[Chimera-users] large structures and two letter chain IDs

Tom Goddard goddard at sonic.net
Thu Feb 9 13:02:53 PST 2017


Hi Petr,

  For handling large structures you can try our next generation ChimeraX and use mmCIF file input.  

	http://www.rbvi.ucsf.edu/chimerax/

It so happens I just ported the Chimera structure morph to ChimeraX and it will be in tonight's ChimeraX build.  But it is quite slow, could take hours or days on your large system.  I am working today on speeding it up.  Do your chains mostly move rigidly?  We use the Yale Morph Server algorithm to divide chains into semi-rigid segments and this can take eternity to compute.  I could add an option that just treats each whole chain as a semi-rigid segment.

  ChimeraX has few capabilities compared to Chimera, but it handles large structures fast, and has movie recording, so it may be usable for making animations.

	Tom


> On Feb 8, 2017, at 3:31 PM, Petr Leiman wrote:
> 
> Dear Chimera Users and Developers,
> 
> I am writing to ask if there is a way to animate multiple conformations 
> of a structure containing 144 chains (~300,000 atoms)? Is it possible to 
> read in such a structure into Chimera and preserve chain IDs? We have to 
> use two-letter chain IDs, something that Chimera does not seem to like.
> 
> Thank you,
> 
> Petr
> 
> --------------
> Petr Leiman
> UTMB
> Galveston, TX77555
> 
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