Re: [ccp4bb] Crystallization problem

> > On Mon, Jan 26, 2015 at 8:22 PM, Monica Mittal > wrote: > >> Hi everyone, >> >> I need an advice on some strange thing happening to one of the protein i >> am working on. I used to purify it and set up trays and get some needle >> shaped crystals and trying seeding and other methods to optimis

Re: [ccp4bb] Crystallization problem

Hi, It happened with me also, thought I had not the needles but the crystals. Temperature matters a lot in these situations, leave the trays unattended for long and also try with various concentration. Make it highest say 15 mg/ml and dilute serially to set with a range of concentrations. Sometime

Re: [ccp4bb] extracting PHENIX structures (help-6435)

Thank you, Rachel. I will try this suggestion out. -Original Message-From: kra...@rcsb.rutgers.eduSent: Mon, 26 Jan 2015 09:22:00 -0700To: patrick.coss...@inbox.comSubject: Re: [ccp4bb] extracting PHENIX structures (help-6435) Dear Patrick, You can try to write a scrip

[ccp4bb] Reminder: Call for access to Synchrotron Beamline Facilities, 2015 - EMBL Hamburg, Germany

REMINDER: Call for access to Synchrotron Beamline Facilities, 2015 - EMBL Hamburg, Germany We would like to remind you of the approaching deadline (*Saturday 31st **January 2015*) for the call for proposals for synchrotron beamline applications at EMBL Hamburg. The call is for applications i

[ccp4bb] Reminder: 3 vacancies at PDBe - closing this week

Hi all, This is just a quick reminder that the application period for our 3 vacancies is closing this Friday at midnight. We are seeking to recruit: - two curators (PDB/EMDB) - http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj&id=53264&aid=15470 - one web front-end developer - http://ig1

[ccp4bb] Sharp: Solomon density modification step

Dear all, A quick question regarding the density modification interface via the Sharp interface. Which resolution range / radius of the solvent sphere/ ncycles should be used for optimal result? The documentation seems to suggest to restrict yourself up to the resolution where good phasing inf

[ccp4bb] Crystallization problem

Hi everyone, I need an advice on some strange thing happening to one of the protein i am working on. I used to purify it and set up trays and get some needle shaped crystals and trying seeding and other methods to optimise them. But recently, it stopped giving crystals even small needles. I am sti

Re: [ccp4bb] PHASER MR solution

Dear Jeorge, you'll find some information about this in http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination . A practical and easy way is described in http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless HTH, Kay On Mon, 26 Jan 2015 11:24:27

Re: [ccp4bb] PHASER MR solution

Dear Jeorge, XDS make no claim to determine the SPACE GROUP but rather the LAUE GROUP, as only the latter is taken into account during data integration. This is definitely so during the indexing step (IDXREF.LP), but even in CORRECT, when systematic absences are sometimes indicated, XDS does not

[ccp4bb] (Off-topic) Analogs of CDP-choline for crystallization

Dear CCP4 members, I’m working on a phosphocholination pathway in which the enzyme utilizes the substrate Cytidine-diphosphate-choline (CDP-choline) as phosphocholione-donor. I’m enquiring about the possible analogs of CDP-choloine for cocrystallization with the enzyme as well as for the inh

Re: [ccp4bb] changing chain type in coot from RNA to DNA and viceversa

Hi Robbie, thanks a lot. I was suspecting that editing the PDB was probably the easiest way to go. I will try that! Best, Almudena 2015-01-26 10:44 GMT+01:00 Robbie P. Joosten : > Hi Almudena, > > You can use Cootilus/Nautilus to rebuild the nucleic acid in your current > density. This is not

[ccp4bb] post doc offer cryo-EM in Paris

Dear all, Please find attached a post doc offer to study cytoskeletal septins by electron microscopy. The project will be carried out at Institut curie (Paris). Someone with a former experience in electron microscopy or willing to be trained in EM is encouraged to apply. Best regards A.Bertin **

Re: [ccp4bb] changing chain type in coot from RNA to DNA and viceversa

Hi Almudena, You can use Cootilus/Nautilus to rebuild the nucleic acid in your current density. This is not a direct conversion, but it should be quick enough. The conversion form RNA to DNA can be done (outside COOT) in a text editor by changing the residue names an deleting the O2' atoms. If

Re: [ccp4bb] extracting PHENIX structures

Dear George and Patrick, It is particularly tricky to do such a search for SHELX because there are different ways of referencing it for refinement (SHELX, SHELX-76, SHELXL, SHELXL-97, SHELXL-2014 etc.) and there are other ways of using SHELX, in particular SHELXD for finding the heavy atom sub

Re: [ccp4bb] PHASER MR solution

Dear Jeorge, I can’t see anything in that output saying whether the systematic absences that would allow you to detect screw axes were covered in your data collection. In any case, it’s not necessary to reintegrate. All that happens when going from P222 to any one of the other 7 possible ortho

[ccp4bb] changing chain type in coot from RNA to DNA and viceversa

Dear all, is there a "fast" way of changing the chain type from RNA to DNA or from DNA to RNA within coot? I have already quite a bit built into density, but it is the wrong kind of nucleic acid. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemi