[Chimera-users] Auto-associate define attribute/render by attribute

Healey, Joseph J.Healey.1 at warwick.ac.uk
Thu Nov 28 03:05:28 PST 2019

Hi Elaine/Eric,

Apologies, that was an error on my part, I forgot that there are case-differences between chains with the same letter ID. They should all match PVC3: the t,u,v,w,x,y chains. Between yours and Eric’s answer though, it sounds like I can’t quite achieve what I’m planning without doing it through a GUI. Perhaps I need to have a re-think about how I go about this altogether.

I don’t suppose there’s any other way besides MAV to auto-associate sequences with structures? In an ideal world, I’d be able to provide an attribute/header type file that looked something like:

# header info
attribute: AttributeName
                :Met      1.23
                :Ala        2.34
                :Ser        3.45
                :…           …

And so on, and have it be able to identify the chains from the sequence of residues in the file.

I would like to use ChimeraX for this in future, but as you say, the scripting/feature set isn’t quite there yet (manipulating large structures speedily is particularly useful to me).

Many thanks for your suggestions so far,


Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB
Research Fellow
Warwick Medical School
University of Warwick
Mob: +44 (0) 7536 042620  | Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>
Email: J.Healey.1 at warwick.ac.uk<mailto:J.Healey.1 at warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738

From: Elaine Meng <meng at cgl.ucsf.edu>
Reply to: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Date: Wednesday, 27 November 2019 at 21:07
To: "Healey, Joseph" <J.Healey.1 at warwick.ac.uk>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Auto-associate define attribute/render by attribute

Hi Joe,
Those chains are two different sequences.

Pvc12 is chains P,Q,R,S,T,U  with  >900 positions in the sequence
Pvc4 is chains V,W,X,Y,Z,a  with 410 positions in the sequence

So I can load the headers from your file for the former sequences (I tried chain T) but not the latter, because your file specifies up to position 436.

Python is beyond my skill set, though… somebody else would have to advise on that.

An aside: I note that it was much easier to tell which chains are the same sequence as each other in ChimeraX, which is also a lot faster on big structures like this.  Unfortunately we don’t yet have it reading custom header files or making the headers into attributes, or else I would suggest using ChimeraX instead.  Below is a screenshot from opening 6j0n in ChimeraX and clicking the “Pvc12” and “Pvc4” links in the Chain Description table that automatically appears when the file is opened.

Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Nov 27, 2019, at 1:43 AM, Healey, Joseph <J.Healey.1 at warwick.ac.uk<mailto:J.Healey.1 at warwick.ac.uk>> wrote:

Hi Elaine,

Thank you for clarifying, I had missed the option for any atom-spec (I was following one of the examples but there didn't appear to be one addressing chains). As you say, this still requires some a priori knowledge of 'what's what' in the structures though. An added complication is that the structures are grouped in to a single model, and need to be split to be treated as different models (though I suppose in practice this makes little difference as its either a case of specifying a chain or a model).

Consequently, this is why I was hoping that sequence-based auto-assignment could be possible. The sequence/alignment headers looks like they have potential, but this leads me to another 2 questions:

- So far, it is complaining that the numeric values I'm using are less than one or greater than the alignment length. The data appears to possibly be longer than the structure (but is shorter than the corresponding gene sequence) so I assume some residues are not present in the mature structure. However, it complains about Position 402 of the file, which should still be in the structure displayed as far as I can tell.According to the docs, numeric values that fall outside [0, 1] should be converted for the histogram, but retained as attributes, so I don't think the numeric values are an issue. Any idea why Chimera is complaining? I've attached the header file I'm using. The model in question is PDB 6j0n (chains T, U, V, W, X, Y).

- Secondly, what would be the equivalent python/chimera command interface for loading header files such that I can render them by these attributes (the latter of which I'm already au fait with).

Thanks again,


On Nov 26, 2019, at 7:40 AM, Healey, Joseph <J.Healey.1 at warwick.ac.uk<mailto:J.Healey.1 at warwick.ac.uk>> wrote:

Hi Chimera team,
I’m working on a script to automatically render proteins in a complex by attributes (in this case, a number of scores obtained from different immunogenicity prediction algorithms). I currently have the script outputting attribute files as intended, but ideally I’d like to define the same attributes across all the chains of the model, which are made up of a number of different proteins.

Is there any way for me to define the attribute file, or utilise some functionality to auto-associate an attribute file with all of the chains which have the correct sequence (similarly to how the sequence alignment input works at the moment?). Currently the attribute file is only using ‘numbered’ coordinates (:1, :2, :3…etc) , rather than the actual sequence.

Since there’s no chain information in the attribute files, I’m not sure how I can go about connecting it to the right structure, other than manually at the moment?
Many thanks,

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