Dear all,
we have to "update" our dryshippers.
There are two models we are consifering: the CX100 from Tayler Wharton
or the MVE SC4/2. Has anybody experience with the dryshipper from MVE?
Thanks a lot in adavance for any insights!
Best wishes, Guenter
Dear all,
taking AlphaFold models for " true" experimental structures seems to
become a serious problem.
I am just returning from a meeting (not a structural biology meeting)
and saw one model after other. And the non-structural biologist used
terms like "we calculated a structure" or "a
for handling as
usual? If you don't have a working N2 gas stream and are on a budget they are
not that hard to build:
https://doi.org/10.1107/S0021889894006357
Cheers,
-James Holton
MAD Scientist
On 1/26/2022 9:25 AM, Guenter Fritz wrote:
Dear Dom,
thanks a lot. Yes, this might work
they are
not that hard to build:
https://doi.org/10.1107/S0021889894006357
Cheers,
-James Holton
MAD Scientist
On 1/26/2022 9:25 AM, Guenter Fritz wrote:
Dear Dom,
thanks a lot. Yes, this might work sending a combipuck alongside with
a good bottle for the local contact.
I was wondering whether the grippers can
/2022 9:25 AM, Guenter Fritz wrote:
Dear Dom,
thanks a lot. Yes, this might work sending a combipuck alongside with
a good bottle for the local contact.
I was wondering whether the grippers can handle a block of propane?
Best wishes,
guenter
Dear Guenter,
Would the use of vials inside combi
/product/combipuck-system/) and some
arrangements with your local contact at the other end, perhaps help
with using propane remotely?
BW,
D
On 26/01/2022 16:53, Guenter Fritz wrote:
Dear all,
we have some delicate crystals which might benefit from freezing in
propane. In former times (when I
Dear all,
we have some delicate crystals which might benefit from freezing in
propane. In former times (when I was still travelling to the beamlines)
we waited until the propane was solid in the vial and then let the
propane thaw in the cryo stream at the beamline.
But how can we do this
, Guenter Fritz wrote:
Dear all,
with ccp4 update 7.1.016 pyrogen was updated from pyrogen-0.0-pre
revision 10365 to pyrogen-0.0-pre revision 10625. I saw that the
--MMFF (usage of Merck forcefield) option is now missing.
Yes, it's the default now (i.e. without mogul).
I get restraints from
Dear all,
with ccp4 update 7.1.016 pyrogen was updated from pyrogen-0.0-pre
revision 10365 to pyrogen-0.0-pre revision 10625. I saw that the --MMFF
(usage of Merck forcefield) option is now missing.
I get restraints from the latest version of pyrogen, which do not work
in refmac. I added a
,
Manfred
Am 14.09.2021 um 14:36 schrieb Guenter Fritz:
Dear all,
does somebody know whom to contact for the software DSX or fconv of
the former group Klebe in Marburg?
Many thanks and best regards,
Guenter
To unsubscribe
Dear all,
does somebody know whom to contact for the software DSX or fconv of the
former group Klebe in Marburg?
Many thanks and best regards,
Guenter
To unsubscribe from the CCP4BB list, click the following link:
Dear all, dear Ian,
I am trying to run edstats from command line. I have read the previous
threads here and I was using the edstats.pl perl script. However I fail.
Here is what I type and what I get (same on a centos machine and my mac).
$ edstats.pl -hklin paefs_018_dimple_refmac.mtz
Dear Antony,
similar to the approach Eleanor has described, lsqman will give you
rotational matrix and translation vector.
http://xray.bmc.uu.se/usf/lsqman_man.html
Best regards, Guenter
Hi,
You can try elNemo server.
Regards,
Nasrin
PhD scholar
On Wed, Jul 8, 2020, 10:16 PM Antony
Dear Artem,
I am a fan of the former "Superformance" column from Merck. The
production / selling of these columns is sourced out to a small company
called Goetec. The columns are not really cheap, but good quality, last
forever, suited also for higher pressures, only glas and Teflon in
Dear all,
I was going through the options in dimple. Is it possible to skip the
checking of the space group by pointless?
Thanks in advance and best regards,
Guenter
To unsubscribe from the CCP4BB list, click the
On behalf of Huib Ovaa (h.o...@lumc.nl):
We are looking for postdoc candidates with a background in protein
chemistry/ structural biology.
There are two projects: One project on MHC-T-cell interactions, and
diagnostics/ immunotherapy using novel sets of protein reagents that we
are
Dear Chris, are there any metal ions in your buffer or in your protein.
We had a similar looking case. A Zn2+ ion bridged two monomers. Our
protein is a Zn2+ binding protein. The Zn2+ originated from some
denatured protein in the drop. No extra Zn2+ was in the crystallization
buffer.
ne."
https://www.imdb.com/title/tt0584455/characters/nm0921942
- Cosmic Cats approve of this message
On Mon, Oct 21, 2019 at 10:00 AM Guenter Fritz
<mailto:guenter.fritz.phenix.c...@gmail.com>> wrote:
Dear all,
I want to put one of our microscopes into the glove box. Does
Dear all,
I want to put one of our microscopes into the glove box. Does anybody
know whether some parts of the microscope optics do not like vacuum in
the air lock ?
Thanks and best regards, Guenter
To unsubscribe
arc-requ...@jiscmail.ac.uk
<mailto:270165b9f4cf-dmarc-requ...@jiscmail.ac.uk>> wrote:
A classic case of this is crambin. Residue 25 of 3nir.
-James Holton
MAD Scientist
On 6/24/2019 1:00 AM, Guenter Fritz wrote:
Dear all,
I am refining a multimer and mass spec data of the sam
Dear all,
I am refining a multimer and mass spec data of the sample indicate that
there is a mixture of two variants which differ in one amino acid
residue. The density that we see is therefore most likely an average of
both variants. I have created a pdb file with "alternate residues" each
Dear Adarsh,
just an add-on to the instructions of the others. Since GNOME is not
anymore compatible with stereo, we use successfully Xubuntu (18.04) with
NVIDIA drivers.
Best , Guenter
Hello everyone
We have just purchased a Dell workstation for crystallography data analysis. We
were
Dear Refmac developers,
I am trying to reproduce some successful refmac runs but cannot get the
previous results despite playing around with the parameters.
I did those runs in Feb 2014 (Refmac 5.8.0049) but unfortunately have
overwritten the log files in a backup. I still have the pdbs, mtz
Dear Deepali,
the best way to define the resolution cut-off is to check whether the
data still contribute to model quality. You can easily check that by the
procedure called "paired refinement" as described by Diederichs and
Karplus (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457925/
should be send to guenter.fr...@uni-hohenheim.de.
Please contact me for any further information.
Best regards,
Guenter Fritz
Dear Vito,
for SeMet have a look here:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Expression_of_SeMet_labeled_proteins
Worked like a charm for E.coli and also for other expression hosts
with minor modifications
Dear Stefan,
just saw this after reading post:
http://www.nature.com/nature/journal/v522/n7557/full/nature14559.html
Best, Guenter
Pramod,
You already got good suggestions on how to handle DNA contamination in protein
preparations.
Let me point out briefly that you haven't demonstrated yet
Dear all,
I want to have a closer look at a conformational change in a multidomain
protein. We see clear changes from different structures but there is
evidence that the conformational changes might be larger than observed.
My idea is to get the transformation matrix of each residue (or of
Hi Stephen,
we crystallized several proteins in a glove box placed in a room with
air condition. We checked the temperature all the times and found that
is had been quite stable.
For one protein that crystallized only at 4 deg C, we setup the
crystallization plate within the glove box and
Hi,
I am using CCP4 on Sci Linux machines and running now into some trouble
with update manager and our firewall.
I connect through a proxy and defined the proxy in the ccp4-setup.sh.
Running update-manager gives me an error message; a new window pops up
telling me Downloaded data is corrupt,
Hi Monica,
what is the reducing agent the protein gets the electron from?
Or is it simply unspecific oxidation of protein side chains?
Do you know what are the coordinating residues of Fe3+ / Fe2+ ?
Dependent on the coordination Fe3+ has some (often very weak) d-d
transitions (400-500 nm)
Dear colleagues,
can somebody give me a hint, whether the program AQUARIUS2 or a similar
/ successor program is available somewhere?
Thanks a lot in advance!
Best regards, Guenter
) was a replacement.
Regards,
Tim
On 11/07/2014 06:47 PM, Guenter Fritz wrote:
Dear colleagues,
can somebody give me a hint, whether the program AQUARIUS2 or a similar
/ successor program is available somewhere?
Thanks a lot in advance!
Best regards, Guenter
Dear Avinash,
you can use Ellman's reagent (DTNB) for GSH.
Have a look here:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Thiols_and_disulfides
For glutathione you don't have to use a buffer with GuHCl.
HTH, Guenter
Dear All,
Greetings and apology for an off topic query. may
Hi,
if one is hesitant to compile it it, pymol is easily installed on a
Linux box via yum ;
enable EPEL repo ( in Redhat derivatives e.g. fedora, Centos, SciLinux)
yum install pymol will install version 1.6 (latest version by
Schrödinger is 1.7)
Best, Guenter
Hi,
I have inquired at
Dear Sun,
I had a similar problem. If you have a good TaBr dataset this should
give you good phases.
You can combine the TaBr phases and Molrepl phases in SHARP.
What worked in my hands very well and is easy to do: SAD using Phaser
and the partial Mol Repl Model.
You find here a input file
Dear all,
and especially all of you involved in the development of refinement
programs,
in low resolution refinement we always include structural information we
actually do not see in the electron density (side chains, riding
hydrogens) since we know that these atoms are there. But what about
board [CCP4BB@JISCMAIL.AC.UK] de la part de Guenter Fritz
[guenter.fr...@uni-konstanz.de]
Date d'envoi : samedi 2 novembre 2013 16:04
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Conserved water positions in low resolution refinement?
Dear all,
and especially all of you involved in the development
Dear all,
one gets different R values, if you re-read in the mtz written out by
refmac after TLS refinement. I think this issue had been a while ago in
ccp4bb, but I can't find the right track.
Here are the details.
1st run:
If we do TLS + restr. refinement in refmac
we get:
Initial
Am 17.07.2013 11:59, schrieb Guenter Fritz:
Hi Stefan and Gottfried,
thanks a lot for the answers. This is the point. Wouldn't it make more
sense to add an extra column that contains the changed Fs?
Best, Guenter
Hi,
it is strongly advised to use the original mtz e.g. scala.mtz
Hi Jan,
you will find some methods for detection of thiols and/or disulfides there:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Thiols_and_disulfides
HTH,
Guenter
Dear all,
I am working on a protein where I have to stabilize the closed
conformation of the protein using
Hi,
have a look into the supplement of the paper by Poul Nissen pointed out.
There are some shell scripts exactly for that purpose.
I had to adapt the scripts a bit, but the instructions are very well to
follow.
HTH
Guenter
Hi Pete
Thanks for the reply.
As for the transformation, I was
On the technical feasibility of storage of original data:
Sure, running Pilatus for an olympic record, we will go home with several T of
data after 24 h (will we?).
Yes, we do already. I just checked the number of images from PILATUS 6M
we have collected so far this year : ca. 1.7 millions.
Dear Zhong Chen and CCP4 users,
I get the very same error on a Centos 5 box. Is there a solution yet?
Best regards,
Guenter
Dear all,
Recently, I used MOLREP to molecular replacement.
My OS is fedora 14 and CCP4 version is the newest one ccp4-6.2.0 .
When I run a pdb file and mtz by MOLREP
Sorry,
I should have had a look also at the CCP4 site:
updated version of molrep from Aug 8.
http://www.ccp4.ac.uk/updates/linux/ccp4-6.2.0/bin/
Cheers
Guenter
Dear Zhong Chen and CCP4 users,
I get the very same error on a Centos 5 box. Is there a solution yet?
Best regards,
Guenter
Dear all,
Dear Padmaja,
I have use Samsung 2233RZ for stereo running on Linux and Windows
systems. Perfomance is great.
HTH
Guenter
Pardon the off-topic query, but I would like to get some feedback
about any personal preference for 3D LCD monitors. I am trying to
decide between the following 3
: fairman@gmail.commailto:fairman@gmail.com
james.fair...@nih.govmailto:james.fair...@nih.gov
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
e-mail: guenter.fr...@uni-konstanz.de
e
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
e-mail: guenter.fr...@uni-konstanz.de
e-mail: guenter.fr...@uniklinik-freiburg.de
http://www.uniklinik-freiburg.de/neuropathologie/live/forschung/ag-g-fritz.html
Tel.: +49 761 270
. Don't really know if that is the problem.
Laurie Betts
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
e-mail: guenter.fr...@uni-konstanz.de
e-mail: guenter.fr...@uniklinik-freiburg.de
http
better data.
A.
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
e-mail: guenter.fr...@uni-konstanz.de
e-mail: guenter.fr...@uniklinik-freiburg.de
http://www.uniklinik-freiburg.de
Sandy,
like mentioned previously, sounds like FeS.
record an optical spectrum. Or even better, check whether there is
somebody on the campus running an EPR machine (equipped for helium
temperature measurements)
Maybe a new FeS protein? FeS is not necessarily required as redox
cofactor. It
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Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
Universitaetsstrasse
reducing agents? Your answers and help in this regard will
be highly appreciated.
Thanks,
Jan
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
in the very beginning.
I want to assign ss to my pdb file in DSSP, but I could not find a
server to run it. Does anybody know a webserver where I could run this
kind of tasks? I use iMAC.
Many thanks!
Jane
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
- mtz is still readable.
I would be glad for any help or advice.
Thanks.
Sergii
P.S. Please, find attached mtz and logs.
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de
, at 09:24, Guenter Fritz wrote:
Hi,
I was looking recently for weak anomalous scatterers, when refined
model is known.
I used phaser as described here:
http://www.phenix-online.org/pipermail/phenixbb/2008-July/001136.html
or running phaser from the ccp4 gui SAD with molecular replacement
partial
/
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
Universitaetsstrasse 10
Postfach M665
D-78457 Konstanz
e-mail: guenter.fr...@uni-konstanz.de
Phone Office: +49-(0)7531 88 3205
Hi Xuan,
I guess your protein is not an E.coli protein. There are several
examples that eukaryotic Zn-proteins expressed in E.coli contain Fe
instead of Zn. I am sceptic whether IMAC with different metal ions will
give the solution of the problem. If you really want to get information
on the
-955-3655
http://web.me.com/bosch_lab/
--
***
Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
Universitaetsstrasse 10
Postfach M665
D-78457 Konstanz
e-mail: guenter.fr...@uni-konstanz.de
Tel.: +49-(0)7531 88 3687
Fax
fold stays intact after removal of one helix.
HTH
Guenter
I would appreciate your opinion
All the best
Francisco J. Enguita
ITQB
Oeiras
Portugal
--
***
PD Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http
Hi,
a follow up question: Which supplier offer Ta6Br12?
Thanks,
Guenter
My post-doc recently produced a splendid (for its resolution)
~5A map of a medium sized protein-DNA complex using Ta6Br12
clusters. And he's got a good toehold on a ~340kDa complex
using the same clusters. So I'm recently
Hi Peter,
you can do that with interhlx:
http://nmr.uhnres.utoronto.ca/ikura/resources/data+sw/interhlx/
There is also a way to determine the interhelical angle with molmol,
http://hugin.ethz.ch/wuthrich/software/molmol/
defining cylinders for the helices.
HTH
Guenter
Hi all
I would be
Dear all,
I wanted to use COOT to add a few residues to a the N-term, just simple
fantasy building. It should be straight forward with the
add-terminal-residue command, however COOT insists on a e-density map.
Any idea to overcome this?
Thanks in advance,
Guenter
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
Universitaetsstrasse 10
Postfach M665
D-78457 Konstanz
e-mail: guenter.fr...@uni-konstanz.de
Tel. Office: +49-(0)7531 88 3205
Tel. Lab : +49
Microbiologiques JM Wiame -IRMW
Av E. Gryzon 1, 1070 Brussels (Belgium)
tél: +32 (0)2 5273634
fax: +32 (0)2 5267273
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
Dear all,
I have installed precompiled ccp4 61 (Redhat from download manager) on Centos5
box, X86_64.
Running ccp4i gives:
[guen...@hypatia ~]$ ccp4i
Top level CCP4 directory is /usr/local/software/CCP4/61/ccp4-6.1.0
Using CCP4 programs from /usr/local/software/CCP4/61/ccp4-6.1.0/bin
Error in
several concerns, one is the autooxidisability of FAD, how fast
FADH2 would be reoxidized by O2 in the air or by the O2 dissolved in
solution. The second cocern is how fast the FAD reaction will go.
Please advise.
Thank you!
Mike
--
***
Priv.Doz.Dr. Guenter
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [EMAIL PROTECTED]
***
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***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Message-
From: CCP4 bulletin board on behalf of Guenter Fritz
Sent: Fri 9/26/2008 3:21 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] losing zinc during crystallization
Hi Sue,
I fully agree with Thierry, you might have to cyrstallize the protein
under exclusion of dioxygen
Hi Sue,
I fully agree with Thierry, you might have to cyrstallize the protein
under exclusion of dioxygen. There are many metallo proteins which have
to be crystallized that way. But a first attempt might be the TCEP as
already suggested by many others. If you need advice regarding
Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
***
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***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http
]
***
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
Universitaetsstrasse 10
Postfach M665
D-78457 Konstanz
e-mail: [EMAIL PROTECTED]
Tel. Office: +49-(0)7531 88 3205
Tel
mutations to make it foldable.Any input would be useful.
Thanks a lot.
Jenny
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
Universitaetsstrasse 10
Postfach M665
D
A mild and quick method is to use dry Sephadex G-25. The material will
swell and take up all the liquid except molecules larger than ca. 5 kDa.
Dear All,
we have GCSF protein produced in inclusion bodies. we solubilise it refold
it and then concentrate it using proflux system. still the
Hi,
if a compound is not in the hic-up data base of the USF
(http://xray.bmc.uu.se/hicup/)
I usually go to NCBI Pubchem database (TCEP e.g. at
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=119411loc=ec_rcs)
, download the sdf file, feed it into a programm that can read it and
put
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***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
Universitaetsstrasse 10
Postfach M665
D-78457 Konstanz
e-mail: [EMAIL PROTECTED
of insights would be very valuable.
thanks,
Neeraj
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
Universitaetsstrasse 10
Postfach M665
D-78457 Konstanz
e-mail: [EMAIL
decreased by 7 deg C.
Godd luck,
Guenter
I am already playing with lowering and/or doing away with the antibiotics.
Any suggestions wrt 18C? The protein is insoluble at 30C.
Thanks.
Raji
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion
.
--
***
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
Universitaetsstrasse 10
Postfach M665
D-78457 Konstanz
e-mail: [EMAIL PROTECTED]
Tel. Office: +49-(0)7531 88 3205
Tel. Lab : +49-(0)7531 88 3687
Fax: +49
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