Hi Elaine, Ah you were quite right. I didn't realise from the docs that "preset" was literally the string itself, I thought it was indicating a variable portion of the name. Solved now! Thanks, Joe Joe Healey M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@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 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 25 May 2017 16:59 To: Healey, Joe Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] custom presets not appearing Hi Joe, I think the issue is the script file name. As mentioned in the docs (see link in your message) it should be named something like Goodsell.preset.cmd Presumably you did the other steps: went to the Presets category in the Preferences (open from Favorites menu) and add the location of your personal preset directory, click Save. I guess logically we could use all the command and python files in the specified directory and not require the “preset” in the name, but currently it is required. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On May 25, 2017, at 1:29 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:

Hi Chimera Team,

I've defined a custom preset (implemented in both python and 'chimera language'), and I've placed in a folder which I have directed the custom preset dialogue to.

E.g, in /Users/joehealey/Documents/Warwick/PhD/Structural_Work/Scripts/Presets/

I have the following script (chimera implemented one):

# Goodsell.cmd

############################################################# # # # Chimera syntax commands for use as a preset. Sets the # # depiction in the style of David Goodsell. # # (The PDB Molecule-of-the-Month style). # # # #############################################################

# Create lower resolution surface models: sym surfaces all resolution 2

# Hide dashed bonds that may appear though the surface setattr g display false

# Apply silhouette edging and colouring set silhouetteWidth 3.5 set silhouetteColor black set silhouette

# Set depth cueing depth and colour

set dcColor black set dcStart 0.5 set dcEnd 1.5

# Set background transparency set bgTransparency

# Set lighting mode for flat rendering lighting mode ambient

# Hide ribbons ~ribbon

# Set surface colour color red ,s

# Make sure molecule is in focus focus

However, as per the documentation ( http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets ) the preset doesn't appear in the presets menu.

I can execute the script as normal with exec, and it works and has the desired effect, but I'd like it to be in the preset menu if possible?

I suspect I'm missing something?

Thanks,

Joe Healey

M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@warwick.ac.uk

Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry)

Twitter: @JRJHealey | Website: MOAC Page | ORCID: orcid.org/0000-0002-9569-6738 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users