Hello all,
I have several questions regarding sugar modeling. These are questions for
both Coot (0.9.4-pre/CCPEM) and Phenix (1.18.2-3874) usage (on a Mac) for
modeling as correctly as possible several N-linked glycosylation (i.e. not
ligand) sugars within a protein, and about the approach as it
Hi All,
We have been noticing lately that our crystal pucks return from different
beamlines coated with the same powdery material. For the record, we
typically undo our pucks, clean the assemblies and dry out the
pucks within a day of receiving the shipping dewar, but notice the same
thing regardl
Lei,
The DeGrado lab developed a tool that would do just what you seek to do and
could function as a PyMOL plugin. I played with it a few years ago after I
found an interesting cation-pi sandwhich in my structure. I e-mailed then
with the author, hoping to link the tool to the entire current PDB
i
The Ollmann Saphire laboratory at La Jolla Institute for Immunology (LJI)
is seeking a technician to work as a part of our team. We are focused on
infectious diseases and immune response in general, viral pathogens that
cause hemorrhagic fever in particular. The lab has a solid core of
structural b
Could it be a member of a coiled coil at some point in its lifetime, as a
part of its function in regulating position or activity of this receptor?
Does the helix have sequence similarity to other coiled coils? see
https://www.uniprot.org/help/coiled for a primer on the topic.
Looks fun!
Emily.
Shijun,
I have processed .h5 format data successfully that was collected at NSLS II
AMX (this beamline has a Eiger 9M, not 16M, incidentally, but I don't think
that this matters). I used XDSGUI without converting to .cbf format. To do
so, and without knowing what the error messages are that you ar
I assume that somehow the two subunits are distinguishable despite their
forming a "homodimer." Otherwise I don't know how you would know that it is
always the same subunit that contains the water molecule. If they are truly
distinguishable, then, the first thing that's come to mind is the
possibil
Hello Randy,
I'm chiming in about the last sentence in your reply:
> Finally, I would suspect that getting a significantly lower LLG for two
> copies of a dimer means that the dimer in your structure is slightly
> different from the dimer in the model.
>
Will you please be more specific about w
I had previously considered to relocate, at least temporarily. But now a
part of me wants to stay and fight for what we (as scientists) have managed
to achieve.
On Nov 9, 2016 12:45 AM, "Tom Peat" wrote:
> I don't know about Europe, but it is very tight Down Under...
>
>
> -Original Message-
e level used in Coot will be lower - and thus seem to be noisier
(perhaps). I suppose that if you want comparable levels from the same
map/mtz file then you should use absolute levels, not rmsd. ***What does
PyMOL's "1.0" mean in electrons/A^3?***
Regards,
Paul."
Regards,
Emily
1/2 Coot's rmsd level)
whether I used the CCP4 map downloaded from the EDS, or generated from the
structure factors with phenix.
Thanks All.
Emily.
> Dale Tronrud
>
> On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote:
> > Hello. I am struggling with an old question--old be
Hello.
I am struggling with an old question--old because I've found several
discussions and wiki bits on this topic, e.g. on the PyMOL mailing list (
http://sourceforge.net/p/pymol/mailman/message/26496806/ and
http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the suggestions
about how to
> Dear All,
>
>
>
> I have a question that is a little bit related to the previous discussion
about crystallisation of a minority fraction monomers. I wonder if there is
a review of some sort (or anything in principle) that would discuss role of
dimerization (or more broadly oligomerization) in pro
As I'm sure you've also found, it's not simple to find one [easily
accessible] program that examines and reports every type of
interaction that might be of interest to you. So I'm sending in a
reference to another web-based tool that I've found complementary to
PISA and the others mentioned here. I
Tianyu,
My suggestion is to determine the molar absorption coefficient empirically
using the Edelhoch method (
http://www.rpgroup.caltech.edu/courses/PBL/bootcamp_June07/pdf/articles/Edelhoch1967.pdf).
This involves measuring the absorbance at 280nm of your native and your
unfolded protein (a nice
Artem,
> In addition to other answers, one of the more esoteric (but surprisingly
> effective) ways to destroy the protein 'skin' on drops is to add a tiny bit
> of Trypsin solution.
>
Will you go a bit further and say what exactly you mean by "a tiny bit of
Trypsin solution"? :-) What is the c
this
type of analysis? ...or are the fits really that different (and maybe green
versus red is not as big as the visual cue would have me assume)?
Emily.
On Thu, Feb 19, 2015 at 11:00 AM, Emilia C. Arturo (Emily) wrote:
> Hello all.
> I'd like to understand what it is I'm
Hello all.
I'd like to understand what it is I'm looking at when I use Coot's density
fit analysis tool. I recognize that there was a post related to this
topic on the Coot bb a while ago --the discussion was on how to interpret
the red-ness or green-ness of the density fit plot (
https://www.mail-
>
> On Mon, Jan 26, 2015 at 8:22 PM, Monica Mittal
> wrote:
>
>> Hi everyone,
>>
>> I need an advice on some strange thing happening to one of the protein i
>> am working on. I used to purify it and set up trays and get some needle
>> shaped crystals and trying seeding and other methods to optimis
If the residues are consecutively numbered (Calculate > Renumber residues),
and are assigned the same chain ID (Calculate > Change Chain ID), Coot
might surprise you and link them on its own.
On Wed, Jan 14, 2015 at 9:39 AM, Zhijie Li wrote:
> Have you done it?
> 1) Click “add residue...”
> 2)
When my daughter was in Kindergarten, her class took a trip to our
facility, and I showed them some of my crystal trays ("What do you see
here? Do you see anything?" "Clear drops ...", they effectively said).
Then I showed them through the microscope several crystals, and I was
pleasantly surprise
Hay,
> Indeed, we also incline to think of it as a monomer in solution,
>
It is in fact possible that different solution conditions favor different
oligomeric assemblies. For example, perhaps your protein, which in one set
of solution conditions prefers the monomer, prefers some other assembly
u
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