[Chimera-users] Downloading HIV PDB 3j3q?

Divjak Maja Maja.Divjak at petermac.org
Wed Apr 3 01:29:29 PDT 2019

Thanks Elaine,

I tried ChimerX at your suggestion and it is able to upload the molecule. The difficulty now is saving it as a PDB. I found it only seems to save some of the subunits in PDB format that I was able to import into Maya. It does save the whole structure as obj, but this file format is not compatible with the import plugin mMaya. I was wondering if there is a way of selecting a number of chains simultaneously and then saving those in a PDB and repeating until the whole capsid is saved out and then reconstruct in Maya? There are a very large number of chains and I seem only able to select one at a time from the drop down menu. Alternatively, can you save as emd files from ChimeraX?

Thanks so much and best wishes,


From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, 2 April 2019 3:16 AM
To: Divjak Maja <Maja.Divjak at petermac.org>; UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
Subject: Fwd: Downloading HIV PDB 3j3q?

From: Divjak Maja <Maja.Divjak at petermac.org<mailto: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<mailto: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,


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.

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.

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