[chimerax-users] XYZ format

[Elaine Meng]

Hi Mike,
As you can probably imagine, the team has not yet discussed some sectors of the universe of possible things that may or may not be in ChimeraX. So I do not have a definite answer for you regarding RMF or XYZ.

We are definitely interested in supporting integrative hybrid modeling and hierarchical structural representations and have been working with several other parties on the formats that may be relevant.  Thus far in ChimeraX, we have been using mmCIF, PDB, and for ensembles, various trajectory formats such as DCD.

Although XYZ is easy to write, I believe it is element-centric and deficient in lacking unique atom (marker) names and the concepts of residues and chains, all of which are highly useful for specifying specific subsets of your points (e.g. indicating different chromosomes or chromosomal regions, different types of markers or fluorophores, etc.) and hierarchies in the data. 

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



> On May 28, 2017, at 3:19 PM, Mike Goodstadt <mikegoodstadt at gmail.com> wrote:
> 
> Hi Elaine,
> Considering your reply further:
> Will ChimeraX include a agnostic plain XYZ import option?
> We work with non-atomistic chromatin confirmations and so are interested in this option.
> What would be your recommendation for a format for non-atomistic particle (xyz) coordinates?
> Also, I have been looking into IMP’s RMF format and comparing it to UMM (http://www.scalalife.eu/content/umm.html).
> Will RMF still receive official Chimera backing in ChimeraX?
> Many thanks,
> Mike
> 
>> On 26 May 2017, at 17:25, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Mike,
>> Not currently.  You can use command “open formats” to list the current ChimeraX formats in the Log.
>> 
>> The data formats are listed with a little more detail in the documentation for “open” (input) and “save” (output) commands. Input formats:
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local>
>> 
>> You may be able to use Chimera (not ChimeraX) to read XYZ and output PDB, if you don’t have any other converter handy.
>> I hope this helps,
>> Elaine