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On Friday, 9 February 2024 at 17:54, Palm, Gottfried wrote:
Dear all,
I have problems preparing my experimental data (XRD) for
deposition. I have two mtz files, which work well for refmac5, with an
FREER column in one
Dear all,
I have problems preparing my experimental data (XRD) for
deposition. I have two mtz files, which work well for refmac5, with an
FREER column in one file and Iplus, SIGIplus, Iminus, SIGIminus
columns in the second file. I merged them into one mtz file with cad
(in ccp4i).
The
Dear all, specifically refmac developers,
I have an unexpected observation, when refining alternate main
chain conformations for residues 22 and following in refmac.
Residue 21 has one conformation, residues 22-25 have two
conformations. There are four chains.
I have coordinates with PRO 21,
Dear all,
I have a modelling problem, which probably has something to do with
the solvent mask.
There is a positive density blob at the surface of my protein, which I
can more or less satisfy with a Hepe (EPE). Hepes is in the buffer,
the sulfonic acid H-bonds to a lysine side chain and a
Dear all,
I have a modelling problem, which probably has something to do with
the solvent mask.
There is a positive density blob at the surface of my protein, which I
can more or less satisfy with a Hepe (EPE). Hepes is in the buffer,
the sulfonic acid H-bonds to a lysine side chain and a
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
Dear all,
I have a few questions handling (non) anomalous data:
By default aimless seems to produce Iplus and Iminus columns. Can I
force it to (also) create an Imean column?
What does refmac do, when it gets Iplus and Iminus (and their sigmas)
as input. Does it take only one of them or does
, applications of
female scientists are particularly welcome.
The deadline for the application is June 24, 2022.
Best regards,
Gottfried
Dr. Gottfried Palm
Synthetische und Strukturelle Biochemie
Institut für Biochemie
Universität Greifswald
Felix-Hausdorff-Straße 4, D-17489 Greifswald
Tel.: 03834 420
Check the electron density (O, Cl, I ?) and the anomalous signal on
your "iodine".
Cysteine has an interesting chemistry and one is oxidation to the
sulfenic acid, CSO, already mentioned. Probably, it is more common
than we tend to expect and may be overlooked, because we don't look
for it and
Dear all,
I don't think, there is much to add to the statement of Bernhard or
James that different protomers in the asymmetric unit (must) have some
difference in there contacts and therefore often in their
conformation. What it doesn't answer is a chicken or the egg question:
do the
Dear Yang Meiting,
I have not solved protein - DNA complexes, but I have seen many
protein densities with more or less ligand bound. When the ligand has
a carboxylate group but doesn't bind tight enough, often an acetate or
sulfate groups binds instead. Depending on how clear you see the
before.
Greetings
Gottfried
Gottfried Palm
Synthetic and Structural Biochemistry
Institute for Biochemistry
University of Greifswald
Felix-Hausdorff-Str. 4
17489 Greifswald
Germany
To unsubscribe from the CCP4BB list, click
Thanks Tim and Oleg for suggestions.
The legacy version works and should be sufficient for my purpose.
Maybe there could be a link or hint in the chapter "Old AMD
processors" to avoid unnecessary questions.
Greetings
Gottfried
On Thursday, 10-12-2020 at 12:46 Kovalevskiy, Oleg
Dear all,
I am running into a "known issue" upon installing ccp4-7.1 on a
pre2010 AMD machine. The download page says
CCP4 7.1: Known issues
...
Old AMD processors
...
We are in the process of preparing an alternative release package for
those processors.
Is there a solution in the
Hi Christian,
couldn't you simply change the position in a text editor after
changing chain IDs in coot? Atom IDs should renumber after reading and
writing in coot, but conversion to cif will probably ignore the atom
IDs anyway.
Greetings
Gottfried
On Monday, 07-12-2020 at 19:19 Pavel
Dear all,
the tenor seems to be, if you see the ligand in any of the
monomers, that's the mode the ligand binds. We have seen other cases,
though, too.
Usually the protein I am thinking of (TetR(D)) crystallizes with one
molecules /a.u. In solution it is an obligate dimer. The dimer is
On Tue, 7 Jul 2020 at 17:16, Palm, Gottfried wrote:
For occasions like Laus, it would be useful to further on have access
to the
CCP4 v7.0 Program Documentation,
even if the programs are not updated as Christian explained.
I was for instance looking for translating coordinates a
For occasions like Laus, it would be useful to further on have
access to the
CCP4 v7.0 Program Documentation,
even if the programs are not updated as Christian explained.
I was for instance looking for translating coordinates as in pdbset,
but couldn't find a replacement in the ccp4i2 gui.
- Look And Feel from
default "openSUSE" to "Breeze Dark". This results in white text on
gray background.
Thanks again
Gottfried
On Thursday, 26-03-2020 at 17:53 Paul Emsley wrote:
On 26/03/2020 16:46, Palm, Gottfried wrote:
I have problems read
believe it is not a problem from coot, rather
from some other setting somewhere, but I don't know where. Can I get a
hint, what to change /set?
Thanks
Gottfried
Gottfried Palm
Universität Greifswald,Institut für Biochemie
Felix-Hausdorff-Straße 4
D-17489 Greifswald
The situation might not be so rare, if you consider 50% Lys and
50% Acetyl-Lys or other post-translational modifications.
Gottfried
On Wednesday, 06-02-2019 at 18:05 Diana Tomchick wrote:
If you have the odd case where one residue (of the same number in the
polypeptide chain) is a Leu and the
problem: The
format of the images has also changed and the new .img files (from the
Saturn92 detector) are not read anymore (whereas they used to be
processable in xds before).
Greetings
Gottfried
Dr. Gottfried Palm
Ernst-Moritz-Arndt-UniversitÀt
Inst. für Biochemie (MNF)
Abt. Biochemie I
of the images has also changed and the new .img files (from the
Saturn92 detector) are not read anymore (whereas they used to be
processable in xds before).
Greetings
Gottfried
Dr. Gottfried Palm
Ernst-Moritz-Arndt-Universität
Inst. für Biochemie (MNF)
Abt. Biochemie I
Felix-Hausdorff-Straße 4
has also changed and the new .img files (from the
Saturn92 detector) are not read anymore (whereas they used to be
processable in xds before).
Greetings
Gottfried
Dr. Gottfried Palm
Ernst-Moritz-Arndt-Universität
Inst. für Biochemie (MNF)
Abt. Biochemie I
Felix-Hausdorff-Straße 4
17489 Greifswald
-greifswald.de).
See also our homepage (http://www.chemie.uni-greifswald.de/~biochem/)
for information on the group and research.
Posting in behalf of Prof. Hinrichs,
good luck Gottfried Palm
Dear all,
I am getting protein crystals in clusters. How can I achieve isolated
crystals.
Thanks
Amit Sharma
As Roger writes One way to separate crystal cluster is to poke them
with a tiny probe. We are often using acupuncture needles as easy
to get and cheap microtools which have very low
Dear Vin
why don't you try glycerol with a carboxylate group, i.e. 2-hydroxymethyl-
3-hydroxy-propanoic acid, change the oxygens to carbons or vice versa
according to the possible hydrogen bonds and then check if you can
make sense out of the resulting molecule.
greetings
Gottfried
Dear Mohd,
to plot the B-factors, I would read the pdb file in Excel (or similar).
Take care that 5.45 is read as a number and not as a string, which
happens at least in German versions because of the . instead of the
German,.
Specify the decimal separator.
The sort by Atmon name to get all
homepage (http:
//www.chemie.uni-greifswald.de/~biochem/).
Posting in behalf of Prof. Hinrichs,
good luck Gottfried Palm
===
WEB-Mailer der Uni-Greifswald ( http://www.uni-greifswald.de/ )
===
Hi all,
another reason to get low readings from the UV meter can be a drift
in the baseline. The photometer is properly calibrated only when
you turn it on, I think. Since we have our machine running in the
coldroom without (usually) turning it off for month, we have observed
wrong 260/280
Dear All,
In the group of Winfried Hinrichs a postdoctoral position/staff scientist
is available in Greifswald/Germany for initially 3 years.
The position involves research and teaching. Knowledge in German
is not mandatory but might be helpful.
You may test your skills with the official
We have a recombinant secreted glycoprotein produced in a mammalian
culture system; the native protein has 12 cysteines which form 6
intramolecular disulfide bonds. We have introduced a new cysteine
residue at a surface position, with the intention of targeting this
residue for an in vitro
([EMAIL PROTECTED]
greifswald.de) before end of September.
See also our homepage (http://www.chemie.uni-greifswald.de/~biochem/endex.
htm) or http://www.rigaku.com/protein/sotm-002.html for an example
of current equipment and research in the lab.
Dr. Gottfried Palm
Ernst-Moritz-Arndt-Universität
a local analytic company.
greetings
Gottfried
Dr. Gottfried Palm
Ernst-Moritz-Arndt-Universität
Inst. für Biochemie (MNF)
Abt. Biochemie I
Felix-Hausdorff-Straße 4
17489 Greifswald
Tel. +49(03834)-864393 Fax. +49(03834)-864373
email [EMAIL PROTECTED
I would like to expand on the question and answer below and compare
your experiences: Looking for ligands in many different soaks / cocrystals
of your protein of interest, you still should do molecular replacement
and a bit of refinement. I agree with Steve, but how much refinement
is
What is the easiest way, these days, to calculate the buried surface
area
between two subunits of a protein?
Thanks, and Happy Friday, Gloria
The PISA server from EBI does a nice job: fast overview, but also
details if necessary.
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
greetings
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