[Chimera-users] cif files

Tom Goddard goddard at sonic.net
Wed Dec 7 11:47:40 PST 2016

Hi John,

  The Chimera mmCIF reader is incredibly slow, taking minutes to read a ribosome structure.  This code was developed outside our lab and is all in Python.  So practically, you would need to download use the multiple PDB format files for structures over 100,000 atoms.  The PDB has made this more difficult for new entries because they get a single ID code and only the mmCIF is easily available if the entry has more than 100,000 atoms.  For fewer atoms Chimera simply fetches the PDB format if you use fetch or command "open 1xyz”, but it fetches the mmCIF for new entries where the PDB format is not readily available.  For those (e.g. 5LZS) you can go to the RCSB web site and use the web page Download menu to get the *.tar.gz file containing several PDB format files representing the model.

  As Elaine said our new ChimeraX is much faster and uses mmCIF by default.  For instance 200,000 atoms of 5LZS opens in 1.5 seconds in ChimeraX.


> On Dec 7, 2016, at 11:39 AM, Elaine Meng wrote:
> Hi John,
> That is one of the major issues addressed in our next-generation program, ChimeraX.
> ChimeraX is not yet publicly available, but we plan to make development daily builds available very soon (this month). However, it is in an early stage and lacks many features. It will take some time to become as functionally rich as Chimera, so how useful it will be for you depends on what types of structural analysis you wished to perform.   If primarily viewing, it may already fill the bill.  We envision people using both packages for a while, depending on their needs.  You can get a feel for what ChimeraX can do now from the website and documentation linked below.
> ChimeraX homepage
> <http://www.rbvi.ucsf.edu/chimerax/index.html>
> Advantages shortlist
> <http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html>
> User Guide
> <http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Dec 7, 2016, at 8:09 AM, John Mercer, Ph.D. <jmercer at duke.edu> wrote:
>> Hi All,
>> Is there a way to usefully (and conveniently) view ribosomes recognizing that Chimera does not support large structure formats like mmcif?
>> -John
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