A research technician position is available in the laboratory of Dr.
Karim-Jean Armache, Assistant Professor in the Structural Biology Program
at the Skirball Institute of Biomedical Research—NYU Medical Center, New
York, USA.
We are looking for creative individuals with a strong interest in
Phenix?
phenix.pdb_atom_selection model.pdb "within(5, (resid 4 and name CA))"
where 5 - 5 Angstrom radius, (resid 4 and name CA) - selection of an atom.
Don't have to be a single atom. More docs on selection syntax is here:
Look at the plots for Rfactor for your last cycle.
Is there a blip at some resoution?
And also look at the plot of v v resolution-- again are
there blips?
People have put a lot of effort in generating informative graphs so use
them!
You should see ice ring effects in the Wilson plot too..
Usually externaly provided has pecedent over library routine ..
you need to label any "amino-acid" as a peptide though to generate the
required links in the protein chain.
E
On Wed, 3 Apr 2019 at 16:09, wrote:
> Dear Deniz,
>
>
>
> In the past, I had similar problems caused by the fact that
Hi everyone again
Hmmm I think we have solved a structure in P1 space, to 2.5 A. However
after refinement the Rfree stuck at 33%-35% with Rwork around 26%. The
structure was solved by MR and current model seems to fit density well. In
Refmac log I found that at the resolution corresponding to
While I agree with testing in lower symmetry (and I'm sure you have), it is
also possible that the asymmetry is too slight or doesn't affect the crystals
contacts, so that the dimer would orient randomly as it packs into the crystal.
In that case, taking the average over all asymmetric units,
In ChimeraX, you can promote a selection to whole residues with:
select up
Repeating the command will expand to whole secondary structure elements,
then whole chains, then whole models. You can reverse this with:
select down
On 2019-04-03 16:13, Gianluca Santoni wrote:
I could be useful
This is easy to do in Pymol again. If you have atoms in selection "nameX", the
command is "select nameX, br. nameX". Very simple.
Best regards,
Petr
From: CCP4 bulletin board on behalf of Gianluca Santoni
Sent: Wednesday, April 3, 2019 5:13:59 PM
To:
I could be useful to then expand the selection to include the full
residues and not just the atoms within the sphere:
byres S1
On 4/3/19 4:21 PM, Steiner, Roberto wrote:
pymol?
example
S1 around 12.3 a. Atoms with centers within 12.3 Angstroms of the center
of any atom in S1
Best
Dear Deniz,
In the past, I had similar problems caused by the fact that when the residue
was “known” to ccp4, it would use the cif file from the ccp4 library instead of
the cif I had created myself. You could check if this might be the case for
you. You find the cif files under
Dear Stephen,
PyMOL can do it. You have to choose your atom and then use following command:
select your-name, (sele) expand 10; where (sele) is your selection - atom or a
group of atoms and 10 is the radius in AA.
Best regards,
Petr
From: CCP4 bulletin
In ChimeraX:
ctrl-click to select your atom, then in the command line below:
select zone sel
Best regards,
Tristan
On 2019-04-03 15:18, Stephen Cusack wrote:
Dear All,
I am looking for an accessible programme that allows selection of
atoms from a PDB file
within a sphere of inputted
pymol?
example
S1 around 12.3 a. Atoms with centers within 12.3 Angstroms of the center
of any atom in S1
Best wishes
Roberto
On 3 Apr 2019, at 15:18, Stephen Cusack mailto:cus...@embl.fr>>
wrote:
Dear All,
I am looking for an accessible programme that allows selection of atoms from a
Dear All,
I am looking for an accessible programme that allows selection of
atoms from a PDB file
within a sphere of inputted radius from a central atom.
Thanks for any help,
Stephen Cusack
--
**
Dr. Stephen Cusack, FRS
Qs..
1) You are using the same dictionaries for both REFMAC and COOT?
2) What happens in refmac if you just use REFI IDEALISE?
And turn on the option for REFMAC to
MONITOR MANY - it might tell you if there is some clash which is overriding
the geometry restraints..
Eleanor
On Wed, 3 Apr 2019 at
Hello,
I'm trying to refine the structure of a protein mutant that has an unnatural amino acid in it. I created a restraint file for the AA and the mutation worked fine in COOT. But when I use refmac5 for refinement, it always changes the bond angle in the sidechain (an azide group, which should
Hi
One way to test if the data processing software has imposed too much symmetry
is to actually look at the images themselves using one of the processing
packages, or process in a lower symmetry and use "viewhkl" (or even "hklview"
if you're old-fashioned...) to view sections of the integrated
I agree. The data processing software might have been confused by the NC 2-fold
and thought that it was crystallographic and of course, after merging the data,
the NC axis will have been made “crystallographic” with superimposed A and B
conformations at 50% occupancy. In this case, reprocessing
Yes - I have had cases like that where reducing the spacegroup symmetry
improved the model a lot!
Eleanor
On Wed, 3 Apr 2019 at 09:47, David Briggs wrote:
> Hi,
>
> This doesn't answer your question directly, but I'd be tempted to reduce
> the symmetry and re-refine in a space group lacking
The Helmholtz Zentrum Berlin für Materialien und Energie, the
Max-Delbrück-Center for Molecular Medicine, the Freie Universität Berlin, the
Chariteand the Humboldt Universität zu Berlin jointly operate three
experimental stations for bio-macromolecular crystallography at BESSY II, one
of
Hi,
This doesn't answer your question directly, but I'd be tempted to reduce the
symmetry and re-refine in a space group lacking that 2-fold axis.
I'd hope that the scaling in the lower space group would give you better stats
as well, but maybe the differences in your case are too subtle?
I
Hi all,
we have a structure with a pseudo internal symmetry along a 2-fold axis
that sits on a 2-fold crystallographic axis. For refinement purposes we
have modeled the parts that differ with 50% occupancy, but before
depositing the structure we wanted to make sure that this is the best way
to
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