As part of the recent Midsummer Make-over of the Protein Data Bank in Europe (PDBe) website, we acquired the domain name pdbe.org and have used it to implement...
1963
Abdul S. Ethayathulla
asethaya@...
Aug 10, 2010 9:48 am
hi I am refining a protein/DNA complex. I have 4 dimers. I want to define one dimer as a NCS unit. I have labelled each molecule in the dimer with different...
1964
Gerard DVD Kleywegt
gerard@...
Aug 12, 2010 9:44 am
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) offers a number of educational resources as part of its wider mandate for outreach and training within...
1965
Rongjin Guan
ziweiguan
Aug 16, 2010 3:05 pm
Dear CNS users, I am refining a 3.1 A structure (from Molecular Replacement) with CNS 1.3, and after rigid-body and annealing, I wanted to do group B...
1966
Ed Pozharski
pozharski
Aug 16, 2010 4:20 pm
Grouped B-factor refinement doesn't work well because it is unrestrained in nature and allows for discontinuites in B-factors of covalently bonded atoms. Just...
1967
Axel Brunger
brunger@...
Aug 16, 2010 4:40 pm
Actually, group B-factor refinement now also includes restraints when using the new "refine.inp" task file in v1.3. I suggest you try various values for the...
1968
r
ramme29
Aug 18, 2010 6:58 am
Hi I do have heterocomplex in the structure and wants to do ncs constrain for individual complex. For example, I do have complex A (segid a) and B (segid b). I...
1969
Gerard DVD Kleywegt
gerard@...
Aug 18, 2010 5:51 pm
There are three more vacancies coming up at the Protein Data Bank in Europe (PDBe; pdbe.org): - Head of PDBe Deposition and Annotation ...
1970
Gerard DVD Kleywegt
gerard@...
Aug 18, 2010 8:30 pm
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is pleased to announce the availability of PISA assembly files, summaries and associated XML ...
1971
Gerard DVD Kleywegt
gerard@...
Sep 17, 2010 3:50 pm
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is pleased to announce the "Structure Integration with Function, Taxonomy and Sequence" (SIFTS)...
1972
evavanamee
Oct 13, 2010 6:37 pm
It is great that the new CNS is now using the PDB format for DNA but it would be even better if it could read its on old DNA coordinates and convert them to...
1973
Axel Brunger
brunger@...
Oct 13, 2010 8:03 pm
Eva, You need to follow the new PDB convention for distinguishing between RNA and DNA residue names. There are both RNA and DNA residues now in the topology...
1974
Gerard DVD Kleywegt
gerard@...
Oct 14, 2010 5:10 pm
Following feedback from students, collaborators and other structural biologists, the Protein Data Bank in Europe (PDBe; pdbe.org) has become aware of a need...
1975
sncal53
Oct 16, 2010 8:26 am
I've got 3 merohedral twin operators for one of my crystals.When I try to do twin refinement in CNS giving twin operator,it only takes one operator instead of...
1976
Francois Berenger
berenger@...
Oct 22, 2010 8:28 am
Laboratory: Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, Japan. (Unit Leader: Dr. Kam Zhang) Job title and Job description: Postdoctoral...
1977
c.hider
Oct 22, 2010 8:28 am
In the enormous amounts of information written on CNS I have found various mentions of a graphical interface. I am very new to the program and am just trying...
1978
readerj14
Oct 22, 2010 8:28 am
Hi all, I have a structure at 2.65A that I'm in the process of refining. It's a complex that has ~1100 residues total, and what looks like a fair amount of...
1979
Nicolas Floquet
nicolas.floquet@...
Nov 9, 2010 12:59 pm
Dear CNS users, i would like to do NMR refinement of our molecules with CNS. These molecules are not peptides. I firts build topologies/parameters with CHARMM....
1980
tusweet
nwilliams1372
Nov 9, 2010 1:00 pm
I need help I am trying to install CNS 1.3 on my Intel Mac with OSX 10.5.8. I am getting an error of "limit: stacksize: Cant Remove Limit (Invalid Argument)"...
1981
Boaz Shaanan
boaz_shaanan
Nov 9, 2010 1:17 pm
Hi, Yes, there is an psf_to_mtf,inp file among the general input files. I assume that should work for you. Â Â Cheers, Â Â Â Â Â Â Â Â Boaz ... From:...
1982
Axel Brunger
brunger@...
Nov 9, 2010 4:19 pm
Please use the latest Intel compilers and the latest Max OS operating system (10.6.4). Alternatively, use the pre-compiled binaries that come with the CNS...
1983
Gerard DVD Kleywegt
gerard@...
Nov 11, 2010 5:53 pm
Hi all, We have two new openings at the Protein Data Bank in Europe (http://pdbe.org - part of the European Bioinformatics Institute in Cambridge, UK) to work...
1984
Debajyoti Dutta
debajyoti_dutta47@...
Nov 13, 2010 9:57 am
Hi all, I have downloaded all the stuffs to install CNS 1.3 for our lab. But unfortunately I cannot find the *.sh file to export cns_solve in bash shell. ...
1985
ijser.editor
Nov 15, 2010 8:21 am
International Journal of Scientific and Engineering Research (IJSER)(ISSN 2229-5518) The International Journal of Scientific & Engineering Research is an open...
1986
Ben Eisenbraun
bpeisenbraun
Nov 16, 2010 7:53 am
... Are you running as root? The cns_solve_env script has this line: limit stacksize unlimited On OS X there is a kernel hard limit on the maximum stacksize....
1987
Ed Pozharski
pozharski
Nov 16, 2010 2:30 pm
This is the old one which will probably work (you need to edit it to match your system). ... -- Edwin Pozharski, PhD, Assistant Professor University of...
1988
Venkataraman
vkabas
Nov 25, 2010 5:34 am
Hi all, This may be the repeated question?. I want to refine the ligand which is covalent attached to sg of cys. I tried the method mentioned earlier in cnsbb...
1989
simona.tomaselli
simona.tomas...
Nov 26, 2010 10:43 am
Hi all, I would like to know which are the differences between cns1.2 and XPLOR-NIH2.26 for NMR structure calculations. thanks simona...
1990
simona.tomaselli
simona.tomas...
Nov 30, 2010 11:58 am
dear all, i am calculating a NMR structure of a protein complexed with two small ligands. I am not able to keep the right conformation of the rings of my...
1991
Venkataraman
vkabas
Nov 30, 2010 12:53 pm
Hi I like to do rigid body refinement for the ligand molecule using CNS either 1.2/1.3. I did tried but it did not do well, it moved S atom far away. I used ...
