[ccp4bb] Opening for a Research Associate (Structural and Biophysical Chemistry) at Novartis Emeryville, CA

We’re looking to hire a B.S./M.S. level Scientist - Structural and Biophysical Chemistry at our Emeryville, CA location. If you or anyone you know is interested please view (and apply to) the opening at: https://sjobs.brassring.com/tgwebhost/jobdetails.aspx? jobId=2477209&partnerid=13617&siteid=5

[ccp4bb] Helium-Temp Cryo-Cooling

Dear Crystallographers, It is my recollection from a while ago that cryocooling to Helium temperatures has modest if any effects on protein structure or diffraction data quality, and I've found a couple of papers just now to that effect. Does anyone know differently? Do the b-factors even chang

[ccp4bb] Postdoctoral scholar position in the Kelch Lab, UMass Med

A postdoc position is available to study the mechanisms of regulation of the DNA replication/repair proteins using cross-disciplinary approaches in the Kelch Lab at UMass Medical School. Successful candidates will use biochemistry, computational biology, genetics, and structural biology to study th

Re: [ccp4bb] Proline derivatives

Thanks everyone for all the suggestion! I have plenty of options now! > On Mar 31, 2017, at 11:06 AM, Lakshmi SwarnaMukhi Pidugu > wrote: > > You could try scifinder. > > Swarna > > On Wed, Mar 29, 2017 at 6:07 PM, Jan van Agthoven > wrote: > Hi Everyone, > Does an

Re: [ccp4bb] prodrg in coot

Jiri, This doesn't answer you question, but in Coot version 0.8.8 (Robbie is right), the default dictionary generator (if one has access to CCP4) is acedrg. This is, I believe, on the whole, something of an improvement over the version of prodrg that is available from CCP4. There is a mechani

[ccp4bb] Postdoctoral Position @ NE-CAT

Postdoctoral position in macromolecular crystallographic computing at NE-CAT, Cornell University The Northeastern Collaborative Access Team (NE-CAT) at the Advanced Photon Source, Argonne National Laboratory is seeking applicants for a Postdoctoral Research Associate to work on the development,

Re: [ccp4bb] prodrg in coot

Dear Jiri, You don't need to buy anything, but you should update your COOT (stand-alone or with CCP4). The current version is 0.8.8. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > chemocev marker > Sent: Monday, April 3, 20

[ccp4bb] prodrg in coot

Dear members I am wondering how to activate the prodrg tool in coot. Does it has to be purchased to get licence??. If I made the ligand in ligand builder and click apply, it gives window info no cprogrg not found. I am using the coot 0.8.4 from the ccp4 site. Does the enhanced ligand tools has to b

Re: [ccp4bb] FW: [ccp4bb] Using a codon-optimised gene to improve protein solubility

Dear Sutapa There has been wonderful suggestions, particularly from Bert, size matters! Considering that all is in order, i would share my experience with retroviral integrase, a sparingly soluble protein when expressed in E. coli. The protein exists in mammalian cells as a multi-protein complex

[ccp4bb] FW: [ccp4bb] Using a codon-optimised gene to improve protein solubility

Dear Supta, If I may make another type of suggestion, we have had success in crystallizing sparingly soluble proteins in the presence of up to 2M urea (Dines et al. Journal of Structural Biology, 2007). It is enough to avoid non-specific associations, but not enough to denature the protein. It

Re: [ccp4bb] Using a codon-optimised gene to improve protein solubility

I think it is very unlikely codon optimisation will improve solubility, so I'd save my money and use it to try other things. Assuming you have tried (much) lower temperatures for expression you could consider dialing down expression via a different promoter or low-copy number plasmid. I assume y

Re: [ccp4bb] DSSP output pdb format

Dear Adriana, That server is ours, at the CMBI. I realize that you are a bit confused about things. Feel free to address me personally (and I am mailing this to the whole list because this offer holds for all the 3D structure related servers reachable via swift.cmbi.ru.nl/gv/facilities). In Skyp

Re: [ccp4bb] Using a codon-optimised gene to improve proteinsolubility

Hi Sutapa, It is very difficult to predict protein solubility in advance. I have worked with different proteins using 'native' sequences and codon optimised 'synthetic' sequences. One of my protein was bHLH transcription factor from Sorghum and codon optimisation didn't rescue the problem

[ccp4bb] DSSP output pdb format

Dear members I assigned the secondary structure to my pdb file by the DSSP application from this webserver http://www.cmbi.ru.nl/dssp.html The application works and gives output the pdb file. The output file just have the reside list not the atom list. I am not able to view the structure from thi

[ccp4bb] AW: [ccp4bb] Using a codon-optimised gene to improve protein solubility

Dear Sutapa, I fully agree with Grant, the first question is whether the naturally-produced protein is soluble and whether your protein is not a membrane protein, or a domain, cut out of a much larger protein? The other question is whether your protein is toxic for E.coli and only the bacteria

Re: [ccp4bb] Using a codon-optimised gene to improve protein solubility

There is also lack of information here. Do you really expect this protein in soluble fraction? Is it a membrane associated or transmembrane protein? Well, I don't have any experience in protein expression using codon optimization. However, Considering the fact that in E.coli it is getting express