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3dmol / 3Dmol.js

WebGL accelerated JavaScript molecular graphics library
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DSN6 map format #738

Closed publcif closed 3 months ago

publcif commented 7 months ago

Does 3dmol support this format?

dkoes commented 7 months ago

No, I’ve never heard of it. Do you have a link to the spec?

publcif commented 7 months ago

Its what the pdb are using instead of ccp4 maps (which 3dmol does render):

https://www.rcsb.org/docs/general-help/x-ray-electron-density-maps

ghutchis commented 7 months ago

Looks like the closest thing to a spec is here: http://www.uoxray.uoregon.edu/tnt/manual/node104.html

wojdyr commented 4 months ago

Its what the pdb are using instead of ccp4 maps (which 3dmol does render):

RCSB added files in this format at some point, I think it was used in the NGL viewer. But more recently they started using a map server that transfers maps in small chunks, in BinaryCIF format.

If you'd like to add DSN6, it's implemented here in xtal.js, and here in my viewer (forked from xtal.js). But I'm not even sure if it still works, because it's never used. CryoEM uses MRC/CCP4 format, and in crystallography almost all programs can calculate maps on the fly from map coefficients in MTZ file. If a map file is occasionally needed, it's typically also in the CCP4 format.

wojdyr commented 3 months ago

FTR, RCSB PDB just announced a plan to drop the DSN6 format: https://lists.wwpdb.org/empathy/thread/PEBDMLMJHJN54HSLU6JKJJJTFPOZXQTB