[Chimera-users] Rendering by arbitrary attributes in external file

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 3 09:08:48 PST 2019

Hi Joe,
Yes, we have an input format that is specifically for this purpose: defining your own custom attributes for coloring, specification, etc.

The format is described here:

… and the file is read in using the “Define Attribute” tool or “defattr” command:

After the file is read, your custom attribute(s) will be listed in the Render dialog.  You may need to Refresh the attribute list if the dialog was already open.

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

> On Jan 3, 2019, at 5:22 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk> wrote:
> Hi chimera team,
> I use the Render by Attribute function frequently for models, but to date, I have only ever used it for rendering attributes determined 'internally' by chimera (hydrophobicity, AA conservation from an MSA etc).
> Is there a way to render residues by an arbitrary set of parameters?
> Imagine for instance, I have a csv that maps a residue number to a value (between 0 and 1). In my case this is antigenicity.
> ResNum, Res, Value
> 1, A, 0.927
> 2, T, 0.872,
> 3, W, 0.738
> ...
> Can I read this file in via python/chimera commands and apply these values from an external file?
> Many thanks
> Joe Healey

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