Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate

2009-08-20 Thread Richard Bayliss
I third it - we used 3.2M + 5% glycerol ammonium sulfate to cryoprotect crystals grown in 1.2M ammonium suphate (Bayliss et al. JBC 2002). This really helped diffraction too. My tip when handling drops at very high salt is to make a little circle of wet tissue paper around your coverslip

Re: [ccp4bb] Unknown density

2009-08-20 Thread Mark J. van Raaij
How about a 3-fold disordered metal ion? Mark On 19 Aug 2009, at 17:07, Sampath Natarajan wrote: Dear All, Currently I'm modeling one structure with 2.6A data. I could find an unknown density which I located in the interface between the three similar subunits. This density shows very

Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate

2009-08-20 Thread Joerg Standfuss
Hi Brenda, Maybe you want to have a look at the cryoprotectant database for protein crystals. http://idb.exst.jaxa.jp/db_data/protein/search-e.php There you can search for your precipitant and get a list of compatible freezing conditions that worked before including the reference. It is

[ccp4bb] Vacancy: Scientific Database Curator- PDBe

2009-08-20 Thread Jawahar Swaminathan
Dear All, I wish to draw your attention to a recent post opening at the Protein Databank in Europe (http://www.ebi.ac.uk/pdbe/) for a Scientific Database Curator. Details of the job and application procedure below: Thanks - Jawahar Swaminathan PDBe, European Bioinformatics Institute, Cambridge

Re: [ccp4bb] cyseteine modification

2009-08-20 Thread Debajyoti Dutta
Dear Sir, Thank you all who have replied. I jast want to enquire that if there is any option in coot to introduce the OH bond with Cys residue as well as to introduce the secondary peptide like bond between carboxylic carbon with amino group of lys. Sincerely Debajyoti Dutta On Wed,

[ccp4bb] Postdoctoral position

2009-08-20 Thread Lan Guan
NIH-funded postdoctoral position is available immediately in a membrane protein transport and structural biology laboratory in the Department of Cell Physiology and Molecular Biophysics at Texas Tech University Health Sciences Center, Lubbock. The laboratory is well equipped with the

[ccp4bb] Vacancy for crystallographer at Boston Univ School of Medicine

2009-08-20 Thread Hwai-Chen Guo
Dear All, I wish to bring your attention to a crystallographer postdoctoral opening at Boston University School of Medicine. Please see the job description below. Thanks, HC Guo Postdoctoral Fellow Position Open Boston University School of Medicine Department: Physiology and Biophysics

Re: [ccp4bb] xplot 84 driver and Bad plot84 file format error

2009-08-20 Thread Brad Bennett
Hi all- Thanks to Charles Ballard, who sent me an xplot driver file with optimization turned off. Once I copied this into my /usr/local/ccp4-6.1.2/bin folder, sourced and reloaded ccp4i, the plots opened up without a problem. Please note that, at least in my hands, just updating to CCP4 version

[ccp4bb] Postdoctoral position at UCLA on membrane protein structural biology

2009-08-20 Thread vincent Chaptal
Posted on behalf of Dr. Jeff Abramson: A postdoctoral position is available in the laboratory of Dr. Jeff Abramson at the Department of Physiology, University of California Los Angeles (UCLA) for a highly motivated individual with a strong interest in structure and function of

Re: [ccp4bb] electron density map

2009-08-20 Thread Artem Evdokimov
Hi, Hard to say w/o moving the thing around, but it could be: pep flips, or even (less likely) wrong chain direction. Incidentally, some of thr the side chains 'just don't look right to me' - interpret that one as you wish but e.g. the leucine in the middle seems particularly wrong (try

Re: [ccp4bb] electron density map

2009-08-20 Thread James Stroud
I agree with Artem. I also don't think you have a register problem. All of the residues show typical 2fofc density for their types, especially considering the 3A data. The disappearing act of the asp carboxyl is typical of solvent exposed aspartates. Assuming the register is correct, you