On 01/09/2023 17:40, Eleanor Dodson wrote:
Is that coot in the latest ccp4 distribution?
By "that" I presume you mean "Coot 0.9.8.92." No, it is not. Currently
it is merely a twinkle in the developer's eye.
I'll try to find some time next week to make a release.
Paul.
On Fri, 1 Sep
Is that coot in the latest ccp4 distribution?
On Fri, 1 Sep 2023 at 17:37, Paul Emsley wrote:
> Dear Eleanor
>
>
> On 01/09/2023 13:19, Eleanor Dodson wrote:
>
> *COOT problem first: or is it REFMAC ? *
> REFMAC outputs coordinates in both pdb and cif format. They are
> identical
> *This model
Dear Eleanor
On 01/09/2023 13:19, Eleanor Dodson wrote:
*COOT problem first: or is it REFMAC ? *
REFMAC outputs coordinates in both pdb and cif format. They are
identical
*This model has ZN linked to CYSs etc..*
The PDB files provides the link records but the cif file does not.
When Xquartz is installed it should be in the applications folder. Have you
tried to reinstall it? It should open an installer gui and proceed normally.
--
Kelvin Lau
Protein production and structure core facility - PTPSP
EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
CH-1015 Lausanne
On 01/09/2023 11:37, Guenter Fritz wrote:
Dear Paul,
I had a strange issue today when refining a structure with latest coot
(0.9.9.91) from CCP4.
Two cysteines with Calpha-Calpha distance of about 6 A do not form a
disulfide bond, but coot wants to enforce a disulfide, although no
I don't know much about CCP4-built binaries on macOS. I do know that one
is supposed to reinstall XQuartz after updating the OS.
Paul.
On 31/08/2023 21:52, Andrea Smith wrote:
P.S. Found this in the log file from Cloud:
dyld: Library not loaded: /usr/X11/lib/libpixman-1.0.dylib
Yes, it is coordinated to the CYS residues. So maybe it does need to be
shown as having links
I was just confused because links for covalent bonds look the same as for
coordinations.
W
On Fri, 1 Sept 2023 at 13:31, Eleanor Dodson
wrote:
> But ZN IS coordinated to the CYS surely? and if you
Just to clarify, I don't think there should be links from the Zn to the
cysteines. The Zn should just be a coordinated metal.
But there is a covalent link from DRG C2 to SG Cys417
Thanks
Wendy
On Fri, 1 Sept 2023 at 13:19, Eleanor Dodson
wrote:
> *COOT problem first: or is it REFMAC ? *
>
But ZN IS coordinated to the CYS surely? and if you dont specify a LINK
refinement will apply VDW repulsion to keep the atoms apart??
E
On Fri, 1 Sept 2023 at 13:30, Wendy Offen wrote:
> Just to clarify, I don't think there should be links from the Zn to the
> cysteines. The Zn should just be
*COOT problem first: or is it REFMAC ? *
REFMAC outputs coordinates in both pdb and cif format. They are identical
*This model has ZN linked to CYSs etc..*
The PDB files provides the link records but the cif file does not.
eleanor@wombat job_187 % grep -i link
Dear Paul,
I had a strange issue today when refining a structure with latest coot
(0.9.9.91) from CCP4.
Two cysteines with Calpha-Calpha distance of about 6 A do not form a
disulfide bond, but coot wants to enforce a disulfide, although no
disufide is defined in the pdb.
Does coot now
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