Re: [ccp4bb] Refmac- solvent mask
Thank you very much James ! -kiran From: James Holton jmhol...@lbl.gov To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, September 26, 2012 9:58 PM Subject: Re: [ccp4bb] Refmac- solvent mask Yes, it's called a partial structure. You input the mask as structure factors and call them FPART in the refmac LABIN input. http://www.ysbl.york.ac.uk/refmac/docs/keywords/xray-principal.html#labin_fparti_phiparti Then enable refining the scale and B factor of the partial structure: http://www.ysbl.york.ac.uk/refmac/docs/keywords/xray-general.html#scpa pay attention to the scale and B assigned to the partial structure in the refmac log. If it blows up (or down) then something is wrong. Also, don't forget to turn off the built-in solvent with SOLVENT NO when you do this. http://www.ysbl.york.ac.uk/refmac/docs/keywords/xray-principal.html#solv You can actually add multiple partial structures and scale them independently, but in my hands things start to get crazy if you have more than 2. -James Holton MAD Scientist On Wed, Sep 26, 2012 at 11:45 AM, Kiran Kulkarni dr.kirankulka...@yahoo.com wrote: Dear CCP4 users, Is it possible to specify a solvent mask to the refmac ? Many thanks in advance for your time and help. Regards, -Kiran
[ccp4bb] Position available: Postdoctoral fellow in New York
*Postdoctoral Fellow: Structural biology of chromatin modifiers.* A postdoctoral position is available in the laboratory of Dr. Karim-Jean Armache, Assistant Professor in the Structural Biology Program at the Skirball Institute of Biomedical Research—NYU Medical Center, New York, USA.We are looking for highly motivated, creative individuals with a strong interest in epigenetics and chromatin biology. We are presently focusing our efforts on chromatin-modifying factors and their complexes with nucleosomes, using X-ray crystallography, complemented with other biochemical/biophysical techniques. Applicants should have a PhD in biochemistry or biophysics with at least one publication in protein crystallography (including PDB entry). The ability to grow crystals, collect diffraction data and determine/refine protein structures is essential. Experience in the biochemical and biophysical characterization of protein complexes is preferred. The candidate must have an excellent command of oral and written English. Applicants should send a single PDF file containing their CV along with a summary of their previous research experience, accomplishments, and experimental expertise. They should also arrange for 3 letters of reference to be sent directly to Dr. Karim-Jean Armache via e-mail at: kjarma...@gmail.com Deadline for applications: October 30, 2012
[ccp4bb] Poor baculovirus stability at 4C?
Sorry for an off-topic question. We began experiencing a sudden reduction in stability of baculovirus stock stored at 4C, like the titer drops more than 5 fold in 3-5 month. The only difference compared with previous preparations is a switch from Gibco SF900-II to a media from Lonza (Insect-XPRESS). Could it be due to the media switch, or something else? What is the best way to store baculovirus? Thank you Alexander Aleshin Sanford-Burnham Medical Research Institute Infectious Inflammatory Disease Center 10901 North Torrey Pines Road La Jolla, California 92037
Re: [ccp4bb] Poor baculovirus stability at 4C?
We began experiencing a sudden reduction in stability of baculovirus stock stored at 4C, like the titer drops more than 5 fold in 3-5 month. The only difference compared with previous preparations is a switch from Gibco SF900-II to a media from Lonza (Insect-XPRESS). Could it be due to the media switch, or something else? What is the best way to store baculovirus? Absolutely could be. For long term storage, add 10% FBS. Helps A LOT. I've used 2 years old stocks stored in serum-containing medium and they worked fine. We don't titer (because it's kind of pointless) but the optimal virus to culture volume ratio has not changed more than twoi-fold. - Dima
Re: [ccp4bb] Poor baculovirus stability at 4C?
Alexander, We produce baculovirus at Gibco SF900-II + 10% heated FBS + 1xPSG and then store at 4C routinely. And it seems to be quite stable. We have a virus that had no change for more than 2 years: we judge by the volume of it needed to infect_cells/produce_protein, no titer measurements. We also avoid exposure to light: definitely cover it with foil if it's transparent door fridge. Vitali On Thu, Sep 27, 2012 at 5:42 PM, aaleshin aales...@burnham.org wrote: Sorry for an off-topic question. We began experiencing a sudden reduction in stability of baculovirus stock stored at 4C, like the titer drops more than 5 fold in 3-5 month. The only difference compared with previous preparations is a switch from Gibco SF900-II to a media from Lonza (Insect-XPRESS). Could it be due to the media switch, or something else? What is the best way to store baculovirus? Thank you Alexander Aleshin Sanford-Burnham Medical Research Institute Infectious Inflammatory Disease Center 10901 North Torrey Pines Road La Jolla, California 92037
