:
> ui mousemode right "contour level"

> mousemode shift rightMode zoom

> set bgColor white

> graphics silhouettes true

> graphics silhouettes width 3

> hide all atoms

> style stick

Changed 0 atom styles  

> style ions sphere

Changed 0 atom styles  

> style ions sphere

Changed 0 atom styles  

> show all cartoons

> show ligand target ab

> show ions atoms

> show sidechain & (ligand | ions) :< 3.5 target ab

> color /a #55c087

> color /b #ffe255

> color /c #f6986c

> color /d #6b80bc

> color /e #aa7fba

> color /g #FFC0CB

> color /h #b2b2b2

> color /i red

> color byhetero

> lighting soft

> lighting depthCue false

> cartoon suppressBackboneDisplay false

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> alias sa isolde sim stop

> alias sb isolde sim stop discardTo start

> alias m2 matchmaker #2 to #1 & sel

> alias m3 matchmaker #3 to #1 & sel

> alias m4 matchmaker #4 to #1 & sel

> alias ct ui mousemode right "contour level"

> alias zm ui mousemode right zoom

> alias cr view $*; clip off; zoom .8

> alias iw isolde write phenixRsrInput #1 2.8 #1 includeH false

> alias rmp4 movie record; rock y 30 384 cycle 384; wait 384; movie encode
> "/Users/jaremko/cryoem/rock_movie.mp4"

> alias sc show (sel-residues & sidechain) target ab

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




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[Eric Pettersen]

Hi Matt,

If you have pairwise alignments, then seq_rmsd will be pairwise, and seq_rmsd for #3 will be the pairwise value with #19. You have two options to get an overall RMSD value. One is to somehow generate a full sequence alignment of all 6 structures (and show the RMSD header). In Chimera you could generate that alignment with the Match→Align tool, but we don't have that in ChimeraX yet. The other option is if the structures have a high degree of sequence similarity, open the sequence of one structure and use the Structure→Associations... context menu entry of that sequence viewer to associate the other structures with that sequence (and then show the RMSD header).
By "obtain a seq_rmsd without alignment", do you just mean have matchmaker assign that attribute without showing an alignment?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Eric Pettersen]

If you are using the daily build, you could use the "sequence align" command to generate an overall alignment.

--Eric

[Elaine Meng]

In case it wasn't clear, the RMSD actually comes from the sequence alignment window:  in the general case (which could include different proteins with different sequences) an alignment is required to indicate which residue goes with which, i.e. which are in the same columns as each other.  So you need a single alignment associated with all of the structures to give an overall alignment and overall RMSD.  As Eric mentioned, you could either have an alignment window in which each structure is a separate sequence, or if the structures have very similar or the same sequence, you could simply show one sequence and associate all of the structures with that one sequence.  Then show the RMSD header in that window and/or color by the resulting attribute values.

[jaremko@…]

Hi Elaine,


Thanks! That's basically what I want to do. I have mutants with the same general conformation, but I want to see the variability by coloring through the overall seq_rmsd attribute. Can this all be done by the command line? Or do I have to work within the alignment window?


Thanks,

Matt

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, April 11, 2022 3:39:09 PM
To: pett@cgl.ucsf.edu; Jaremko, Matt
Cc: meng@cgl.ucsf.edu
Subject: Re: [ChimeraX] #6581: Showing RMSD

#6581: Showing RMSD
-----------------------------------------+----------------------
          Reporter:  jaremko@…           |      Owner:  pett
              Type:  defect              |     Status:  feedback
          Priority:  normal              |  Milestone:
         Component:  Structure Analysis  |    Version:
        Resolution:                      |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+----------------------

Comment (by Elaine Meng):

 {{{
 In case it wasn't clear, the RMSD actually comes from the sequence
 alignment window:  in the general case (which could include different
 proteins with different sequences) an alignment is required to indicate
 which residue goes with which, i.e. which are in the same columns as each
 other.  So you need a single alignment associated with all of the
 structures to give an overall alignment and overall RMSD.  As Eric
 mentioned, you could either have an alignment window in which each
 structure is a separate sequence, or if the structures have very similar
 or the same sequence, you could simply show one sequence and associate all
 of the structures with that one sequence.  Then show the RMSD header in
 that window and/or color by the resulting attribute values.
 }}}

--
Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_trac_ChimeraX_ticket_6581-23comment-3A4&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=hXpNoqNcgGzlmQlyhaTJdA&m=DgtnXLtX0PCn9-dhlZik685MvbG8KVRUtuPBiuGgBds&s=IjOieDVLagSlUzViJUZx4QzAQnQK_9Q-IdbJg9IIstQ&e= >
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ChimeraX Issue Tracker

[Elaine Meng]

It might be easier through the GUI, as in less of of learning curve for the commands (and I believe you would still need to show the GUI) but yes, it can be done with commands.  Here is a pairwise example where I match one conformation of a protein onto another and then show sequence for one and associate the other with the sequence, then show RMSD header, then use the resulting attribute.  You would need to generalize; you already have the multiple superposition and only need to show the sequence of any one of those structures, but then would need to associate all of the others with that sequence (there would be multiple "seq associate" commands in your case).  Here are the example commands:

open 2gbp
open 2fw0
mm #2 to #1
seq chain #1/A
seq associate #2/A
seq header rmsd show 
color byattribute seq_rmsd #2 palette 0,blue:3,red:10,yellow

If you look at the sequence command help, these commands all allows specifying an alignment ID. I can omit it in this case because there is only one sequence window shown.  You can also omit it similarly, if you only show one sequence window.  Use command "help sequence" to see the help page for all these seq commands.

[jaremko@…]

Hi Elaine,


Great, thanks! I will try this. This should work with 3 or more structures also, right? I would use seq associate #2,3/a, for example?


Thank you!

Matt

________________________________
From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Tuesday, April 12, 2022 11:29:17 AM
To: ChimeraX-bugs@cgl.ucsf.edu
Cc: pett@cgl.ucsf.edu; Jaremko, Matt
Subject: Re: [ChimeraX] #6581: Showing RMSD

It might be easier through the GUI, as in less of of learning curve for the commands (and I believe you would still need to show the GUI) but yes, it can be done with commands.  Here is a pairwise example where I match one conformation of a protein onto another and then show sequence for one and associate the other with the sequence, then show RMSD header, then use the resulting attribute.  You would need to generalize; you already have the multiple superposition and only need to show the sequence of any one of those structures, but then would need to associate all of the others with that sequence (there would be multiple "seq associate" commands in your case).  Here are the example commands:

open 2gbp
open 2fw0
mm #2 to #1
seq chain #1/A
seq associate #2/A
seq header rmsd show
color byattribute seq_rmsd #2 palette 0,blue:3,red:10,yellow

If you look at the sequence command help, these commands all allows specifying an alignment ID. I can omit it in this case because there is only one sequence window shown.  You can also omit it similarly, if you only show one sequence window.  Use command "help sequence" to see the help page for all these seq commands.

[Elaine Meng]

My previous reply said you would have multiple "seq associate" commands, but yes, it is also possible just to give one "seq associate" command with multiple chains specified, as you suggest.  If you want to associate the sequence with *all* of the "A" chain structures that are present in ChimeraX, you could even specify them collectively by omitting the model numbers, e.g. "seq associate /A" 
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#associate>