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
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
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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
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?
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
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
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 ?
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
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The Photon Sciences Directorate at Brookhaven National Laboratory is seeking an
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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
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
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
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
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 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
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
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
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
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).
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