[Chimera-users] Fwd: Downloading HIV PDB 3j3q?

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 1 09:16:19 PDT 2019

> From: Divjak Maja <Maja.Divjak at petermac.org>
> Subject: Downloading HIV PDB 3j3q?
> Date: April 1, 2019 at 5:23:39 AM PDT
> To: Elaine Meng <meng at cgl.ucsf.edu>
> Hi Elaine,
> It's me again! Hope you had a nice weekend...
> I'm having some trouble downloading the HIV capsid file, PDB 3j3q. When I try to import it to Chimera it begins downloading, but the molecule never quite appears, even though it ends up in the entry list. The screen stays blue like it has yet to be uploaded. If I try to upload it from the list, again, nothing appears. I realise the molecule is very large, but I think I'm missing something important here?
> Thanks so much for your help, as always,
> Maja
> Dr Maja Divjak 
> BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS)
> Biomedical Animator
> Office of Cancer Research

Hi Maja,
(forwarding to the address that should be used for for Chimera questions)

It is probably just too big for the memory on your computer to open this structure in Chimera.

Depending on what you’re trying to do with this capsid, maybe you could try using ChimeraX instead of Chimera.  It handles large structures much more efficiently, but it does not have the same set of features as Chimera.
<http://www.rbvi.ucsf.edu/chimerax/index.html <http://www.rbvi.ucsf.edu/chimerax/index.html>>

If you are just trying to get the atomic coordinates of the entire capsid, they are already in the file(s) you could download directly from the RCSB PDB without using any visualization program. 
<https://www.rcsb.org/structure/3j3q <https://www.rcsb.org/structure/3j3q>>

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