I am thinking this could be done using pdbset to apply symops and origin
shifts, etc, with a bit of checking in Coot, creative chain-ID's and some trial
and error? Or using Coot to apply symops and save the resulting pdb's with
different chain ID's and then concatenate them into a mini-lattice?
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
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wwPDB validation reports are now provided in PDBx/mmCIF format for all
new depositions in OneDep. This change makes validation data more
interoperable with the PDB archival format. Data are more logically and
better organized in the PDBx/mmCIF reports, and therefore more
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Dear all,
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Hi Boaz
Thank you.
That works in Chimera (first superpose, then symmetry expand) but not in
CCP4MG (independently of the order of the operations).
It would be nice to have an equivalent option implemented in CCP4MG.
Best regards
Stefano Trapani
Le 2021-06-02 16:20, Boaz Shaanan a
Hi Stefano,
Did you try first to expand a unit cell in each lattice (using its symmops) and
then superimpose two molecules from each lattice? Perhaps the expanded lattice
wil move with the moving molecule?
I don't know how to do this in ccp4mg but I think it's possible in Chimera.
My 2p.
Dear Stuart
That does not work.
"Transform coordinates" seems to move molecules, but not the crystal
symmetry elements (no update of the crystal symmetry operation
matrices), so that crystal symmetry expansion after "Transform
coordinates" does not generate a rotated/translated version of
Does "Contents one unit cell", then "Extend unit cell" do this?
Stuart
On Wed, 2 Jun 2021 at 14:14, Stefano Trapani wrote:
>
> Yes, that is the way I usually do, but it can be cumbersome.
>
> It would be easier if I could first superpose two molecules from the two
> crystals, and then decide
Dear Stefano,
It might be possible to do what you want in a roundabout way:
i) Apply matrix to molecule: Molecule Icon -> Transform coordinates ->
Enter transformation
ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file.
iii) Load in the saved molecule
iv) For the new
Yes, that is the way I usually do, but it can be cumbersome.
It would be easier if I could first superpose two molecules from the two
crystals, and then decide in which directions to expand by crystal
symmetry (I want to compare layers and rows of molecules).
Best regards
Stefano
Le
Dear Stefano,
I do not know if it is possible, but as a workaround, you could first expand
your object by crystallographic symmetry and then do the superposition.
Best,
Herman
Von: CCP4 bulletin board Im Auftrag von Stefano Trapani
Gesendet: Mittwoch, 2. Juni 2021 14:31
An:
Dear all
I would like to visually compare (using some molecular graphics
software) the crystal packing of two different crystal forms of the same
protein.
In order to identify the similarities/differences between the crystal
packings, I need to change the default unit cell origin and
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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
Dear Marcin,
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 may require
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