Re: [ccp4bb] about point mutation

Hello Arun: Actually, I am not sure about " i couldn't get my desire point mutation". You mean you didn't get the pcr product or you could get the pcr product but there is no mutation. If you didn't get the PCR,Just lower the annealing temperature to 55 degree. And try extension temperature 72

[ccp4bb] Post-doctoral position in Biochemistry & Structural Biology - Antioxidant Proteins

Please excuse cross postings and feel free to forward. Dr. Soares Netto was a NIH Postdoctoral Fellow in the Laboratory of Biochemistry (NHLBI) with Dr. Stadtman from 1992-1996. *Post-doctoral position in Biochemistry and Structural Biology with emphasis on Antioxidant Proteins.* *University of

[ccp4bb] npr videos of crystals growing

All - See the link below; there was a story on NPR Science Friday about a photographer who took videos of ice crystals forming under cross-polarizers. Then, they said they want listeners to send in cool science videos - I bet there are some of you out there (not me) that would have the equipment t

Re: [ccp4bb] output sigmaa and D values?

Hi Pavel, Thanks - I'd missed that one when I was checking the phenix documentation. Also, I may be slower than usual today, but I don't see an output column for sigma_a. Is there a relationship between alpha and beta and sigma_a? Pete Pavel Afonine wrote: Hi Pete, yes, I wrote one a whil

Re: [ccp4bb] output sigmaa and D values?

Hi Pete, yes, I wrote one a while ago: phenix.reciprocal_space_arrays https://www.phenix-online.org/documentation/reciprocal_space_arrays.htm it does exactly what you asked for and much much more. Let me know if you have questions. Pavel On Fri, Feb 24, 2012 at 9:28 AM, Pete Meyer wrote: >

Re: [ccp4bb] about point mutation

Phusion requires that the primers are phosphorylated for mutagensis to work, unlike Pfu. If you cannot phosphorylate them use Pfu as recommended by Charlotte Not really. Phusion *protocol* requires phosphorylated primers but seemingly the only reason for that is that they needed to find a way

[ccp4bb] output sigmaa and D values?

Does anyone know of a program that will output sigma_a and D values for individual reflections (yes, I know they're usually calculated as bin values)? Or, for that matter, an option to an existing program I haven't found in the documentation yet? Thanks, Pete

Re: [ccp4bb] about point mutation

Phusion requires that the primers are phosphorylated for mutagensis to work, unlike Pfu. If you cannot phosphorylate them use Pfu as recommended by Charlotte Dan

Re: [ccp4bb] Extra positive density seen after TLS refinement?

Dear Naveed A Nadvi I think that your results highlight the fact that modelling the disorder/complex ordering of your crystal is relevant and in general, that we should take care in optimizing B factor refinement as a strong factor for model improvement. In this sense I would not relay in

Re: [ccp4bb] about point mutation

Dear Arun, I find stratagene method using Pfu turbo enzyme much more successful then using phusion. If you go to their website they even have a tool to design the 'perfect' primer! Happy cloning! On 24/02/2012 10:54, "Tim Gruene" wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ar

Re: [ccp4bb] about point mutation

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Arun, it's been a while for my last PCR, so take my comment with caution: 33bases seems very long for a primer especially if it is only for a point mutation. Could you trim it down to 20-25 bases? I would cut at the downstream side. Tim On 02/24

[ccp4bb] Post-Doc Position available at the BMLS, University Frankfurt, Germany

At the Buchmann Institute of Molecular Life Sciences (former Frankfurt Institute of Molecular Life Sciences; Goethe University Frankfurt/Main) there is an opening for a Post Doctoral Position (E13 TV-G-U, fulltime). The position is available from April 1, 2012, and the initial appointment i

[ccp4bb] PHENIX error: No refinement carried out (may need free R flags)

Hello Fellow PHENIX users (and others!) I had been using PHENIX to generate iterative build composite OMIT maps. I was able to perform these runs with automated settings for two of my data. With the third one (1.2 A structure) I get an error. I am pasting a part of the message below:

Re: [ccp4bb] Extra positive density seen after TLS refinement?

Dear Crystallographers, Thank you for your responses. The density map levels were 0.11e/A^3 (3.00 A) for both images with and without TLS refinement. When I superposed the deposited structure I could see the extra density was due to water moleucles that were seen in the higher resolution deposi

[ccp4bb] about point mutation

can any one help me in suggesting that what mistake i have did in my mutagenic pcr . actually my problem is my primer annealing temperature is 81degree. im using phusion pol enzyme. i have made many trial, i.e., made annealing at 68 and then followed 2 step pcr method and then added 1micro lit o

Re: [ccp4bb] molrep question - how get our ducks in a row?

Hello Gloria, I usually let Coot display the nearest symmetry molecules (as CA) and save those that fit: Option "Save Symmetry Coordinates..." and pick the molecule to save. Best regards, Daniel -- Daniel Schlieper email: daniel.schlie...@tuxomania.net Biochemische Pflanze