A postdoctoral position is available immediately to work on structures of
bacterial microcompartments and to pursue other projects involving protein
design and assembly. Bacterial microcompartments are poorly characterized
virus-sized protein shells that serve as organelles inside many bacterial
c
Hi Qing Lu,
try Autorickshaw: http://www.embl-hamburg.de/Auto-Rickshaw/
It can perform the complete structure solution procedure if the quality of
your data is sufficient and I consider it very user-friendly, especially
for beginners .
Regards,
Uli
> Hi All,
>
> I am new to protein crys
>The simplest explanation would be that those particular atoms are not in any
>TLS group, and therefore they have only an isotropic ADP component.
Unfortunately, the '0 0 0' for the anisotropic component in ANISOU record is
for all of my protein atoms.
>If that is not the case, please show the c
On Thursday 20 May 2010, Shiva Kumar wrote:
> Dear Crystallographers
>
> I am trying to print out my total B factors using TLSANL (version: 6.1) in
> CCP4- 6.1.1. My TLSANL’s input file.pdb is coming from refmac (version:
> 5.5.0072) using the TLS & restraint refinement option and isotropic B
Dear Crystallographers
I am trying to print out my total B factors using TLSANL (version: 6.1) in
CCP4- 6.1.1. My TLSANL’s input file.pdb is coming from refmac (version:
5.5.0072) using the TLS & restraint refinement option and isotropic B factors.
The TLSANL’s output file.pdb contains the f
http://www.ebi.ac.uk/chemblntd
And the related publication
Thousands of chemical starting points for antimalarial lead identification
http://www.nature.com/nature/journal/v465/n7296/pdf/nature09107.pdf
Good luck with the goldmine !
Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public H
I don't like the site finding option in autosharp, takes too long in most of my
cases.
So my approach is locate sites via SHELX, then feed them into Sharp.
Sorry Gerard :-)
Jürgen
On May 20, 2010, at 10:02 PM, Jeremiah Farelli wrote:
> I second autoSHARP/SHARP. It makes great initial maps, an
I second autoSHARP/SHARP. It makes great initial maps, and once you get it
running, it is totally worth it.
Hello,
If you have Phenix, try phenix.find_ncs (sorry for the non-CCP4 answer).
The example run in the PHENIX documentation is:
phenix.find_ncs anb.pdb mlt.mtz
This will then write out the NCS operators in various flavours.
Basically if you have a list of Se sites it calls RESOLVE, but ha
Dear all,Does anyone know if NCSFIND is still available or how I can get it. If not is there another program that I can use to determine noncrystallographic symmetry between Se-sites.Thanks in advance,Karin
I think this is somehow tortured, especially by a quick reading of
Dale's explanation.
All natural epimerases, isomerase and racemases use a mechanism based
on L-amino acids to deal with a mirror-symmetric (quasi-, sometimes)
reaction. In another word, these enzymes use a non-mirror symmet
Dear crystallographers,
For those of you who have shared personal frustration with cryoEM map
availability, or for those of you who would simply like to see science
proceed as it should, here's your opportunity to sign an on-line petitition.
Please feel free to send the link below to any of your
The Organizers of the workshop:
"Frontiers in Automated Crystal Handling and Visualization"
May 26-27, 2010
National Synchrotron Light Source, Brookhaven National Laboratorty
Hamilton Conference Room Bldg 555 Chemistry Department
would like to invite you to participate in this exciting works
What is a good resource for identifying what seem to be ions (Na+, Cl-,
CO3-, NH4-) and not simply water molecules in a crystal structure?
James W. Murphy, Ph.D.
Associate Research Scientist; Dept. of Pharmacology
Facility Manager; Macromolecular Crystallography Facility
Yale Uni
Dear Cathy/EMDATABANK team:
It is hard to comprehend the option for keeping maps on hold for up to 2
years. It seems any depositor would do this for pure selfish reasons: keep
the data to themselves, don't allow anybody to verify the data for a long
time, and have the exclusive right to do experi
A PhD studentship (3 years) is available at the Institut de Biologie
Structurale (http://www.ibs.fr) in Grenoble, France. The project is to
explore the structural dynamics of the medically important enzyme
acetylcholinesterase by a panoply of complementary biophysical methods,
including kinetic c
Dear Eleanor -
That is correct. The pseudo-sg is P6, and the structure has been
refined in this sg. The intensity difference between the strong and
weak subsets is quite significant that for most data sets, auto-
indexing routines will miss the weak spots and pick the pseudo-sg
instead.
sent on behalf of the EMDATABANK.org team:
The EM Databank (EMDB, http://www.emdatabank.org/) is a resource for the
archival deposition and retrieval of EM maps and associated metadata. It was
established in 2002 by the European Bioinformatics Institute (EMBL-EBI, UK),
and is now run jointly by
Dear Qing Lu,
Now that several suggestions, both ccp4 and non-ccp4, have been made,
may I suggest that you (also) try autoSHARP, available free of charge at
http://www.globalphasing.com/sharp/
It includes the invocation of SHELXD to solve the substructure, and takes
you
This looks a bit strange..
If you have a hexamer in the asymmetric unit, in P3, then that means
all symmetry copies lie in the same plane. To generate the Patterson
peak, 2/3,1/3,0 the hexamer must be centred at 1/3,1/3, z
(with symmetry equivalents 0,-1/3,z and -1/3,0,z )
I would expect y
pdbset xyzin mol1.pdb xyzout mol1-tran1.pdb
SHIFT frac x,y,z (where x,y,z is the patterson peak)
end
OR
pdbset xyzin mol1.pdb xyzout mol1-tran2.pdb
SHIFT frac -x,-y,-z (since -x,-y,-z is also a the patterson peak)
end
Nicolas Soler wrote:
Dear CCP4bbs,
I am dealing with a case involving pseu
Minor correction: SHELX software are not part of CCP4 but if you have
them installed as part of your crystallograhic software, you can call
them from the CCP4 GUI.
You can obtain the SHELX suite free to academic labs from Ggeorge
Sheldrickbe
Email George Sheldrick. George M. Sheldrick
Jürge
Crank is a good tool for doing this automatically. Follow the
instructions here:
http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Automated_experimental_phasing_with_Crank
Qing Lu wrote:
Hi All,
I am new to protein crystallography. I would like to know the steps
involved in solving a MAD da
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