Hi Grant,
This is part of the recurring side chain discussion. There is no consensus in
the community about what the optimal approach is.
In your current approach you are adding a model parameter (occupancy) to
improve the fit with the experimental data (remove negative difference
density). You
Hi Grant,
sounds like you did the right thing (as far as I can guess given the amount
of information you provided).
In a nutshell, both, B-factors and occupancies, model disorder. The
difference is that occupancies model larger scale disorder (such as
distinct conformations) than B-factors (smear
Hello all,
I'm currently working on a structure which if I stub a certain side chain
phenix/coot shows me a large green blob which looks strikingly similar to the
side chain, when I put it in and run another refinement the blob turns red.
Basically I was just playing around and I changed the oc
Hi All,
I am running the latest ccp4 ( auto-updated using the new autoupdate tool
built into ccp4i)
I was running what should be a routine scalepack to mtz conversion and I
got an error which I have never seen before with ctruncate.
When I run the same job with old truncate it succeeds.
Any id
Hi Petr,
Thanks for noting this - yes it has existed for a while, sad to say.
(I was using the standard space group name to convert between clipper
symmetry and mmdb symmetry - that was a mistake - I should have been
using the Extended Hermann–Mauguin symbols).
Fixed in r4489.
Paul.
On 19
To add another datapoint, a couple of weeks ago, I saw a friend's
MacBook Pro (probably 2007) had a battery case open up just like that.
My 17-inch MacBook Pro (2008) case is also bent in a million different
ways, and I have already had to change the bottom case once (for $130,
and at no labor
Hi Andre,
There is set of plasmids allowing coexpression in yeast
they are described in the following article
Constructionand characterization of bidirectional expression
vectors in Saccharomyces cerevisiae
Aimin Li1,2, Zengshan Liu1, Qianxue Li2, Lu Yu1, Dacheng Wang2 & Xuming Deng
1,2
in FE
Hi,
We have been thinking of implementing recombinant protein expression in S.
cerevisiae in our lab, and I would like to ask if there is a choice of vector
designed for co-expression of any two intracellular binding partners, similarly
to the pETduet-1 vector for E. coli.
If you feel this is no
On 19/11/12 11:12, Jenny Harmer wrote:
Thank you for the information. They are only coordination bonds between the
atoms, which I wouldn't personally class as a physical bond.
I am also using WinCoot which does not have the option for Make Link under the
Modelling tab in Extensions. Is this a
On 19/11/12 13:13, Petr Leiman wrote:
Dear Developers of Coot,
I believe that coot has never been able to display the crystallographic
symmetry of a R32:H shelxl .res file. As a result, water picking does not work
properly for such a file. Everything else seems to work fine. This is not a
hug
Beamline Scientist Position for Macromolecular Crystallography Beamlines at
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The Photon Sciences Directorate at Brookhaven National Laboratory is seeking an
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Dear George,
Thank you very much for your continuing development of the shelx suite. A lot
of users (yours truly included) are happy to continue using .res files in coot.
It's just the "stupid" R32/H32 spacegroup that causes coot to misbehave a
little. And I am simply very surprised of why this
On 11/18/12 20:48, 王瑞 wrote:
> OK,thank you all of you. I have installed one copy of HKL2000 on our
> desktop computer. But for my notebook's low 1366*768 resolution, the
> HKL2000 can't work ! So what could I do to resolve it ?
>
http://www.pcworld.com/article/261763/samsung_shows_off_series_9_lap
shelxl-2012 does include the space group in a way that Coot understands
when it writes a .pdb file. This version is in the final beta-testing
stage with a lot of new features (mainly for small molecules) and no
known bugs, so I hope to release it soon. If anyone would like to try it
now please
Dear Developers of Coot,
I believe that coot has never been able to display the crystallographic
symmetry of a R32:H shelxl .res file. As a result, water picking does not work
properly for such a file. Everything else seems to work fine. This is not a
huge problem, but it would be nice to be ab
Thank you for the information. They are only coordination bonds between the
atoms, which I wouldn't personally class as a physical bond.
I am also using WinCoot which does not have the option for Make Link under the
Modelling tab in Extensions. Is this a function of the Linux version?
On 19/11/12 10:32, Jenny Harmer wrote:
I would like to add CONECT records to my pdb file to indicate interactions
between protein side chains and a co-factor (all of the related proteins
contain them).
I don't think CONECT records are the canonical method to specify such a
think (if you mean
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Dear Rex,
which monomer do you refer to? LBT.cif loaded by coot looks very
similar to LACTOS03 in the CSD, doesn't it?
Regards,
Tim
On 11/19/2012 11:22 AM, Rex Palmer wrote:
> Does anyone know why the ligand alpha lactose in COOT has at least
> on
Dear Acoot,
There is a paper by Monika Budayova-Spano
(http://scripts.iucr.org/cgi-bin/paper?fw5105) on using temperature as a
crystallisation variable that also has a number of useful references.
HTH,
Esko
_
Esko Oksanen, PhD
Instrument Scientist - Neutron Macromol
I would like to add CONECT records to my pdb file to indicate interactions
between protein side chains and a co-factor (all of the related proteins
contain them). I am using Coot to refine the structure but have access to other
programs. Is there a program to introduce these records into the pdb
On 18 Nov 2012, at 00:28, William G. Scott wrote:
> I'm trying to get a sense for how frequently this sort of thing occurs:
In recent months we had two of the early MacBook Airs that suffered from the
same problem with the case bulging alarmingly. We've also had a mid-2007
MacBook Pro battery
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Dear Rui Wang,
the window size of the main HKL2000 window is indeed fixed. One
relatively simple workaround is to use a virtual screen size,
provided you use X11. Check your /etc/X11/xorg.conf and add an
entry, say, 'Virtual 1400 1024' in the Displ
Dear Acoot,
In the website of the company Centeo, you can find the slides of a short
presentation I had given three years ago on temperature and macromolecular
crystalllisation. You may find some info there:
http://www.centeo.com/_fileupload/Temperature%20Control%20in%20PXTL.pdf
There is a lot
Does anyone know why the ligand alpha lactose in COOT has at least one sugar
ring that is not fully symmetrical. The CCDC deposited alpha lactose molecule
has both rings perfectly symmetrical chairs.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead
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