Hi Marco,
Did you try putting the MR solution into ModelCraft for automated building?
You say that the N-terminal domain does not fit the map, but does it look
like this region is resolved, i.e. could you build it interactively in
Coot? If you have good maps then I would expect automated model-bui
It would also be good to check the monomer library (expanded with any
user-supplied dictionaries). Cases where an element in columns 77-78 exists
and it does not agree with the component definition should probably be
flagged up.
Cheers,
Paul
On Wed, 15 May 2024 at 12:39, Marcin Wojdyr wrote:
>
What Oleg says is right. The phases may be too poor to Bootstrap from. Oleg
also reminded me that the MR solution may be incorrect. I would check the
following:
What were the TFZ and LLK scores for the MR solution (if you used Phaser
for MR)?
What are the R-factors after molecular replacement? Do
Hi Sam,
ARP/wARP should work well at 1.9A resolution. If it did not then there are
things to check such as whether the space group is correct and whether
there are major deviations in the Wilson plot.
Do you have a suspected sequence for chain B? If so, I would provide that
to the programs to hel
career stage.
The *application deadline has been extended to the 14th July* (this
Friday). Application details can be found on the School website.
https://www.ccp4.ac.uk/schools/ccp4-summer-school/application.php
Many thanks,
Johan Turkenburg, Jon Agirre and Pau
I believe there are many advantages to storing things *internally* as data
objects with metadata instead of as columns of an MTZ file. How many
students know what FP,SIGFP mean? And how many know that the FP,SIGFP
columns in Refmac's HKLIN are not the same as the FP,SIGFP columns in
HKLOUT? In an i
Hi Paul,
You have probably solved this already, but in case you are interested I
have written a script to superpose AlphaFold models using PDBe mmCIF
annotations, AlphaFold DB and Gemmi (link below), as I had already done
something similar in a previous project. It is probably better to use
3D-Bea
Hi Eleanor,
This is how you would do something similar in gemmi with ccp4-python:
import gemmi
mtz = gemmi.read_mtz_file("input.mtz")
dataset = mtz.add_dataset("mydataset")
dataset.crystal_name = "mycrystal"
dataset.project_name = "myproject"
dataset.wavelength = 1.44555
for column in mtz.column
The -origin-hand option is also useful for comparing molecular replacement
solutions that may have different origins.
I think the slides in Andrey Lebedev's presentation help to visualise this
problem (specifically slides 49 & 50).
https://www.ccp4.ac.uk/schools/DLS-2020/course_material/day03.01%2
Hi Joël,
You can go to Calculate -> Scripting -> Python and enter:
set_draw_cis_peptide_markups(0)
Kind regards,
Paul
On Thu, 12 Mar 2020 at 09:58, Joël Bloch wrote:
> Hi Dave
>
> Thanks a lot for the hint. The Cis-bond should be correct, as it is a
> buried glycine residue in a crystal struc
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