Dear all,
I have a couple of questions regarding deposition of a structure
with a posttranslational modification.
1. I understand, that PCMs (protein chemical modifications) and PTMs
are now handled in a standard way, but what is the standard way? Is
there a link giving insight into these rul
on Cooper.
jon.b.coo...@protonmail.com
Sent with Proton Mail [1] secure email.
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 colu
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 validati
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, 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 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 mai
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 def
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 it
Dear all,
the University of Greifswald is currently seeking to appoint a full
professor (m/f) of biochemistry (Biochemie III). You can find the
official advertisement at
University-Homepage:
https://www.uni-greifswald.de/universitaet/information/stellenausschreibungen/professuren/stellenausschre
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 be
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 differe
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
phospha
Dear all,
our previous Rigaku X-ray diffractometer is being offered by the
VEBEG (auctions of used stuff from federal institutions in Germany)
for the highest bid. It is only in German, but open to all bidders.
https://www.vebeg.de/de/verkauf/suchen.htm?DO_SUCHE=1&SUCH_MATGRUPPE=1170&SHOW_AUS
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 (STFC,RAL,SC
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 meanw
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 Afonin
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
forme
Eleanor
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 trans
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.
Gr
Theme - 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 re
Dear all,
I have problems reading some of the text in coot.
Example situation: I open the Ramachandran Dynarama. The I hover with
the mouse over one of the dots for a residue. A small box appears, but
the text is white on very light grey background. Most of the time
impossible to read. I beli
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
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