Re: [ccp4bb] Off Topic: Fixed point sequence alignments

Hi, Indonesia is great for this. http://xray.bmc.uu.se/dennis/ Cheers, Martin On Jan 25, 2011, at 10:50 PM, Katherine Sippel wrote: Hi all, I was wondering if you know of a program that can do protein sequence alignments around experimentally determined equivalent residues (i.e.

[ccp4bb] Postdoctoral position in RNA structural biochemistry at the Karolinska Institutet

and a CV with publication list. Contact details of two references should also be provided. Send the application as an email with attachments to martin.hallb...@ki.se Review of applications will begin immediately and continue until the position is filled. . B. Martin Hallberg, PhD Department of Cell

Re: [ccp4bb] tRNA expression

Hi, Can you explain what you want to do? Do you just want more of some tRNA corresponding to a codon that is rare in E. coli you can use the pRare2 plasmid that you can easily isolate from the Rosetta2 strain (or use Rosetta2 directly if you don't mind). If you just want some extra tRNA

Re: [ccp4bb] Question on calculation of RMSD

I think it is still hard to beat lsq_imp as implemented in 'O'. http://xray.bmc.uu.se/alwyn/A-Z_of_O/everything_e-l.html#anchor1342614 Cheers, Martin On Nov 15, 2010, at 2:32 AM, Clement Angkawidjaja wrote: DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the

Re: [ccp4bb] High Rmerge with thin frames

Dear Sergei, Did you check the mean intensity as function of spindle position statistics in the CORRECT.LP file? Any (even minute) shutter problems will affect these thin frames significantly. If this is indeed the problem, you could then try to set: PATCH_SHUTTER_PROBLEM=TRUE for the CORRECT

Re: [ccp4bb] High Rmerge with thin frames

in XDS (which should have no problems with fine phi-slicing) to use the PATCH_SHUTTER_PROBLEM=TRUE that Martin Hallberg suggested, which looks a bit like a fudge to me (but I expect Kay to correct me on that!). It is not the normal thing in XDS but it is perhaps a relatively common solution

Re: [ccp4bb] Source for trimethyl lead acetate

it. Matthew Vetting . Martin Hallberg, PhD Department of Cell and Molecular Biology Karolinska Institutet Stockholm Sweden http://tinyurl.com/yzn9y5j

Re: [ccp4bb] met auxotroph S.cerevisiae strain?

Hi Tommi, In S. cerevisiae you need a sam1(-) sam2(-) mutant. You can contact the authors of the paper in this link to get them: http://www.pnas.org/content/104/16/6678.long Cheers, Martin On Oct 5, 2010, at 3:47 PM, tommi kajander wrote: Hello all, Would anyone happen to have a met

Re: [ccp4bb] smeared bacteria pellets in protein expression

Dear Hannes, I am afraid it can still be phage problems. There are many kinds of phages that infect E. coli and some of them behave like you describe: not always lysed cells but from time to time and coming and going. The phage may anyway be present but in its lysogenic state and only entering

Re: [ccp4bb] Zalman LCD availability

BTW, has anyone tried out the higher resolution 24 inch 3D model from Zalman that appears to be available from this reseller in Japan?: http://mikimoto-japan.com/beans/products/product_dsp.htm and this reseller in the UK: http://www.cleverpc.co.uk/index.php?productID=5338 My guess it that it is

[ccp4bb] Postdoctoral position in RNA structural biochemistry at the Karolinska Institutet

a cover letter and a CV with publication list. Contact details of two references should be also provided. Send the application as an email with attachments to martin.hallb...@ki.se Review of applications will begin immediately and continue until the position is filled. . B. Martin Hallberg, PhD

Re: [ccp4bb] SHELXL eating REFMAC5 waters - whom to trust?

is less than 1.1. I have in the past been comforted by this statement by George... You can also try the SHELXWAT module. Cheers, Martin . Martin Hallberg, PhD Department of Cell and Molecular Biology Karolinska Institutet Stockholm Sweden http://tinyurl.com/yzn9y5j On Nov 12, 2009, at 8:53

Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.

Hi, On Jun 25, 2009, at 6:41 PM, Ian Tickle wrote: But I thought what you wanted was to reconstruct the diffraction pattern (i.e. streaks, TDS, ice rings, zingers, warts all) as a pseudo-precession image, not just display a representation of the integrated intensities. That surely would be

Re: [ccp4bb] XDS and ESRF ID23-1 images

. Martin Hallberg, PhD Assistant professor Department of Cell and Molecular Biology Karolinska Institutet von Eulersv. 1 SE-171 77 Stockholm Sweden Fax: +46-8-339380

Re: [ccp4bb] Refmac and MSE?

Hi, Have you specified the right form factor for Se given the wavelength used in your experiment? anomalous formfactor [Name] [f'] [f''] You can also try the new option where you can do simultaneous SAD phasing and refinement. See: http://tinyurl.com/8on2cr You will have to upgrade from your

Re: [ccp4bb] AW: [ccp4bb] suggestions for UV spectrometer

phone: +1 604 827 4267 email: [EMAIL PROTECTED] http://crg.ubc.ca/VanPetegem/ . B. Martin Hallberg, PhD Assistant professor Department of Cell and Molecular Biology Medical Nobel Institute Karolinska Institutet Von Eulersv. 1 SE-171 77 Stockholm Sweden Fax: +46-8-339380

Re: [ccp4bb] Mg++ binding to N7 of G

a try to carefully collect a data set using a wavelength around 1.5-1.6 Å (or simply your home source depending on how good it is). Cheers, Martin . B. Martin Hallberg, PhD Assistant professor Department of Cell and Molecular Biology Medical Nobel Institute Karolinska Institutet Nobels väg 3 SE

Re: [ccp4bb] XDS and overlaps

and/or spatially overlapped macromolecular diffraction patterns. by Dominique Bourgeois. Link: http://scripts.iucr.org/cgi-bin/paper?BA0019 Best regards, Martin . B. Martin Hallberg, PhD Assistant professor Department of Cell and Molecular Biology Medical Nobel Institute Karolinska Institutet

Re: [ccp4bb] XDS and overlaps

. Dodson). Why I'm worried about XDS separating relatively overlapped spots is the funny intensity stats that may result from this (as George Sheldrick and Martin Hallberg has pointed out)? The incomplete HKL2000-processed data (70%) still has intermediate values for the intensity stats

Re: [ccp4bb] Thermofluor

highly a sensitive RT-PCR machine for the thermofluor experiment (sypro orange). That would imply excitation below 500 nm (ideally 470) and detection at about 570 nm, right? I know several simple machines have a problem with the 570 nm... Jeroen. . B. Martin Hallberg, PhD Assistant

Re: [ccp4bb] off-topic-Heat shock protein gets precipitated

precipitation.Also appreciate worth suggestions from groups working with chaperonins.Thanx in advance. Shivesh kumar . B. Martin Hallberg, PhD Assistant professor Department of Cell and Molecular Biology Medical Nobel Institute Karolinska Institutet Nobels väg 3 SE-171 77 Stockholm Sweden

Re: [ccp4bb] Mico-focus beamline

try to make a seed stock and then a dilution series of that. Good luck! Martin . B. Martin Hallberg, PhD Assistant professor Department of Cell and Molecular Biology Medical Nobel Institute Karolinska Institutet Nobels väg 3 SE-171 77 Stockholm Sweden

Re: [ccp4bb] Removal of bacterial chaperone

Institute . B. Martin Hallberg, PhD Molecular Cell Biology Program Department of Cell and Molecular Biology Karolinska Institutet SE-171 77 Stockholm Sweden

Re: [ccp4bb] Advice on img proc software

diffraction from one, 2, 3 an array of objects? Cheers, br Bernhard Rupp www.ruppweb.org . B. Martin Hallberg, PhD Molecular Cell Biology Program Department of Cell and Molecular Biology Karolinska