Re: [ccp4bb] DDM

2012-03-26 Thread Joao Dias
in the literature values between 0.5-2% being used successfully. Good luck. Cheers, Joao Joao Dias, Ph.D. Senior Scientist Heptares Therapeutics Ltd BioPark, Broadwater Road, Welwyn Garden City, Herts, AL7 3AX UK This document contains company confidential and/or proprietary information. It is

[ccp4bb] "Structural Biologist/Protein Biochemist" position at Heptares Therapeutics Ltd.

2011-05-26 Thread joao dias
ld also be of benefit. Further information can be found on our website (www.heptares.com). To apply for this position, please send your application to h...@heptares.com, quoting reference number 2011/1B Best wishes, Joao Dias, Ph.D. Senior Scientist Heptares Therapeutics Lt

Re: [ccp4bb] Cannot running NTA to purify the protein having His-tag?

2007-02-28 Thread Joao Dias
Before loading the Ni-NTA column you should exchange the medium buffer (some media have histidine which will compete with your protein) to a more suitable buffer, like your loading buffer (Buffer A is 50mM phosphate buffer pH 7.5 and 300mM NaCl is OK). If your His-tag is not accessible, then

Re: [ccp4bb] Maps look different from auto-mtz vs EDS vs FFT in Coot or CCP4MG.

2007-05-24 Thread Joao Dias
Dear Kendall, I would suggest you to run a simulated annealing omit map around the region you are interested. The model bias will be reduced and you will get a more clear answer. Ciao, Joao Joao M. Dias Ollmann Saphire Lab The Scripps Research Institute 10550 North Torrey Pines Rd. IMM-2 La J

Re: [ccp4bb] FreeR flag value swap

2007-09-27 Thread Joao Dias
Petra, You do not need any conversion. It is true that the default FreeR flag used by the two programs is the opposite (1 or 0), but I when you run CNS/Phenix or Refmac you can say specifically which flag you want to use. You just have to say in your input file which flag you want to use. No

Re: [ccp4bb] multiple sequence alignment from multiple pairwise structural alignments

2008-03-04 Thread Joao Dias
Hi Stephen, I will add to the previously mentioned ones the MSD ssm server at EBI? http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver You also have the Godzik tools if your proteins have flexible regions. FATCAT http://fatcat.burnham.org/ and POSA http://fatcat.burnham.org/POSA/ Good luck, Joao

Re: [ccp4bb] Deglycosylation

2008-09-25 Thread Joao Dias
Hi Eugenio, It will depend on the expressing system you are using: mamalian cells, insect cells, yeast. For enzymatic deglycosylation I suggest you to do first do a small scale test, using the following enzymes: PNGase F is extremely efficient. EndoH (you can try EndoHf which is cheaper and )

Re: [ccp4bb] temperature after 30 minutes using microscopes ?

2009-01-21 Thread Joao Dias
Jurgen, From your question I assume that you are having problems with the warming up of the crystal tray due to the microscope light. Did you consider the use of an external cold light source like the KL1500 LCD? I do not feel anything warming up. Which microscope are you using? The LED sy

[ccp4bb] Protein crystallographer position at Heptares Therapeutics

2014-03-28 Thread Joao Dias
iculum vitae including the names and contact details for two referees. Please send your application in pdf format, to h...@heptares.com<mailto:h...@heptares.com> quoting reference number 2014/2B. The closing date for applications is 18th April 2014. No agencies, please. Thanks, Joao Dr J

Re: [ccp4bb] Unusually low B factors with phenix

2012-11-02 Thread Joao Dias
Hi, I am using the latest version of phenix 1.8.1-1168 for the MacOSX and I see a similar behaviour with the B-factors. Which version do you suggest to update to? There might be a problem with over-refinement and one workaround might be to limit the Rfree-R=0.05, but your Rfree will likely to incr