[Chimera-users] Clustering docking results using "headless" Chimera

Conrad Huang conrad at cgl.ucsf.edu
Thu Jun 28 11:07:08 PDT 2012

Assigning secondary structure is pretty ingrained, but if you _really_ 
want to do it, you can open the attached "noksdssp.py" file before your 
models and it will prevent ksdssp from being called.  Just remember that 
it's a HACK :-) and may have side effects if you do anything else that 
might depend on secondary structure type.

The size problem, on the other hand, needs a little more analysis. 
Would it be possible for you to send me a large dataset so that I can 
try out a few things?



On 6/28/12 6:23 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
> Hi Conrad,
> Thanks again for your hard work. This works very well for me. I really
> like the clustering algorithm in Chimera because it adjusts the clustering
> threshold automatically and does its thing very quickly.
> Speed is very important for my purposes, so it was necessary to comment
> out the MatchMaker part of the script (thanks for including that; I'm glad
> it seems like that wasn't the majority of your work!). Another thing
> slowing down the clustering was the invocation of "ksdssp" upon opening of
> the individual PDBs. Is there an option to skip that?
> Finally, I want to run this on at least 1000 PDBs. After about 50, Python
> had gobbled up more than 1 GB of memory and my laptop slowed to a crawl. I
> was able to kill it, but this may be a concern for production work. We
> intend to run this on a high-memory node of a cluster, but is there some
> way to reduce the memory used?
> Thanks for everything!
> Darrell

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