[ccp4bb] How to config CPU to run ccp4 with multi-processor

Dear all I just installed CCP4 6.4 on Ubuntu 12.1. The program can work. I found it just used 1 processor instead of 4( Intel i5) for data solving. Does anyone know how to config CPU so that all processors can be used. Thanks Chang

[ccp4bb] How to config CPU to run ccp4 with multi-processor

Dear all I just installed CCP4 6.4 on Ubuntu 12.1. The program can work. I found it just used 1 processor instead of 4( Intel i5) for data solving. Does anyone know how to config CPU so that all processors can be used. Thanks Chang

[ccp4bb] in vitro Tyr phosphorylation

Does anyone know of a good way to phosphorylate the Tyr on a protein for structural studies? Is there a generic kinase that can be coexpressed or purified for phosphorylation? The pCMF Amber codon system is very expensive and Glu really doesn't mimic pTyr all that well. Any ideas/help would be a

Re: [ccp4bb] Cryo solution for crystals grown in magnesium formate

On Mon, Dec 16, 2013 at 1:36 PM, Xiao, Junyu wrote: > Dear all, sorry if this topic does not interest you. I wonder whether > anyone has experience with freezing crystals grown in ~0.2 M Magnesium > Formate. Garman and Mitchell suggested that "A major anomaly is solution > 44, 0.2 M magnesium fo

Re: [ccp4bb] Cryo solution for crystals grown in magnesium formate

Junyu, I haven't tried it personally with this particular solution, but I have found that 30% glucose can pretty much cryoprotect any condition I have tried it with. If necessary, add cryoprotectant solution (mother liquor + 30% glucose) gradually to minimize osmotic shock and potential crack

[ccp4bb] Cryo solution for crystals grown in magnesium formate

Dear all, sorry if this topic does not interest you. I wonder whether anyone has experience with freezing crystals grown in ~0.2 M Magnesium Formate. Garman and Mitchell suggested that "A major anomaly is solution 44, 0.2 M magnesium formate, which requires 50% glycerol for cryoprotection" in th

Re: [ccp4bb] Heavy atom sites

Didn't mlphare use to print those values in the log file ? Jürgen On Dec 15, 2013, at 4:29 PM, David Schuller mailto:dj...@cornell.edu>> wrote: I have some SIRAS data of a known structure. I want to get the isomorphous and anomalous occupancy and phasing power from my data. What's the best softw

Re: [ccp4bb] ccp4 v6.4.0 cannot extract mtz

Yes Uli. I have the same issue, but not solve it yet :-( Partha On Mon, Dec 16, 2013 at 10:52 AM, ulrich.goh...@mdc-berlin.de < ulrich.goh...@mdc-berlin.de> wrote: > Dear colleagues, > > Trying to run the latest version of ccp4 (6.4.0), say Refmac, I get the > following error when I fill in th

Re: [ccp4bb] MrBUMP not running after update

Dear Ronan Thank you! Happy holidays! Jie - Original Message - From: "Ronan Keegan" To: Sent: Monday, December 16, 2013 3:40 AM Subject: Re: [ccp4bb] MrBUMP not running after update Dear Jie, Thanks for spotting this problem. I've made a fix for MrBUMP that should address the

Re: [ccp4bb] MrBUMP not running after update

Dear Jie, Thanks for spotting this problem. I've made a fix for MrBUMP that should address the problem. It will be included in the next CCP4 update which will go out tomorrow (Tuesday 17th of December) all being well. Best wishes, Ronan On 10/12/13 01:34, jie liu wrote: Dear All I just i

Re: [ccp4bb] ccp4 v6.4.0 cannot extract mtz

Dear Uli, On Mon, 2013-12-16 at 15:52 +, ulrich.goh...@mdc-berlin.de wrote: > Dear colleagues, > > Trying to run the latest version of ccp4 (6.4.0), say Refmac, I get > the following error when I fill in the file box for the data file: > > "CCP4i encountered an error when trying to extract t

Re: [ccp4bb] CAD

Hi, It looks like you're missing your LABIN line. Pete Ashu Kumar wrote: Dear all, I am trying to use CAD to apply b-factor sharpening to my 3.7 A data. Following is the script which I am running. cad hklin1 test.mtz hklout test_out.mtz <

[ccp4bb] CAD

Dear all, I am trying to use CAD to apply b-factor sharpening to my 3.7 A data. Following is the script which I am running. cad hklin1 test.mtz hklout test_out.mtz <

[ccp4bb] ACA 2014, Industrial Research from Young Scientists

The Industrial Special Interest Group and Young Scientists Special Interest Group of the American Crystallographic Association will be hosting a scientific session on Sunday, May 25, 2014 during the ACA Meeting in Albuquerque, New Mexico which will highlight research by young scientists (undergr

[ccp4bb] ccp4 v6.4.0 cannot extract mtz

Dear colleagues, Trying to run the latest version of ccp4 (6.4.0), say Refmac, I get the following error when I fill in the file box for the data file: "CCP4i encountered an error when trying to extract the data from data.mtz. You can view the output from the mtzdump program" etc. + crash of th

Re: [ccp4bb] Heavy atom sites

I would find the sites from the PHIC - you need to use CAD to add Fcalc PHIC and FOM to the original data with Fnative Fderiv DANOderiv etc I usually then use SCALEIT to scale native and derivative to Fcalc - then you know you are roughly on an absolute scale Then feed those sites into Phaser_EP

Re: [ccp4bb] AW: [ccp4bb] Wrong Space Group?

See previous answer re spacegrroup - if phaser has output coordinates with SG P6522, but you are refining against the originally processed data that may well have SG P6122 in the header. Refmac DOES NOT check this ( Why not Garib! ) Eleanor On 16 December 2013 09:47, wrote: > Dear Bonsor,

Re: [ccp4bb] AW: [ccp4bb] Phaser output problem

Things to check - number of molecules to search for. You can use Matthewscoeff to get a suggestion - MOLREP does it autromatically . Space group - has Phaser chosen as best SG an alternative to that in your header? Eleanor On 16 December 2013 11:03, wrote: > Looks like you need to search for

[ccp4bb] AW: [ccp4bb] Phaser output problem

Looks like you need to search for more molecules. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Amanda Blythe Gesendet: Montag, 16. Dezember 2013 11:46 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Phaser output problem I am trying to solve a structure by mole

[ccp4bb] Postdoctoral positions in structural biology/ cryo-EM at OIST

Dear structural biologists, there are two positions for postdoctoral researchers available with an emphasis on high-resolution cryo-EM at OIST (Okinawa Institute of Science and Technology Graduate University, Japan). We are a highly motivated young international team and benefit from an excell

[ccp4bb] AW: [ccp4bb] Wrong Space Group?

Dear Bonsor, I fully second James suggestions but have a few additional comments: If you get a solution in P6522 with one molecule, you should get the same solution in P65 with 2 molecules. One of the "crystallographic" symmetry operators would then be "non-crystallographic". The current version

Re: [ccp4bb] Heavy atom sites

Hello David, I would use the SAD target function of refmac5 for the anomalous occupancy. As of isomorphous occupancy and phasing power, I don't know. Best, Tim On 12/15/2013 10:29 PM, David Schuller wrote: > I have some SIRAS data of a known structure. I want to get the > isomorphous and anomalo