Dear Gergely,
>
> Thank you for these examples! It is reassuring to see that multiple
> crystallographic models do not break validation for example. I assume only
> the validation of the first model and first reflection file is shown. I can
> imagine that it is still a substantial change and
Dear Ethan,
This is an interesting discussion. I agree the word uncertainty covers very
broad concepts, but I try to narrow down what I mean.
My starting point is that a reflection file contains point estimates of
diffraction intensities or structure factor amplitudes. Refinement and model
To: Gergely Katona
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Meaning of a pdb entry
Dear Gergely,
For authoritative advice you'd need to ask the PDB. Below is my take.
> I am not sure if it is possible to use MODEL-ENDMDL loops in pdb or mmcif
> format for storing multiple crystallographic
Dear Gergely,
For authoritative advice you'd need to ask the PDB. Below is my take.
> I am not sure if it is possible to use MODEL-ENDMDL loops in pdb or mmcif
> format for storing multiple crystallographic models.
It's possible, there are a few examples such as 2VTU. They represent
"ensemble
On Monday, 31 May 2021 10:53:46 PDT Gergely Katona wrote:
> Dear Ethan,
>
> Thank you for your comments! I started a new thread, it was unfortunate that
> I brought this up in a discussion about B-factors. I really wanted to discuss
> something that is model agnostic and how to represent
Dear Gergely,
you can concatenate (mm)CIF files, without violating the grammar. Thus,
if you want to deposit multiple models at once, just run 'cat 1.mmcif
2.mmcif 3.mmcif > allmy.mmcif' for deposition. This works for CIF, and
is accepted e.g. by the IUCR journals.
Best,
Tim
On Mon, 31 May
Dear Ethan,
Thank you for your comments! I started a new thread, it was unfortunate that I
brought this up in a discussion about B-factors. I really wanted to discuss
something that is model agnostic and how to represent uncertainty by sampling.
I consider an ensemble model with multiple
