Converting PDB/mmft with a specific dict

[chaconlab]

I would like to convert mmft/PDB (and back) following exactly the https://mmtf.rcsb.org/v1.0 conventions/dictionaries. As a stupid test I download mmtf file from RCSB and re-formated but the output is almost 2 times larger (I am guessing is related to the bit encoding). I need to convert PDB into mmft and also mmft to PDB but exactly conforming RCSB dictionary. Is it possible with your nice tool?

Thanks for your help

Pablo

Here at http://chaconlab.org are my coordinates just in case you want to contact me...

Proposed Example Code

python3.6 converter.py 2fxm.mmtf temp.mmtf

import sys import atomium

print ('Converting', sys.argv[1], sys.argv[2]) pdb = atomium.open(sys.argv[1]) print(" ", pdb.model) pdb.model.save(sys.argv[2])

[samirelanduk]

Hi - thanks for trying out atomium!

I'm not sure I quite understand the task to be performed. If you want to convert a PDB to MMTF you can indeed do as you suggest in the example code:

import atomium
pdb = atomium.open('1xxx.pdb')
pdb.model.save('1xxx.mmtf')

This will create a MMTF version of the PDB that should be perfectly valid. Perhaps I have misunderstood your Issue?

Sam

[chaconlab]

Hi Sam,

Sorry my problem was originated because I want to use a NGL RCSB script and it requires that mmtf have concrete mmtf fields. Now I reduce the problem to transform a raw pdb (just the coordinates) to mmtf and then transform back this mmtf into pdb. Is it possible? In addition, I will love to transform a raw multiple pdb model (a trajectory in pdb format) into mmtf, are you planning to incorporate this feature to atomium.

Thanks for your help,

Pablo

El jue., 15 ago. 2019 a las 15:58, Sam Ireland (notifications@github.com) escribió:

Hi - thanks for trying out atomium!

I'm not sure I quite understand the task to be performed. If you want to convert a PDB to MMTF you can indeed do as you suggest in the example code:

import atomium pdb = atomium.open('1xxx.pdb') pdb.model.save('1xxx.mmtf')

This will create a MMTF version of the PDB that should be perfectly valid. Perhaps I have misunderstood your Issue?

Sam

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