Dear Anandhi,
you might be interested in PMID: 29752562.
BW,
Oliviero
On 09.11.2018 01:30, Anandhi Anandan wrote:
Hello everyone,
I am trying to solve the structure of a protein with a bound ligand at
2.65 A resolution. XDS was used for data reduction, phaser-MR for
molecular replacement a
Hi,
The "B factors" reflect the rapidity of the decrease in intensity of
scattering with increasing resolution. The scattering of a crystal
becomes unmeasurable at a lower resolution if its intensities drop
faster. This results in a connection between the resolution of a data
set and the aver
Hello everyone,
I am trying to solve the structure of a protein with a bound ligand at 2.65 A
resolution. XDS was used for data reduction, phaser-MR for molecular
replacement and Phenix for refinement. The refinement was done with the
default settings ( individual B factors, occupancy and TLS
Dear Frank,
pdb_redo webserver does. However you have to cheat to provoke it: The
resolution remark in the PDB has to be 0.10A beyond what it was used
before. You can use also use the command line version of pdb-redo to
tweak settings for your calculation (the expert option).
However it woul
On Thursday, 8 November, 2018, 3:56:39 PM GMT, Pavel Afonine
wrote:
Perhaps
phenix.pdbtools model.pdb rotate=... translate=...
which should work with any PDB or mmCIF file.
I couldn't figure out what angles goes as input for "rotate=" and "translate="
option of the phenix.pdbtools.
Does any refinement software automatically do the CC* resolution
exploration ("paired refinement") that Kay did in the original paper?
Now that /would/ be fantastically useful.
On 08/11/2018 12:44, Pavel Afonine wrote:
Clément,
I'm guessing this is because it isn't clear what CCwork/CCfree c
Hi,
I am studying how HIV-1 Protease Inhibitors were developed so rapidly,
3-5 years vs. normal 10-15 years, enabling the HAART Drug Therapy to be
introduced in 1996? Can you suggest articles or contacts on how
/_cryocrystallography_/ (with synchrotrons) accelerated the first HIV
Protease
Perhaps
phenix.pdbtools model.pdb rotate=... translate=...
which should work with any PDB or mmCIF file.
Pavel
On Thu, Nov 8, 2018 at 11:36 PM Tim Gruene wrote:
> Dear Kaushik,
>
> you could try moleman2 from the Uppsala Software Factory,
> http://xray.bmc.uu.se/usf/moleman2_man.html - maybe
Dear Colleagues,
We would like to draw your attention to the workshop "Cryo-EM in
Industry & Academia", that we are organizing at EMBL Heidelberg, 6-8
February 2019. The workshop will focus on success stories and new
technologies, but also on challenges industry is facing using cryo-EM.
The w
Dear Kaushik,
you could try moleman2 from the Uppsala Software Factory,
http://xray.bmc.uu.se/usf/moleman2_man.html - maybe it keeps those cards
in the PDB file.
Best,
Tim
On 11/8/18 4:23 PM, KAUSHIK H.S. wrote:
> Hello,
>
> I want to transform (rotate+translate) structures determined by NMR.
Hello,
I want to transform (rotate+translate) structures determined by NMR. I tried
using pdbset from the commandline. The program seems to remove "MODEL" and
"TER" lines from the coordinate file. Is there a way to make pdbset retain
these lines? or am I missing something obvious?
I could spl
Clément,
I'm guessing this is because it isn't clear what CCwork/CCfree can tell you
that Rwork/Rfree can not. Needless to say we all more or less have a good
idea about what the ok values for Rwork, Rfree and Rfree-Rwork (as function
of resolution) while it is much less clear (to me at least) when
Hi Clement,
Refmac actually does write out CCwork and CCfree out in its log files, so you
can already check to see whether this you can use these metrics as you propose.
We use these values in PDB-REDO to do paired refinement. IMO this is a better
way of finding a high-resolution cut-off than g
Hi all,
This probably have already be discussed, but can't find trace of it :
Is there any reason I am not aware of that refinement software (thinking of
both phenix and refmac) do not output CC work / free ?
We all accepted CC 1/2 for resolution cut (whether it's 30 or 10 %) which
tend to lead to
Dear All
Registrations are now open for the Instruct Biennial Structural Biology
Conference to take place in Alcalá de Henares (near Madrid) 22-24 of May 2019.
Confirmed speakers includes: Sjors Scheres, Julia Mahamid, Eva Pereiro, Andrej
Sali, Teresa Carlomagno, Alex de Marco, Dave Stuart an
15 matches
Mail list logo
