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

Healey, Joseph J.Healey.1 at warwick.ac.uk
Wed Nov 27 01:43:00 PST 2019

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,


 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 | ORCID: orcid.org/0000-0002-9569-6738

On 26/11/2019, 17:55, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

    Hi Joe,
    Not sure I understand completely, but did you know that you could include chain in the specification in the attribute file?  E.g. instead of “:3” it could be “:3.A”  for residue 3 in chain A.  It is any command-line specifier, so it could also include the model number.
    You would still have to figure out the numbering correspondence to write the attribute files, however.
    An alternative approach is to create a custom header file for the sequence or sequence alignment in Multalign Viewer, which would automatically also become an attribute of any associated structures.
    I hope this helps,
    Elaine C. Meng, Ph.D.                       
    UCSF Chimera(X) team
    Department of Pharmaceutical Chemistry
    University of California, San Francisco
    > On Nov 26, 2019, at 7:40 AM, Healey, Joseph <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, 
    > Joe

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