[Chimera-users] A script for deleting discontinuous/disconnected parts of a map, similar to the hide dust function in Chimera

Elaine Meng meng at cgl.ucsf.edu
Sat Nov 24 08:09:37 PST 2018

Hi MImi,
In general, if you can figure out a series of Chimera commands to run, then you can automate over multiple input files as described here:

To figure out what commands to use, you’d first try them interactively on some example data set.

Hide Dust is available as a command, “sop hideDust”

However, it only hides (does not actually remove the data).  As explained in the “sop hideDust” documentation (link above) you may instead want to show only the dust and use that part as a mask.  After showing only the dust as described there, then you could use the “mask” command to mask the original volume and create a new map:

Then you could save (“volume” command “save” option) the new map, “close” both original and new maps, “open” the next map, etc.  How you set threshold level is witih “volume” command “level” option, but I don’t know how you would decide what level to use.  That is likely going to be the sticking point of trying to automate your procedure.


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

> On Nov 23, 2018, at 6:04 PM, CHI-MIN HO <mimilinh at ucla.edu> wrote:
> Hello Chimera Team,
> I would like to write a script that can automatically remove smaller blobs (disconnected parts) of a volume, exactly likely how the hide dust function works in chimera, except I want it to be automated. I would like a script that can automatically determine a good threshold, then rank the parts/volumes in the box by size, and then remove all but the largest volume, and save the result as a new volume. 
> Do you have any existing code or sample code that accomplishes anything like this that you could point me toward? Or if not, would you be able to advise me as to the best way to achieve this?
> Thank you in advance!
> Best wishes,
> ~Mimi

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