Greetings to all !
I have docked some ligands into the active site of a protein identified
through literature using AutoDock Vina. The available PDB protein structure
does not have a co-crystallized ligand, and it is the only structure
available for my study. I have obtained good docking results,
> By the way, did you mean by "outliers" those from the PDB validation
> report? I have had a feeling that their criterion is a bit too strict.
> Could anyone from the PDB tell how the outlier of the ARG sidechain is
> calculated?
Looking at the planeRMSD values of ARG side chains in several
valid
Vladyslav
I would be very interested in seeing the PDB report that you received. If
you wish to share, please send it directly to me.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Hi Luiso,
All correct, thank you for replying
Cheers,
Maria
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Dear Dave,
Unfortunately this is not possible in current version of CCP4 Cloud. However,
since DUI runs on user's machine anyway, it would be possible to start it from
the locally installed CCP4 and only import results into Cloud. This way, DUI
work directory can be re-used, and new results re-
Whatever it is worth, I agree with Dale. I see those "Major validation issues"
all the time. Some structures at medium resolution (2-3A), and some are at high
(1.1-1.4A). Not all Arg residues are "in violation". At low and medium
resolution cases it is hard to argue. But high resolution electron
Hi David,
DUI is capable to pick up where it was before, but only if is launched exactly
from the same path as before. If I understand correctly CCP4 cloud was designed
(before DUI was programmed) to handle locations of where programs are launched
differently.
The only solution that come to my
Hello,
Thank you for your feedback.
Yes, I meant those that appear in pdb validation report.
I will try to inspect surrounding residues as well as run with suggested
keywords and let you know how it went.
Thank you!
Best regards,
Vladyslav
From: CCP4 bulletin b
Hi All,
In CCP4i2 it is possible to re-open the results from a previous DUI session by
cloning the job and selecting the "Continue from previous dials session" option
from the drop-down. I'm trying to find a way to do this in CCP4 cloud for a
tutorial - perhaps it's not possible?
Any suggestio
Hi,
I would like to support Dr Yamashita's statement and emphasize that
Arg side chains really do deviate from planarity from time to time, and
it is possible that your side chain is an "outlier" because it really is
non-planar. In the paper Yamashita mentioned ("Arginine off-kilter:
guani
Hi,
I assume the planarity you mentioned is what is discussed in Moriarty
et al (2020) https://doi.org/10.1107/S2059798320013534
As shown there, it is known to have some deviation. In Refmac (or in
the CCP4 monomer library) it is restrained using a torsion angle with
5 degree sigma instead of the
Hello,
I am refining a structure and I have ARG planarity outliers in the sidechain.
Could someone please tell me how should I set the planarity restraint in
REFMAC5 (version 5.8.0403) to correct them?
Should I use: plane [value1] [value2] in the advanced settings? If so, what
values 1 and 2 sh
On 17/08/2023 11:18, Palm, Gottfried wrote:
>
> I copied the EDO.cif from the library and changed the C1-C2 torsion
> angle definition to
> EDO sp3_sp3_4 O1 C1 C2
> O2 180.000 10.0 1
>
> After loading EDO in coot via "import cif dictionary
Dear all,
I have a problem in fine tuning the cif file for my new ligand. I
try to force a specific torsion angle, but coot doesn't "obey". The
ligand has more than 50 atoms , so I tried with simple ethane diol,
EDO.
I copied the EDO.cif from the library and changed the C1-C2 torsion
angle def
Hi
Since this is the ccp4 bulletin board, it’s always worth mentioning CCP4MG for
producing images & movies of macromolecules. Comes with the package, and you
can get help from the author directly if you have any issues.
Harry
> On 17 Aug 2023, at 02:09, khaja faisal tarique
> wrote:
>
> Th
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