[chimerax-users] XYZ format

[Tom Goddard]

Hi Mike,

  We are working on making ChimeraX handle intergrative hybrid model format, an extension to mmCIF being developed by the wwPDB intended to handle coarse grain models.

	https://pdb-dev.rcsb.rutgers.edu <https://pdb-dev.rcsb.rutgers.edu/>

	https://github.com/ihmwg/IHM-dictionary <https://github.com/ihmwg/IHM-dictionary>

The Sali lab is working on this new file format and it is not clear if the IMP RMF format will continue to be used.  There currently aren’t good standard formats for describing coarse-grain models.  A recent (April 2017) Nature chromosome 3D structure article

	http://www.nature.com/nature/journal/v544/n7648/full/nature21429.html <http://www.nature.com/nature/journal/v544/n7648/full/nature21429.html>

has data at the NCBI GEO database with the chromosomes represented in PDB format:

	https://www.ncbi.nlm.nih.gov/gds/?term=GSE80280 <https://www.ncbi.nlm.nih.gov/gds/?term=GSE80280>

  Tom



> On May 28, 2017, at 3:19 PM, Mike Goodstadt 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 <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  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 <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
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On May 25, 2017, at 4:10 PM, Mike Goodstadt  wrote:
>>> 
>>> Hi!
>>> Many thanks for the great work on this new version.
>>> Does ChimeraX support XYZ files?
>>> Chimera did but I get an “unrecognized filetype” error in ChimeraX.
>>> Best regards,
>>> Mike Goodstadt
>> 
> 
> Mike Goodstadt
> mikegoodstadt at gmail.com <mailto:mikegoodstadt at gmail.com>
> skype: mikegoodstadt
> +34 653 756 614
> 
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