[ccp4bb] Problem in MAKE_U_POSITIVE

Hi there - a transient message appears during anisotropic refinement CCP4 6.1: Refmac_5.5.0071 Problem in MAKE_U_POSITIVE that seems to have no further consequences. I guess that means that some elements in a U tensor lead to a divergent behavior, but details evade me. Just curious..

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

You may try Andrey Lebedev's Zanuda program from www.ysbl.york.ac.uk/YSBLPrograms/index.jsp If the problem is related due to false origin related with the presence of strong pseudo-translation then this program may be able to sort this out. In some cases it may also correct space group (if t

[ccp4bb] Industrial crystallographer position available

Exelixis is an exciting biotechnology company with primary locations in San Diego and the San Francisco Bay Area of California, USA. The Structural Biology department has an immediate opening for a computationally-skilled crystallographer at our South San Francisco site. The successful candidat

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

1) do you have unexplained peaks in your native Patterson? (calculate from your model and compare, if in doubt) 2) do you have both streaky and sharp reflections present on a subset of your images ? if answers to both questions are yes, then you might have a case of LTD/OD twinning. The la

Re: [ccp4bb] Refmac Problem - Permission Denied

The problem is that every directory in lib/data/monomers has to be world "writeable" in order to use nfsv4 for refmac to run. Something that clearly I don't want to do... And why just the monomers directory is refmac trying to write something, or is it a broken nfslock I can easily fix t

[ccp4bb] anaerobic crystallization

Hi, Does anyone have tips or suggestions for getting started with anaerobic crystallization? Searching through the archives, I was able to find some discussion about various glove box options (http://tinyurl.com/ccp4-glovebox), but not about the process itself (we already have a box). To simp

[ccp4bb] Staff Scientist and 2 Research Technician positions in Vienna

* Staff Scientist and 2 Research Technician positions in the Laura Bassi “Center for Optimised Structural Studies*“ *The Center for Optimised Structural Studies (COSS)* is a joint, FFG (www.ffg.at ) funded venture between Max F. Perutz Laboratories at the University of Vien

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

Eleanor Dodson wrote: This phenonema doesnt necessarily mean you have lattice-tranlation defects - pseudo translations are quite common with perfectly good crystals. Lattice translation defects usually imply your "crystal" has two or more layered different crystals in the beam.. It can be best

[ccp4bb] post-doctoral fellowship in Ann Arbor, Michigan

Post-doctoral Associate ? Macromolecular Crystallography Life Sciences Institute, Ann Arbor Michigan We are looking for a highly motivated postdoctoral research fellow to join our laboratory at the Life Sciences Institute, University of Michigan in Ann Arbor, Michigan. We are interested in pr

[ccp4bb] Protein Crystallography course via the web at Birkbeck College

Dear all, registration is currently open for the postgraduate certificate course in Protein Crystallography via the web at Birkbeck that starts on Monday October the 5th. It is for the duration of 1 year during which all aspects of protein crystallography will be covered from the fundame

Re: [ccp4bb] Scale datasets from different crystals

These are just warnings: Scala will combine them & average the unit cells Phil On 18 Aug 2009, at 13:10, Donald Damian Raymond wrote: I tried to scale the two datasets in scala after combining the two unmerged datasets with the sort MTZ program, but scala thinks the two datasets are from

[ccp4bb] Is my data twinned or not?

Dear all, I have a small three helix bundle domain (~14 kDa) which after data analysis I believed crystallized in either P41212 or P43212 (a=b=121.8 c=118.0) with between 4 and 8 molecules in the ASU and I have data to 3.2A. However after looking at a native Patterson there is a non-origin peak

[ccp4bb] Off Topic: Pittsburgh Diffraction Conference, October 29th - 31st, University of Georgia U.S.A.

Dear Colleague, Both B.C. Wang and I would like to direct your attention to a meeting that we are hosting at UGA on October 29-31, 2009. The scientific sessions include RNA crystallography, small angle scattering, neutron diffraction, protein complexes and more. As the announcement below

Re: [ccp4bb] space groups not supported by Refmac5

Just to clarify this again: the question of "standard" settings for primitive orthorhombic space groups (& the I2/C2 choice) was raised by Ian Tickle in earlier discussions. He pointed out that the IUCr standard was to choose a < b < c for primitive orthorhombic irrespective of which axes a

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

This phenonema doesnt necessarily mean you have lattice-tranlation defects - pseudo translations are quite common with perfectly good crystals. Lattice translation defects usually imply your "crystal" has two or more layered different crystals in the beam.. It can be best detected by an analysis

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

Eleanor Dodson wrote: You must have a pseudo translation vector of ~ 0.02 0.5 0.0 That relates solution 1 and 2, and 3 and 4. That makes it hard to determine space group - there will be absences along 0k0 because of the translation so the space group could be P 2i 2 2i or P2i 21 2i But which

Re: [ccp4bb] Weird expression behavior

Hi Ezra and others, Just thought I'd let you know that I have noticed that one or two of those E. coli proteins that love to bind Ni-affinity resin do not bind to Cobalt resin. Of course, there is always a price to pay (for the Co resin, in this case) :)! Cheers, Raji --- Raji Ed

Re: [ccp4bb] Weird expression behavior

A little tangental You mentioned lowering the temperature - how low... Stratagene markets a call line - Arctic Express - that adds chaperones that are more active at lower temps. I know someone who overcame inclusion body problems by expression at 16 using these cells. (I know someone els

[ccp4bb] Thanks_Re: [ccp4bb] Cold Cabinet Vs Fridge, FPLC

Dear all, I wish to thank everybody for all the suggestions, pictures and ideas! Dianfan

Re: [ccp4bb] Weird expression behavior

I do have rare codons for E.coli in my construct, indeed I have two stretches of 3 and 4 rare codons (arginines mainly), thus, I tried the expression in BL21(DE3)-codon plus and Rosseta. But the result was the same (GST or MBP alone). Thanks again 2009/9/2 Ezra Peisach > Been there, done that,

Re: [ccp4bb] Weird expression behavior

Been there, done that, got the T-shirt. I do not believe there is a protease like 3C in E. coli. That said - do you have any rare codons in your protein - that might cause the stall/termination in expression - leaving you a large amount of tag. Have you followed through with purifictaion to s

Re: [ccp4bb] CNS to PDB format conversion

That could be due to anything - a really useless message.. You arent trying to rerun an older refmac script are you - the rerun job button was broken at some point. If you "reset defalt parameters" and then set up the job again it might work.. Eleanor Manoj Saxena wrote: Hi Thanks for yo

Re: [ccp4bb] MAMA-mask

You need to run mapmask to extend the mask to cover an assymetric unit using the overlap option. CCP4i instruction here: http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Electron_density_manipulation#Converting_a_non-crystallographic_mask_to_a_crystallographic_mask This is becoming a very FAQ. I

Re: [ccp4bb] CNS to PDB format conversion

Manoj Saxena wrote: Hi all, How to convert CNS coordinate file to PDB file format that can be used for refinement in refmac. Is there any utility in CCP4 or other GUI based interface that can convert CNS output file to PDB . Thanks . Manoj Penn Sate University Biochemistry State College P

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

You must have a pseudo translation vector of ~ 0.02 0.5 0.0 That relates solution 1 and 2, and 3 and 4. That makes it hard to determine space group - there will be absences along 0k0 because of the translation so the space group could be P 2i 2 2i or P2i 21 2i But which ever SG it is thedata

[ccp4bb] Weird expression behavior

Hello crystallographers in general and E.coli-protein producers in particular, I would like to share with all of you a strange behavior of two of my expression constructs, looking for some advice or just know if anybody has experienced something similar: The scenario is the following one, I am tr