Re: [ccp4bb] Negative electron Density for Zinc

2012-08-28 Thread Pavel Afonine
Hi Deepthi, 1) refine anisotropic ADPs for Zn, 2) make sure charge is accounted for, 3) refine f' and f'' for Zn (that means you need to use anomalous data in refinement). If 1-3 do not help, add 4) refine occupancy of Zn, 5) make sure you visualize your map using correct levels. This should so

Re: [ccp4bb] Negative electron Density for Zinc

2012-08-28 Thread Lijun Liu
Please correct me if I am wrong. If I am understanding correctly, your refinement was against the data of SAD which used a wavelength to collect anomalous dispersion. Such kind of data have anomalous source atoms collected at a lower "real" atomic struc

Re: [ccp4bb] Jelly body refinement?

2012-08-28 Thread Gunnar Schroeder
Just a quick comment on low resolution refinement: The concept of Deformable Elastic Network (DEN) refinement is quite similar to jelly-body refinement in the special case of gamma=0, for which the network is not deformable. In contrast to jelly-body refinement, the DEN restraints are however a

[ccp4bb] Negative electron Density for Zinc

2012-08-28 Thread Deepthi
Hi Everybody Thank You very much for your suggestions. I did play around with Zinc occupancy by giving 0.5 to each of them. I got rid of the negative electron density. But i think it still needs to be refined. Thank You very much once again Deepthi

[ccp4bb] Negative electron Density for Zinc

2012-08-28 Thread Deepthi
Hi everybody, I am working on a mutant protein structure which is 56 aminoacids long and solved the structure using SAD( Single wavelength anomalous dispersion) with zinc ions. We used SHELX software to locate the Zinc atoms and solved phases. We got the structure as a monomer. The resolution of

[ccp4bb] Post-doctoral position in Lyon, France

2012-08-28 Thread Laurent Terradot
Post-doctoral position in Structural Biology of Bacterial Pathogenesis at the IBCP (Lyon, France) ** *A FINOVI (http://www.finovi.org) funded postdoctoral position *is available immediately in the group of Laurent Terradot at the Institut de Biologie et Chimie des Protéines (IBCP), Lyon, (htt

[ccp4bb] Open Position EMBL

2012-08-28 Thread Panne Daniel
EMBL is seeking to recruit a postdoctoral researcher to join the group of Daniel Panne. EMBL is a leading international research organization with a collaborative atmosphere. We are seeking to recruit an outstanding candidate with a strong interest in structure determination. We focus on multi-p

Re: [ccp4bb] DNA geometry

2012-08-28 Thread Arka Chakraborty
Hi There is a server version of X3DNA called w3DNA...does the same job.. Best Arko On Tue, Aug 28, 2012 at 10:09 AM, Miguel Ortiz Lombardía < miguel.ortiz-lombar...@afmb.univ-mrs.fr> wrote: > Le 28/08/12 09:57, cuisheng2007 a écrit : > > Dear all: > > > > Is there software or web-server that c

Re: [ccp4bb] DNA geometry

2012-08-28 Thread Miguel Ortiz Lombardía
Le 28/08/12 09:57, cuisheng2007 a écrit : > Dear all: > > Is there software or web-server that can measure DNA geometry (PDB > coordinates) precisely, such as groove width, helix diameter, helix > axis, base tilt angle, helix rise per base pair… > > It is surely doable to measure and estimate the

Re: [ccp4bb] DNA geometry

2012-08-28 Thread Kristof Van Hecke
Dear Sheng, On the website of the NDB (Nucleic Acid Database), there's plenty of links to software tools like 3DNA, Freehelix,.., which will do the trick. (I would recommend 3DNA) http://ndbserver.rutgers.edu/services/index.html Regards Kristof On 28 Aug 2012, at 09:57, cuisheng2007 wr

[ccp4bb] DNA geometry

2012-08-28 Thread cuisheng2007
Dear all: Is there software or web-server that can measure DNA geometry (PDB coordinates) precisely, such as groove width, helix diameter, helix axis, base tilt angle, helix rise per base pair. It is surely doable to measure and estimate them manually, but I am just wondering if there are better