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

Healey, Joseph J.Healey.1 at warwick.ac.uk
Fri Jan 24 06:18:05 PST 2020

Hi Eric/Elaine,

That’s perfect thanks – just what I needed to know!


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: Eric Pettersen <pett at cgl.ucsf.edu>
Reply to: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Date: Thursday, 23 January 2020 at 18:46
To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Cc: "Healey, Joseph" <J.Healey.1 at warwick.ac.uk>
Subject: Re: [Chimera-users] Auto-associate define attribute/render by attribute

Like Elaine says, skipping the assignment entirely is perfectly acceptable.  If it’s easier to assign something than skip it, assign None.


Eric Pettersen
UCSF Computer Graphics Lab

On Jan 23, 2020, at 10:03 AM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

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<mailto: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)?

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?
        setattr(res, “attributeName”, score)

Many thanks,


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