[Chimera-users] Command-line equivalents of interative action

Healey, Joe J.R.J.Healey at warwick.ac.uk
Thu Jul 13 03:40:23 PDT 2017

Hi Chimera Team,

I've been following this great tutorial:


To render a structure by conservation. I'd like to run this non-interactively for a number of proteins though. Could you tell me what the python or 'chimera code' equivalents would be?

For instance, I would provide a structure (or structures in a session) and MSA in fasta format already, so without interactive menus I'd like to:

  1.  Open the structure(s) and MSA
  2.  get the conservation from MultAlign (the actual conservation metric doesn't particularly matter to me at the moment)
  3.  Render any open models by conservation, say using the cyan-maroon colour scale
  4.  Additionall depict as smooth worms with defined min and max radii

If this is possible!



Joe Healey

M.Sc. B.Sc. (Hons) MSRB
PhD Student
MOAC CDT, Senate House
University of Warwick
Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738
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