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

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 23 10:03:47 PST 2020

Hi Joe,
Maybe I’m misunderstanding the issue, but can’t you just skip assigning a value to that residue if it does not have a score?  That would be the same as omitting the residue from an attribute assignment file.

It depends how you want to use the attribute: do you want those residues to have the attribute but assigned as none, or do you want them simply not to have that attribute?

An analogous situation is the amino acid hydrophobicity attribute. The following command-line specifier designates residues (such as water or nucleic acids) that lack a Kyte-Doolittle hydrophobicity assignment:


… and the Render by Attribute tool and rangecolor command both have options as to what you want to do with such “no-value” atoms or residues.

To summarize, you may not need to assign some kind of null value, but simply skip assigning anything.
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 23, 2020, at 2:51 AM, Healey, Joseph <J.Healey.1 at warwick.ac.uk> wrote:
> Hi Chimera team,
> I’ve made some good headway with the subject of this previous thread (a relatively simple Bio.pairwise2 alignment approach seems to serve to associate chains reasonably well. One further thing I’d like to clarify, is how missing data is stored for a residue attribute in the case of the renderbyattribute functionality?
> e.g. if I have the structure sequence, and the scores (just using integers as a simple example for now):
> model.residues = MEREYV
> Scores = 192984
> I can assign those scores reasonable easily as discussed with something to the effect of:
> for res, score in zip(model.residues, scores):
>      setattr(res, “attributeName”, score)
> If in the case I have scores with missing data however, what value for missing is acceptable/expected by chimera (“”, None etc)?
> E.g:
> Scores = 192-84
> In which case I envisage doing something like:
> for res, score in zip(model.residues, scores):
>     if score == “-“:
>          setattr(res, “attributeName, “”)  # Or whatever the allowable character/value is?
>     else:
>          setattr(res, “attributeName”, score)
> Many thanks,
> Joe

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