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
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
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
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
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
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
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.
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
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
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
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
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
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
I second autoSHARP/SHARP. It makes great initial maps, and once you get it
running, it is totally worth it.
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,
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
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
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
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
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