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
lecule 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
at few Angstrons of the protein.
Em 12-12-2011 19:01, Jacob Keller escreveu:
How do you know where to put the axis?
JPK
On Mon, Dec 12, 2011 at 2:34 PM, Fred wrote:
Hi Tim,
Thanks for your message and sorry if I wasn't clear. I don't have neither
the axis orientation nor the rotat
y distance
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:
I only want to produce an artificial tetramer.
Em 12-12-2011 19:41, Jacob Keller escreveu:
Can you clarify your reason for doing this?
JPK
On Mon, Dec 12, 2011 at 3:36 PM, Fred wrote:
Hi James,
In my first post "arbitrary orientation into the cell" only means not
paral
uence
region, which 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
trace 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
it and apply the desired symmetry. However, unless
XFIT, I 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
tension time up to 9
min. 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.
7;t
want start 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 mutagene
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
ental 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
Fred wrote:
Dear CCP4bb,
Could someone please, point me to some references about non-symmetric
tetramers? If I have a tet
uprising, a particle 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
ee mutually perpendicular twofolds than a fourfold (e.g.
the favorite classic hemoglobin has no fourfold anywhere).
And there is no fundamental reason that a tetramer has to
have any particular symmetry.
Phoebe
Original message
Date: Thu, 29 Jul 2010 13:04:02 -0300
From: Fred
So, that was my previous question.
Em 29-07-2010 14:14, Phoebe Rice escreveu:
You don't have to keep the same number of symmetrical
contacts.
Original message
Date: Thu, 29 Jul 2010 14:13:56 -0300
From: Fred
Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round
To: C
07-1r.pdb !! NSD = 1.213
egp5S214-1r.pdb !! 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 symme
ny help is appreciated.
Fred
enced 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 // schrieb am *Di,
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
x) ? Just launch the executable and it runs,
no questions asked...
Thank you,
Fred.
To unsubscribe from the CCP4BB list, click the following link:
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Desmond - their installation is simple and they 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 t
*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
s 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, clic
Thanks 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
ology 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, V
file format. Contains h, k, l, Fobs, Sigma F etc
dsn6 is a map file (density, such as electron density, Patterson density).
Hence you cannot convert between the two.
You use the mtz file to compute a map, then use mapman from Uppsala to
convert the map to a dsn6 file.
Fred.
--
Fred. Vellieux, es
(no harm meant there, this is not targetted
at anyone).
Please note that I have also posted to cnsbb in order to get more replies.
Help is really needed since I do not know why I get these extra OXT atoms
introduced in the model.
Please read on further:
Date: Mon, 5 Mar 2007 13:34:54 +0100 (CET
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":
&
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 reas
e
true phases. Since F's are phased quantities and since phases are more
important than amplitudes, non random amplitudes plus non random phases
(both from map inversion of averaged maps) lead to better electron density
maps.
Fred.
--
Fred. Vellieux, esq.
===
guarantee at this stage
that there will be a publication however!
Thank you all in advance,
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) 438785494
=
gt; phaser.out << EOI
MODE MR_AUTO
HKLIN rescut.mtz
LABIN F = FP SIGF = SIGFP
PACK 6
ENSEMBLE TET1 PDBFILE trimer.pdb IDENTITY 0.221
COMPOSITION PROTEIN MW 168960 NUM 2
SEARCH ENSEMBLE TET1 NUM 1 ROOT phaser_trimer
SOLU 6DIM ENSE TET1 EULER 327.076 56.322 181. FRAC 0.12840 -0.
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
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,
found at the cmake stage,
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&A=1
ce 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 - Ba
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
Hi,
To make it short:
If you want a computer you wish to bring home so that you can do plenty of
things (i.e. not crystallography-related in addition to crystallography):
Windows because you can edit videos easily, or play games, or (I don't)
because there is plenty of (free) software available.
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
> N
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
An alternative:
vi my_pdb.pdb (carriage return)
:%s/HETATM/ATOM /g (carriage return)
:wq! (carriage return, or ZZ i.e. shift zz)
This does the trick. Simple operations like this can be done easily with
an editor. I don't know Windows editors (because I don't use Windows).
F.
> Dear all
>
> Is
Wow, an email from the future !
[Sorry...]
> Subject: [ccp4bb] diagram of dsDNA
> From: "cuisheng2007"
> 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
> dsDNA/Protein
> complex,
Hi all,
The question is in the Subject line of this email: which version of Coot
should I download and install on a Scientific Linux 6.3 box ?
Ta very much in advance,
F.V.
--
F.M.D. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
38027 Grenoble Cedex 01
France
Tel: +33 438789605
your 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
.
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
uld 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, Czec
f you 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:
awings ?
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.
--
Med
-terminus: 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.
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
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
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
m.edu/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
rest
idea 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,
igurations)? 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:
http
Linux. 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 yo
nd saved).
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
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/
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
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
#x27;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:
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