Dear Rohit Kumar Singh,
you can remove a couple of residues before and after the outlier and
rebuild it. You can also switch on Ramachandran restraints in Coot and
run real-space refinement. If this does not help, I would delete a
single residue within the region in question, run real-space refine
Hello all,
if outlier is in between 5 to 6 %, how someone can fix it.
As the resolution is low (3.0-3.5 A).
On Mon, Jan 12, 2015 at 7:53 PM, Robbie P. Joosten wrote:
> Hi Dialing,
>
> 86% favoured can actually be quite okay for an initial model. As long as
> it doesn't have 14% in the disallowe
Hello Bing,
It is possible to do it with the software version 5.01, but I guess that it
should be available on all version.
Under the Evaluation software, open your result file. In the menu "file" go
down to export, select the curve that you want to export and save it. It is an
asci file that y
Hi all,
Sorry for this off topic! I need you guys to help me to export the x/y value
from AKTA UNICORN since I want to redraw it in EXCEL. Is it possible? How to do?
Also I don't need and like the software which can extract the data from the
images or pdf files, because it is not precise.
Than
>at the beginning of my experience of S-SAD about 10 years ago, it was not too
>difficult to do S-SAD phasing with inhouse data provided the resolution was
>better than 2.0A, while it did not always work with synchrotron data. Purely
>personal experience.
I assume that the synchrotron data were
Hi Jacob,
at the beginning of my experience of S-SAD about 10 years ago, it was
not too difficult to do S-SAD phasing with inhouse data provided the
resolution was better than 2.0A, while it did not always work with
synchrotron data. Purely personal experience.
However, the inhouse machines I am
>the top-hat profile is one of the reasons why inhouse machines produce better
>quality data than synchrotrons. However, the often much increased resolution
>you achieve at the synchrotron is generally worth more than the quality of the
>data at restricted resolution.
>
>Cheers,
>Tim
Several su
Hi all,
To follow up on my question from last week, Dr. Emsley's work-around worked
great for me. Increase map sampling in coot, export, and then proceed in
pymol without using the map_double command. I end up with gigantic map file
sizes (~160MB), and it's more work to make all my maps this way,
While most (all?) CCP4 programs use the MMDB library for reading
PDB files, handling of incorrect PDBs is not consistent.
Default settings in MMDB (and in clipper) are strict, but most of the
programs use a combination of options that make it more liberal (SetFlag()).
Marcin
On Mon, Jan 12, 2015
Yes, you can provide your own bulk solvent model as a "partial
structure" to REFMAC.
http://www.ysbl.york.ac.uk/~garib/refmac/docs/keywords/xray-principal.html#labin_fparti_phiparti
http://www.ysbl.york.ac.uk/~garib/refmac/docs/keywords/xray-general.html#scpa
http://www.ysbl.york.ac.uk/~garib/ref
We are huge fans of the Retsch Planetary Ball Mill grinder. Grinds yeast cells
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-Mary Munson
UMass Medical Schoo
The Bead Beater has a 15, 40, and 350 mL chambers. I haven't used mine
to homogenize yeast, but I suspect it is similar in performance to E.
coli disruption. (Different bead sizes are used for yeast than
bacteria.) We get excellent, gentle disruption of E. coli in 8 minutes
total. A French Pres
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Hi Jan,
Privateer relies on Clipper-minimol, which in turn uses MMDB. According to
MMDB's error code description list (
https://www.ebi.ac.uk/pdbe/docs/cldoc/object/cl_obj_irets.html) :
Error_WrongEntryID 3 A PDB or mmCIF record that ought to display
this entry's ID, shows an ID contradic
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..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street,
Dear all,
I am experiencing some troubles with running Privateer. It seems to fail
to read a PDB file. The Error message:
Reading xxx.pdb... MMDBfile: read_file error: xxx.pdb :3
terminate called after throwing an instance of 'clipper::Message_fatal'
Aborted
Any ideas?
Best regards,
Jan
Dear All,
I am looking for an equipment that can do *Saccharomyces cerevisiae* cells
lysis (say about 100-200ml lysate volume). I have used the Constant Systems
cell disruptor TS 0.75kW model (at another facility) that can go up to
40kpsi. It works perfect for my yeast cell lysis experiment. We
Dear Bernhard,
further thinking about the Babinet scaling effects, I have to correct my
conclusion in the last sentence:
On 12.01.2015 14:21, Dirk Kostrewa wrote:
If, however, the unmodelled part is less well ordered (which is the
more common case), it's contribution will mainly affect the mo
Hi Dialing,
86% favoured can actually be quite okay for an initial model. As long as
it doesn't have 14% in the disallowed region, the vast majority of
residues will be correct, or close enough to the correct answer that
they can be fixed easily. Of course, such a model will need tweaking,
bu
Dear Bernhard,
I think, the main difference of an unmodelled part between the mask bulk
solvent correction and the Babinet bulk solvent correction is, that the
mask approach can use quite detailed structural information, whereas the
Babinet approach uses only two additional scale factors. Let'
Dear All，
If an initial PDB has only 86% residues in the Ramachandran favored region, it
would mean there is a significant error (for example significant length of
protein fragment in the total protein assigned to the wrong electron density
map position) , right?
Dialing
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On 12 Jan 2015, at 10:09, Bernhard Rupp
mailto:b...@ruppweb.org>> wrote:
What still evades me is, why exactly is the Babinet immune to these effects of
excluding/masking-out unmodelled parts?
The Babinet correction is also a function of the MODELLED part, just the
opposite sign. So an incomplet
What still evades me is, why exactly is the Babinet immune to these effects of
excluding/masking-out unmodelled parts?
The Babinet correction is also a function of the MODELLED part, just the
opposite sign. So an incomplete model
de facto equals an over-estimated solvent. Is it just the high e
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