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 mikegoodstadt@gmail.com skype: mikegoodstadt +34 653 756 614
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 ----- 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 <mikegoodstadt@gmail.com> 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
Thank you for the information! Best regards, Mike On Fri, 26 May 2017 at 17:25, Elaine Meng <meng@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 ----- 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 <mikegoodstadt@gmail.com> 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
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 <meng@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 ----- 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 <mikegoodstadt@gmail.com> 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@gmail.com skype: mikegoodstadt +34 653 756 614
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@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@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
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@gmail.com <mailto:mikegoodstadt@gmail.com> skype: mikegoodstadt +34 653 756 614
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Thanks Tom!
On 30 May 2017, at 23:06, Tom Goddard <goddard@sonic.net> wrote:
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@gmail.com <mailto:mikegoodstadt@gmail.com> skype: mikegoodstadt +34 653 756 614
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
participants (3)
-
Elaine Meng -
Mike Goodstadt -
Tom Goddard