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
machine and
not the latest v1.5). However, olex2 (the installation program) does not
come with Shelx program executables, and I could not locate the
installers for the shelx software on Windows.
Hence I am running SHELXL in line command mode on my Linux box.
Thank you again,
Fred.
On 12/03
don't know if this is feasible or
even advised. Probably not.
Thanks,
Fred.
--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic
To unsubscribe from the CCP4BB list, click the following link:
https://www.jisc
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/
d).
Just in case.
Fred.
On 17/01/2024 10:17, Frederic Vellieux wrote:
Dear all,
Perhaps a reader of the bb will have a solution for this problem. ccp4
is version 8.0 and is up to date. All graphics programs (coot, but
also other non-ccp4 software such as chimeraX, Pymol...) run fine on
the Alma
x. I don't know how many times I've
had to re-install Alma Linux...
Jan Dohnalek mentioned that the ugly graphics could be due to a lack of
memory problem. I am investigating that.
Cheers,
Fred.
On 1/17/24 11:47, Stuart McNicholas wrote:
Dear Fred,
Many apologies for your difficulties
tions)? If so I'd like to know what was successful.
Thank you.
Fred.
--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic
To unsubscribe from the CCP4BB list, click the following link:
https://www.
dea of how to specify that a
part of a coordinate file is the ligand, so that DiscoveryStudio 2021
recognises it as such and allows me to proceed?
Thanks,
Fred.
--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czec
/tomcat/biocomp/convert
Sometimes the conversion doesn't take place and I have no idea why.
HTH,
Fred.
On 5/19/23 11:28, Frank von Delft wrote:
Hello - as in the subject line, does anybody know of, or have, code
that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the
restraints CIF
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
play of the proteins appears with
the residues involved in the interface. This is followed by a PISA
calculation from within CCP4MG. The surface of only one of the
components in the p-p-i can be displayed, which is exactly what I was
looking for.
Thanks for all the suggestions.
Regards,
Fred.
On
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
nus: fails. It complains about the
ACE cap. Removing the cap solves that problem but then CHARMM fails
because of "HIS". If CHARMM fails because it doesn't like any
amino-acids then I don't know how I can use the program. But still I'd
like to use it because I have to.
Thanks,
Fred.
--
MedC
At some stage I ran PRODRG, introduced the cif file in the file
components.cif used by LigPlot (LigPlus). I also replaced the coordinate
files by those returned by the PRODRG run. Always with the same cryptic
error message provided by the software (oops, app).
Thanks,
Fred.
--
MedChem, 1st
wish to produce figures for a presentation or for
publication.
Ta,
Fred.
--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic
To unsubscribe from the CCP4BB list, click the following link:
https
be the cause of the problems with the current crystals etc but who
cares? It may be that (for example) a small molecule inserts itself in
the right place to give you the desired result.
Worth trying.
HTH,
Fred.
--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic
files for each component separately
merge these into global parameter and topology files for the system
run initial Energy Minimization
run M.D. simulations
analize the trajectories of the small molecules.
Thanks in advance.
Fred.
--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec
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,
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
*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
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
executable and it runs,
no questions asked...
Thank you,
Fred.
To unsubscribe from the CCP4BB list, click the following link:
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,
although it is present on my system)
Thank you for the prompt responses.
Fred.
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
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
of contacts between layers
in the crystal. Is it something that has already been observed in other
crystals?
Best regards,
Fred
-
Frédéric Kerff
Chercheur qualifié F.R.S.-FNRS
Cristallographie des protéines
Centre d'Ingénierie des Protéines
Université de Liège
17, Allée du 6 Août - Bat B5a
4000
Thanks for all the replies and sorry for rerun of a thread. I however have two
additional questions:
- Why is the pdb still available without any obvious sign of the fraud?
- Why is the paper stil available ?
Fred
-
Frédéric Kerff
Chercheur qualifié F.R.S.-FNRS
Cristallographie des
.
Closing date for this post is Tuesday 15 January.
Additional information and full details about the application process can be
found at https://jobs.york.ac.uk/
Please don't hesitate to contact me directly for further information.
Fred Antson / YSBL
help.
Fred
-
Frédéric Kerff
Chercheur qualifié F.R.S.-FNRS
Cristallographie des protéines
Centre d'Ingénierie des Protéines
Université de Liège
17, Allée du 6 Août - Bat B5a
4000 Liège (Belgium)
Tel.: +32 (0)4 3663620
Fax: +32 (0)4 3663772
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
Two Wellcome Trust funded postdoctoral positions are available at York
Structural Biology Laboratory, to work with Dr Fred Antson. Both posts are
available for 3 years, with potential to extend for a further 2-years.
One project focuses on investigating protein-nucleic acid interactions within
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
another discussion but, is there any reason for differences
in the transformation efficiency between the parental and the mutated
(cleaned) plasmids?
All the Best,
Fred
Em 03-02-2012 16:14, Fred escreveu:
Hi CCP4 list,
Thanks everyone who have answered my post concerning to mutagenesis.
From quick
. Is there anything else I can try?
Any help is appreciated!
Regards.
Fred
P.S.: Agilent's e-mail support is not working.
P.P.S.: this might not be of other's interest, address the answers,
please, to my e-mail only.
) Purify your PCR product before transformation if possible or use 3 of
4 microL of it. This is more or less the amount of DNA showed in the
uploaded image.
Kind regards,
Fred
P.S.: I'll let you know the results.
don't know which program else has these capabilities. So the
steps described here in are not of general application, but has solved
my problem.
Best wishes and Marry Xmas,
Fred
vectors inside a cell and give it rotation properties.
However, Xfit seems to be frozen and integration with pdbset would be
painful.
Regards,
Fred
Em 14-12-2011 07:32, Tim Gruene escreveu:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Fred,
this sentence of yours, All pdb's are superposed
also will be part of the tetramer interface. I'll try to
make things work.
Once more, sorry for any inconvenience and thank you very much.
Kind regards,
Fred
to
be at a certain distance of the molecule. This sounds conceptually
simple, but I would like to do that in batch mode for hundreds of PDB's.
Could someone, please, tell me the easiest way/program to do that?
Thanks in advance,
Fred
into the
cell and give it the 4-fold propriety. Quite simple, but don't which
program to use.
Regards,
Fred
Em 12-12-2011 18:23, Tim Gruene escreveu:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello Fred,
if you know the rotation matrix, you can use pdbset with its 'rotate'
keyword.
It is not clear
nor the rotation matrix. I would like to create them
but don't know how and which program to use. Theoretically a have to create
a axis (vector) at some distance of the molecule into the cell and give it
the 4-fold propriety. Quite simple, but don't which program to use.
Regards,
Fred
Em 12-12-2011
of the origin, pass a vector/axis through it and take the 3 others
molecules by symmetry. That's trivial, given the point, the orientation
and the property of the rotation. Don't know which program to use.
Regards,
Fred
Em 12-12-2011 19:18, James Stroud escreveu:
This is not trivial. Assuming
. That's trivial, given the point, the orientation and the property
of the rotation. Don't know which program to use.
Regards,
Fred
Em 12-12-2011 19:18, James Stroud escreveu:
This is not trivial. Assuming an arbitrary origin, the simplest 4-fold
symmetry operation (4-fold rotation) has 5 free
envelop does
have a 4-fold axis.
I appreciate if you could add some more comments on this.
Thanks in advance,
Fred
On Wed, 28 Jul 2010 15:31:45 -0300
Fredccp4bb.l...@gmail.com wrote:
Dear CCP4bb,
Could someone please, point me to some references about non-symmetric
tetramers? If I
with 222 symmetry does not
have 4-fold symmetry. There are 3 mutually perpendicular 2-fold axes
that intersect at the origin (of the particle, of the molecule) [and
for the nomenclature, these axes are named the P Q and R axes].
Fred.
Fred wrote:
Thanks all of you who promptly replied my question
at the origin (of the particle, of the
molecule) [and
for the nomenclature, these axes are named the P Q and R
axes].
Fred.
Fred wrote:
Thanks all of you who promptly replied my question.
I should have been more precise. I was referring to the
symmetry
(of the particle, of the
molecule) [and
for the nomenclature, these axes are named the P Q and R
axes].
Fred.
Fred wrote:
Thanks all of you who promptly replied my question.
I should have been more precise. I was referring
!! NSD = 1.270
egp5S208-1r.pdb !! NSD = 0.710
Em 29-07-2010 13:11, Kushol Gupta escreveu:
Fred,
Two cents - I think the P1 SAXS solution should strongly guide your choice
of symmetry constraint above all else in this case: do any of the
symmetry
Dear CCP4bb,
Could someone please, point me to some references about non-symmetric
tetramers? If I have a tetramer composed by 4 identical subunits, it'll
always have a P4 point group symmetry?
Thank in advance,
Tomb
the same problem before, which I solved just
increasing urea from 6M to 8M. Now, I have reached GndHCl 6M and no
binding at all.
I'm currently running a SDS-PAGE with samples eluted from Talon and let
you know the results.
All the Best,
Fred
--- Fred /ccp4bb.l...@gmail.com/ schrieb
Just to let you know. No way, Talon also don't work. I am gonna try the
GE His-trap column.
Fred wrote:
Hi everyone,
Thanks for answer my question. Just to add some more notes regarding
to my expression system. The insert-vector (pET28) has been sequenced
and the his-tag is N-terminal
is appreciated.
Fred
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
On Mon, 5 Mar 2007, James Irving wrote:
Hi Fred,
From memory, this can occur due to long bond lengths in the model being
interpreted as chain breaks, try editing the generate.inp or
generate_easy.inp script and increase the value for break_cutoff:
{* cutoff distance in Angstroms
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
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