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MDAnalysis / mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.
https://mdanalysis.org
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support mmtf format #907

Closed orbeckst closed 7 years ago

orbeckst commented 8 years ago

@arose suggested on twitter to use MMTF for storing big structures. "The Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structural data quickly and accurately."

There is a python implementation available: https://github.com/rcsb/mmtf-python

kain88-de commented 8 years ago

they have another format -.-? What is with the mmCIF that is still in development for large macromolecular complexes?

orbeckst commented 8 years ago

On 20 Jul, 2016, at 14:20, Max Linke notifications@github.com wrote:

they have another format -.-? What is with the mmCIF that is still in development for large macromolecular complexes?

If you look at the comparison graph for loading mmCIF vs mmtf I would say it’s on the way out – but I don’t know how feature-complete mmtf is. I really did not dig into it in any more detail.

Oliver Beckstein * orbeckst@gmx.net skype: orbeckst * orbeckst@gmail.com

arose commented 8 years ago

Hey @kain88-de, mmCIF is still the archival format and there are no plans to retire it in any way! We created MMTF for the specific purpose of fast transmission over the internet (and whole archive analyses). It loads and parse real quick, allowing you to look at the 2.4M HIV Capsid in a Browser. MMTF does not contain all the metadata from mmCIF files but rather most of the data generally used.

orbeckst commented 8 years ago

@arose, many thanks for the background information on MMTF! Very useful.

On 20 Jul, 2016, at 14:58, Alexander Rose notifications@github.com wrote:

Hey @kain88-de, mmCIF is still the archival format and there are no plans to retire it in any way! We created MMTF for the specific purpose of fast transmission over the internet (and whole archive analyses). It loads and parse real quick, allowing you to look at the 2.4M HIV Capsid in a Browser. MMTF does not contain all the metadata from mmCIF files but rather most of the data generally used.

Oliver Beckstein * orbeckst@gmx.net skype: orbeckst * orbeckst@gmail.com

orbeckst commented 8 years ago

@richardjgowers I assigned you to this issue because you've been working on #907 and you already have some expertise – feel free to assign other folks and tag with 'help needed' or similar.

richardjgowers commented 8 years ago

@orbeckst OK, I'm trying to stop procrastinating on 363 so anyone else can finish this off if they want.