[ccp4bb] Lithium versus Sodium

2012-01-11 Thread Scott Pegan
Hey all, Does anyone know of a good article that deals with differentiating between a lithium ion and sodium ion for density in a X-ray structures? Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry & Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254

[ccp4bb] a question on Average Occupancy-weighted avg temperature factor (Deviation)

2012-01-11 Thread Dialing Pretty
Dear All,   For the RCSB depositation report, it gives the "Average Occupancy-weighted avg temperature factor (Deviation)".   Will you please tell me what range the "Average Occupancy-weighted avg temperature factor (Deviation)" should be and what is the significance of that value?   I am lookin

[ccp4bb] brainpool research associate position

2012-01-11 Thread intekhab alam
Dear members Have a look on the advertisement for the position of research associate in structural biology. Interested candidates please reply to kh...@korea.ac.kr. Informal enquiries can also be made. Structural Bioinformatics Lab, Department of Biotechnology & Bioinformatics, Korea University,

[ccp4bb] Gordon Research Conference on Diffraction Methods in Structural Biology

2012-01-11 Thread Ana Gonzalez
We are excited to invite you to the biannual Gordon Conference on Diffraction Methods in Structural Biology, which will be held at Bates College in Lewiston, Maine from July 15-20. Behind all the new biological systems that are being studied by diffraction methods nowadays lie a compendium of met

Re: [ccp4bb] Choice of heavy atom derivatives

2012-01-11 Thread Francis E Reyes
> They show a nice diffraction, but appear to be perfectly twinned. In most cases, structures can be solved (and biological questions answered) in twinned cases. I wouldn't be discouraged. > I have crystallised a SeMet derivative, but I have not been able to collect > sufficiently good data, to

Re: [ccp4bb] Sub-angstrom resolution

2012-01-11 Thread Colin Nave
Dirk Yes. Equating the square root of the measured intensity (photons/spot) to the structure factor was sloppy nomenclature on my part. One should look at Darwin's formula for the intensity (photons/spot). The adverse term in it is Vxtal/Vcell (ratio between crystal and cell volumes). Regarding

Re: [ccp4bb] Sub-angstrom resolution

2012-01-11 Thread Thomas Womack
On 11 Jan 2012, at 11:36, Thomas Womack wrote: > > On 11 Jan 2012, at 02:13, Artem Evdokimov wrote: > >> There are two sides to this qustion: the scientific one is actually easier >> to answer in generic terms - but I also would like to point out the very >> recent example of a mystery that re

Re: [ccp4bb] unusual bond lengths in PRODRG cif file (Another possibility - direct use of QM)

2012-01-11 Thread Oliver Smart
On Mon, 9 Jan 2012, krish wrote: You can use Phenix.elbow or phenix.reel to load the coordinates of the small moleucle and optimize with AM1 (semi-empirical), then you should get reasonable geometirc parameters suc as bond length, bond angles and etc.   Hope this helps !   Cheers, Kri

Re: [ccp4bb] DDM crystals

2012-01-11 Thread Jacob Keller
What exactly is your question--I saw tons of "crystals" of DDM and PEGs, I think especially P400, if I recall correctly. JPK On Wed, Jan 11, 2012 at 7:12 AM, Patrick Loll wrote: > Does anyone have any experience with formation of crystals of dodecyl > maltoside in the presence of PEG? > Pat > >

[ccp4bb] DDM crystals

2012-01-11 Thread Patrick Loll
Does anyone have any experience with formation of crystals of dodecyl maltoside in the presence of PEG? Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Gradu

Re: [ccp4bb] Choice of heavy atom derivatives

2012-01-11 Thread Miguel Ortiz Lombardía
Le 11/01/12 12:23, Federica Basilico a écrit : > Hi everyone, > > I have crystals of a protein of 176 residues, with 5 Cys, 8 His, 3 Met. > Native crystals grow in 10% MPD, 100mM Bicine pH 9.0. They show a nice > diffraction, but appear to be perfectly twinned. > I have crystallised a SeMet deriva

Re: [ccp4bb] Sub-angstrom resolution

2012-01-11 Thread Thomas Womack
On 11 Jan 2012, at 02:13, Artem Evdokimov wrote: > There are two sides to this qustion: the scientific one is actually easier to > answer in generic terms - but I also would like to point out the very recent > example of a mystery that required very high resoluton (and orthogonal > techniques)

[ccp4bb] Choice of heavy atom derivatives

2012-01-11 Thread Federica Basilico
Hi everyone, I have crystals of a protein of 176 residues, with 5 Cys, 8 His, 3 Met. Native crystals grow in 10% MPD, 100mM Bicine pH 9.0. They show a nice diffraction, but appear to be perfectly twinned. I have crystallised a SeMet derivative, but I have not been able to collect sufficiently g

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-11 Thread dusan turk
Hi Guys, I just want to make aware that apart form PRODRG etc there exist also PURY server http://pury.ijs.si/, which offers a possibility to create restraints for heteromolecules. It accepts PDB files, smiles format. Alternatively JME editor can be used to draw your compound. PURY: a databa

Re: [ccp4bb] Sub-angstrom resolution

2012-01-11 Thread Dirk Kostrewa
Dear Colin, Am 10.01.12 18:08, schrieb Colin Nave: 3. The structure factors are lower for large unit cells. This will mean they will be harder to detect, particularly if there is a high background. But aren't the total structure factors of a unit cell the sum of the atomic structure fact