Kendall is absolutely correct..
Faisal
On 3/30/11, Kendall Nettles wrote:
> There is a paper from John Kuriyan on co-expressing a phosphatase with c-Src
> kinase domain to enable bacterial expression of homogenous protein (
> PMID:
> 16260764). Also look at work from E. Goldsmith (PMID: 16829129
Yes, but this is not how you do it. I assume you have a stereo image to start
with generated from (eg) pymol. and you are trying to float the labels at the
same "z" as specific
atoms or objects. It is simple. Place the two labels for the two images at
the same y value (y up, x across in my n
Thanks.
We have this type of stereo glasses. It is good for watching the figures on
paper, but very difficult to adjust the figures' labels on computer screen.
On Wed, Mar 30, 2011 at 10:29 PM, Bosch, Juergen wrote:
> Watch out, this is an advertisement !
> http://hamptonresearch.com/product_det
Watch out, this is an advertisement !
http://hamptonresearch.com/product_detail.aspx?cid=26&sid=145&pid=439
Jürgen
On Mar 30, 2011, at 10:24 PM, Jiamu Du wrote:
For side by side stereo figures.
Thanks.
On Wed, Mar 30, 2011 at 9:42 PM, Ingrid Attinost
mailto:ingrid_attin...@hotmail.com>> wrote:
http://hamptonresearch.com/product_detail.aspx?cid=26&sid=145&pid=439
These work pretty well and are cheap.
Bert
On 3/30/11 10:24 PM, "Jiamu Du" wrote:
For side by side stereo figures.
Thanks.
On Wed, Mar 30, 2011 at 9:42 PM, Ingrid Attinost
wrote:
Dear Jiamu,
What kind of stereo are you
For side by side stereo figures.
Thanks.
On Wed, Mar 30, 2011 at 9:42 PM, Ingrid Attinost <
ingrid_attin...@hotmail.com> wrote:
> Dear Jiamu,
>
>
> What kind of stereo are you refering to? Do you mean anaglyph stereo (like
> the kind of stereo used nowadays when watching 3D movines at the theate
Hi Xiaopeng, and those who are using the new interruptible "fit_protein..."
or "stepped_refine..." in wincoot 0.6.1:
I just took a look at wincoot 0.6.1's fitting.py file
(WinCoot\share\coot\python\fitting.py). It seems that in the old
"fit_protein()" and "stepped_refine_protein()" functions,
Dear All,
I want to buy a stereo glasses for making stereo figures, especially for the
labeling. Is there a company sell it?
Thanks and best wishes.
Dear all,
I have two fold NCS in ASU. I could find phase by molecular replacement,
but I have to build other chains by myself, since the model is not complete.
During model building in coot, I built one chain in one NCS, and I merged
this chain into the previous molecule. Now it is the "chain M'.
We don't have a problem getting them to stick to the plates in
serum-free media, or in 5% FBS media. The more challenging part is
getting the plating density just right, too low and the plaques are
too big, to high and they are too small. Or if the cells dry out, or
if your agarose overlay is too
Mark,
alternative conformations and associated with them occupancies are to
describe the larger scale disorder (the one that goes beyond the B-factor's
capability to cope with).
Multi-model PDB files is another option.
Best,
Pavel.
On Wed, Mar 30, 2011 at 2:15 PM, VAN RAAIJ , MARK JOHAN <
mjvanra
yet, apart from (and additionally to) modelling two conformations of the
side-chain, the B-factor is the only tool we have (now).
Quoting Pavel Afonine:
> Hi Quyen,
>
>
> (...) And if B-factor is an estimate of thermo-motion (or static disorder),
>> then would it not be reasonable to accept th
Hi Guys,
we are learning to work with Sf9 cells and Carol in my lab wanted me to ask
you the following question. Many thanks for any help, G
I need to titer a baculovirus stock in my suspension-adapted Sf9 cells. I
know that these can be encouraged to attach better to tissue culture plastic
if
On Wednesday, March 30, 2011 11:04:30 am James Holton wrote:
> perhaps a better name for the "disordered side chain problem" would be
> "dark density"? This name would place it properly amongst "dark
> matter", "dark energy" and other fudge factors introduced to try and
> explain why our "stand
Hi Quyen,
(...) And if B-factor is an estimate of thermo-motion (or static disorder),
> then would it not be reasonable to accept that building the side-chain and
> let B-factor sky rocket might reflect reality more so than not building it?
>
NO. Your B-factors are valid within a harmonic (sma
I completely agree, although if the IUCr or PDB decides otherwise, I'd be happy
to oblige.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.
Standardization is great! That is why the way we describe positions,
occupancy, and B factors has already been standardized. The core of this
discussion is that some people want to use these parameters to describe
details other than position, occupancy and motion. Since all the parameters
on A
I don't have strong preference either way, but if one has good density
for backbone and no density for a corresponding side-chain, would it
be reasonable to believe that the side-chain might actually exists and
that it has no visible density at a certain contour level might be
because it wa
How about a converter between the two "file formats"? Perhaps something
like this:
if(occ==1 && B < 30) print;
-James Holton
MAD Scientist
On 3/30/2011 11:30 AM, Mark J van Raaij wrote:
perhaps then there should be 2 pdb files for each structure:
- a "users" pdb containing "correct" models b
I'm amazed at the pedestal people put their precious coordinates on --
isn't the first thing you learn about MX that our models are rubbish
parametrizations of the actual content of the crystal? And thus they
will remain as long as we have the R-factor gap, and no amount of
coordinate-sigmas
perhaps then there should be 2 pdb files for each structure:
- a "users" pdb containing "correct" models but tailored for easy use by
non-crystallographers
- a "depository" pdb containing the "best" model the crystallographers can (or
has bothered to) come up with, of course conforming to certain
I'm afraid this is not a problem that can be solved by "standardization".
Fundamentally, if you are a scientist who has collected some data (be it
diffraction spot intensities, cell counts, or substrate concentration vs
time), and you have built a "model" to explain that data (be it a
constel
On Wednesday, March 30, 2011 08:29:11 am Phoebe Rice wrote:
> I've now polled 4 fairly savvy "end users" of crystal structures and there
> seems to be a consensus:
>
> - they all know what B is and how to look for regions of high B
> (with, say, pymol) and they know not to make firm conclusions
Hello Mark,
I absolutely agree with this. The worst thing is when everybody is
following their own personal rules, and there are no major guidelines for
end-users to figure out how to interpret those parts. I assume there are no
absolute guidelines simply because there isn't any consensus among
What about setting both the occupancy to 0 *and* setting the b-factors
to some special arbitrary number, say, 500? Then people would pick up
easily on the side chains being dubious, and the refinement would not
be affected by them.
Jacob
On Wed, Mar 30, 2011 at 10:29 AM, Phoebe Rice wrote:
> I
perhaps the IUCr and/or PDB (Gerard K?) should issue some guidelines along
these lines?
And oblige us all to follow them?
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91
I've now polled 4 fairly savvy "end users" of crystal structures and there
seems to be a consensus:
- they all know what B is and how to look for regions of high B (with, say,
pymol) and they know not to make firm conclusions about H-bonds to flaming red
side chains.
- None of them would ever t
I agree there are probably much better and simpler ways of doing this.
But to answer the question, you could probably use MrBUMP to do this, using the
local PDB file option. It will require a bit of scripting to deal with all the
file names, and will take forever.
Other points:
1) you don't nee
Dear CCP4 members,
The deadline for this position has been extended until the 15th April and the
first round of interviews will now be held on the 17th May in Lund, Sweden.
Please note that the position is permanent with the organisation rather than a
short term contract. Further general inform
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