[Chimera-users] biounit

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 14 15:52:00 PDT 2017


Hi Arthur,
It’s probably too big for your computer and/or for reasonable speed of interaction in Chimera (display changes, rotation etc.).  The structure is so large that it’s being downloaded in mmCIF format and Chimera is rather slow to open mmCIF.  It might load eventually if you waited a really long time (many minutes?), but then rotation etc. would still be slow.

Our new software ChimeraX is developed to handle such large structures and mmCIF format much better and faster, but it also depends on having a reasonably up-to-date computer.  Download could still be slow depending on the speed of your connection with the database.  As for the computer, we recommend using one from the “last 3 years” although it is certainly possible it might work on older computers too.  ChimeraX commands have a lot of similarities with Chimera commands, but there are differences, and most functions are command-only (not in the menu).  Nevertheless, should be easy to try downloading the program and seeing if it runs on your computer, and if so, entering command “open 4v9d” to see how that goes.

ChimeraX is still in pre-release but available to download, and it has a lot of display options and image-saving.  The ChimeraX home page has links to download and User Guide on the left: 
<http://www.rbvi.ucsf.edu/chimerax/index.html>

The bottom example in the ChimeraX image gallery is a ribosome:
<http://www.rbvi.ucsf.edu/chimerax/gallery.html>

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

> On Aug 14, 2017, at 3:19 PM, Arthur Szabo <agszabo at outlook.com> wrote:
> 
> Elaine
> 
> Thank you
> 
> A follow up question. PDB 4V9D is a structure of a bacterial ribosome. Some 35Mb.
> 
> Can this be handled, or is the size to large to download.
> I tried to fetch it by PDB index, but it just seemed to stall or was way too large.
> 
> Regards
> 
> arthur




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