Hello,
You could look at this family of enzymes,
http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.jc.b.b.html
[the sulfolactate dehydrogenase-like family]
No Rossman fold there.
HTH,
Fred.
Dear all,
I have biochemically characterized one enzyme that can dephosphorylate
NADP+ / NADPH.
Wow, an email from the future !
[Sorry...]
Subject: [ccp4bb] diagram of dsDNA
From: cuisheng2007 cuisheng2...@yahoo.com.cn
Date: Mon, October 1, 2012 9:33 am
To: CCP4BB@JISCMAIL.AC.UK
Dear all
When I was playing around with Nucplot to generate diagram for
).
So if there are other suggestions to solve this br of a problem, they
are most welcome!
Fred.
--
Fred. Vellieux, esq.
=
IBS J.-P. Ebel CEA CNRS UJF / LBM
41 rue Jules Horowitz
38027 Grenoble Cedex 01
France
Tel: (+33) (0) 438789605
Fax: (+33) (0
On Mon, 5 Mar 2007, Fred. Vellieux wrote:
Hi James,
I tried to increase the parameter value to 3.0 A. The resulting file gives
the same behaviour (and the newly introduced OXTs are within 0.05 A of the
N atom of the following residue) so I think the distances are reasonable.
So
plus non random phases
(both from map inversion of averaged maps) lead to better electron density
maps.
Fred.
--
Fred. Vellieux, esq.
=
IBS J.-P. Ebel CEA CNRS UJF / LBM
41 rue Jules Horowitz
38027 Grenoble Cedex 01
France
Tel: (+33) (0) 438789605
Fax: (+33
use Voidoo however I do not know where to download an
initial (and fairly comprehensive) cavity.lib file which I'd modify if
need be. The links on the USF web site appear to be broken.
I am running Linux.
Thanks for the advice,
Fred
Hi,
We already have problems with the volume taken by our standard backups
(they take too much space and we haven't been able to push the walls
outwards in the Institute - I don't know why they keep telling us that
our data should be in some clouds up in the sky). Hence I was wondering
about
Dear all,
These are the replies received so far:
Daniel Rigden (U. of Liverpool) suggested to do the conversion using
https://www.webqc.org/molecularformatsconverter.php . It didn't work for
me, the small molecule may be too complex (error message when reading
the .mol file);
Petr Kolenko
*Hello,
I am looking for the Superimposé web server (from Charité, Berlin).
*
*This web server must have moved from the place where it is supposed to
reside, farnsworth.charite.de , not found.
Does anyone know where this web server resides now ?
TIA,
Fred.
*
Hello,
Follow up concerning my query to the bb (in case anyone is interested),
reply received from Robert Preissner through Philip E. Bourne and Joel
Sussman:
The Superimposé server was stopped in May 2018.
Fred. Vellieux
On 2/28/20 7:47 AM, Fred Vellieux wrote:
*Hello,
I am looking
y work
reasonably well.
---> Jack Tanner (U. Missouri-Columbia): "You might want to review the
literature on using MD to study diffusion of O2/CO in myoglobin." (I had
started in fact)
[---> Lorenzo Briganti: the reply seems to have been lost along the way].
Hoping this will be use
Dear all,
I need to run MD calculations in order to follow the trajectories of a
very small molecule inside a protein. From previous calculations (not
MD) I have starting positions for this small molecule that all seem in
agreement with a possible path of motion inside the protein.
Now I
s to all who replied. Superposition using the nucleid acid part of
complexes can be very informative.
Have a nice day further,
Fred. Vellieux
--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic
is the "best" way of doing this.
Your suggestions will be appreciated, thanks.
Fred. Vellieux
--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic
To unsubscribe from the CCP4BB list, click the
Hello,
I need to perform some MD calculations and then trajectories of some
small molecules analyzed.
What I have is
1. protein
2. cofactor (FAD)
3. small molecule (either single O2 atom or single Chlorine atom)
4. crystallographic waters
The software I can access is either Gromacs (with yum
Hi folks,
Sorry about the non-ccp4 question. I don't know where to ask.
I have to perform MD simulations but I am totally on my own here. The
one program that appears to be free (in terms of license) seems to be
CHARMM. GROMACS (testing with the examples found in the internet) did
not work
Hi,
In addition to all that's been suggested so far: when I was facing such
problems I always tried the (commercially available) additive screens
(additive kits, whatever they are called nowadays). This means setting
up quite a few crystallisation experiments (you already have conditions
in
Hello there,
After running autodock vina on certain small molecules, the graphics
software I am using (e.g. Pymol, Coot) draws far too many bonds on the
docked small molecule. See enclosed screen capture.
Is there any way to prevent this from happening? This isn't very
satisfactory of you
Hi folks,
I'm trying to run Ligplot on a PDB file that contains a residue with
type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2
years now (which means that I had to reinstall, with an expired license,
and get familiar with it again). I get the following error message
Hi,
Other people on this BB may run into the same problem.
CentOS 7 end of life is announced to happen in July 2024.
I have to migrate my Linux box to another Linux "flavour".
I've had a look at the possibilities:
- migrate to another RHEL (rpm-based) Linux, with "elevate-linux" and
looking for a method allowing me to identify and display
the interface forming residues of one of the protein components. Plus a
surface representation of that part, for the 3D structure.
Thanks in advance for any tips.
Regards,
Fred. Vellieux
--
MedChem, 1st F. Medicine, Charles University
ture of the
complex available) I am looking for a method allowing me to identify
and display the interface forming residues of one of the protein
components. Plus a surface representation of that part, for the 3D
structure.
Thanks in advance for any tips.
Regards,
Fred. Vellieux
--
MedC
Hello Pavel,
You may want to have a look at PDB structure 6YCR: the macrocyclic
peptide inhibitor is modelled as two conformations. The entire peptide.
HTH,
Fred.
On 8/24/22 00:02, Pavel Afonine wrote:
Dear community,
I’m looking for an example of a crystal structure where a large group
Folks, apologies for the non-CCP4 software question.
I have tried to contact the BIOVIA DiscoveryStudio support team, somehow
my browser does not allow me to open their "contact form".
I am trying to visualize and perform an analysis on a protein:smaller
molecule complex. The smaller
Hello Frank,
We have to convert betwen file formats very frequently (usually several
times daily) and:
1) we didn't need any restraints CIF file for that;
2) the tools we are using are
http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html
Hello,
Overhanging "sticky" ends are mentioned frequently when it comes to
obtaining infinite helices that are useful in crystallization. For
example in
https://home.ccr.cancer.gov/csb/nihxray/Tips-and-Tricks_Crystallization_Protein-DNA_updated.pdf
.
Cheers,
Fred.
On 09/02/2024 10:59,
Dear Stuart,
I did test that (removing the .CCP4MG2 directory and its contents) and
it gave the same ugly graphics.
There are problems with Alma Linux and the "Secure Boot" on this Hewlett
Packard Z4 computer. This I have noticed. The secure boot option wants
to load a signed graphics
Dear all,
In case anyone experiences problems with Alma Linux, NVIDIA graphics
boards and the NVIDIA graphics driver, here is what worked:
somehow, the nouveau graphics driver seems to sneak back in, even if
blacklisted. When nouveau is in use, the ugly graphics are obtained with
ccp4mg.
Hi folks,
I have a simple question: is there an electronic bulletin board for
small-molecule crystallography? I have checked the list of CCP projects
and there is no CCP-project for small molecule crystallography in the list.
I am trying to run SHELXL, and it fails with the cryptic message
t remember (the Linux flavour here is
Alma Linux 9, not Debian).
Fred.
On 12/03/2024 10:56, David Waterman wrote:
Hi Fred,
CCP4 distributes the shelxl binary on Linux. I've not checked yet, but
perhaps it is also part of CCP4 on Windows?
Cheers
-- David
On Tue, 12 Mar 2024 at 09:38, Fred Vellie
did your input files
come from?
Cheers
-- David
On Tue, 12 Mar 2024 at 09:01, Fred Vellieux
wrote:
Hi folks,
I have a simple question: is there an electronic bulletin board for
small-molecule crystallography? I have checked the list of CCP
projects
and there is no CCP
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