Hi
This is more or less what I do in PyMOL, but I was looking for some
quicker and more user-friendly tool.
A (less cumbersome ?) procedure is the following (thanks to Arwen
Pearson for the hint). It requires external manipulation of the PDB
files and some matrix calculations (I have not tes
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?
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 écr
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.
Cheers,
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 th
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
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 file:
bulletin board IM AUFTRAG VON Stefano
> Trapani
> GESENDET: Mittwoch, 2. Juni 2021 14:31
> AN: CCP4BB@JISCMAIL.AC.UK
> BETREFF: [ccp4bb] superpose crystal objects in CCP4MG or other software
>
> Dear all
>
> I would like to visually compare (using some molecular graphics sof
@JISCMAIL.AC.UK
Betreff: [ccp4bb] superpose crystal objects in CCP4MG or other software
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
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 orienta
10 matches
Mail list logo
