Re: [ccp4bb] Ecoli protein staining with AntiHis?

Depends on which antibody you're using. Different manufacturers tend to light up different stuff. We very rarely see just one band - typically it's a bunch of weak bands as well as smears. How strong is the band? Can you cut it out of the gel and do a tryptic digest and MS identification? If the

Re: [ccp4bb] How to run SIGMAA twice in a row? (fwd)

Hi Huiying, Thanks, I think I understand what your approach was. I guess I was overly-concerned about model bias during density modification of model phases (I can explain to myself both why it's valid and why it's not; but haven't been able to resolve the obvious contradiction there); although w

[ccp4bb] Drug Target Crystallography and Structure Based Drug Discovery June 28-29 2007

Dear All: A two day workshop on the cutting-edge developments in crystallography and structure-based drug design will be held on June 28-29, 2007 in La Jolla California. The workshop will be conducted jointly by myself and Dr. Ruben Abagyan (Professor of Molecular Biology at The Scripps Research I

[ccp4bb] Ecoli protein staining with AntiHis?

Hi Everyone, I see a band that lights up in my anti-His Western blots. While I investigate what else the band might be (truncated protein etc.), does anyone know whether there is an E. coli protein that migrates ~ 30-40kDa (SDS-PAGE), which binds to anti-His antibodies? Thanks. Raji

Re: [ccp4bb] How to run SIGMAA twice in a row? (fwd)

Hi Pete, The sigmaa-weighing scheme implemented in SigmaA routine is the very means to remove the potential model bias. Also, the model phases we used in the phase combination were simply from a backbone poly-Ala model generated from the best parts of the MAD-phased density (some of them from

Re: [ccp4bb] GUI problem with SIGMAA

Hi Eleanor, Thanks for doing the test. I did the same thing through run & view com option as Chris Rife suggested. SIGMMA did wonderful job once I was able to provide the second run with the correct FOM from the first round of MAD phase combination. The density quality (after SOLOMON) calculat

Re: [ccp4bb] How to run SIGMAA twice in a row? (fwd)

> structure" running mode of SIGMAA. This is the run we really wanted to combine > the model phases with the MAD phases before going through further density > modifications with SOLOMON or DM. I would have thought that you'd want to do this the other way around (density modification on MAD before

Re: [ccp4bb] recommendation for heavy atoms used in lithium sulfate and ammonium sulfate

Tiancen If you have enough crystals to experiment with, just do a normal series of heavy atom derivatives, starting with good old favorites such as mercury and platinum. As an added touch of class you can try tungstate - it's like sulphate, but has fat W so it can be used probably just like a hali

Re: [ccp4bb] exposing your Tev site

Lukacs, Christine wrote: Quick question about Tev sites – We have a situation where our N-terminal TEV site is inaccessible to the protease. Looking at a close homolog, we realized that our first protein residue is already involved in a beta sheet. From peoples’ experience – how FEW residues

Re: [ccp4bb] recommendation for heavy atoms used in lithium sulfate and ammonium sulfate

Tiancen, How critical is it that the crystals remain in the sulfate salts? I ask because we recently had success with an RNA crystal that was very intractable to heavy atom soaks because of very high lithium sulfate growth conditions, and the fact that cryo-protection was best done by increasing

[ccp4bb] exposing your Tev site

Quick question about Tev sites - We have a situation where our N-terminal TEV site is inaccessible to the protease. Looking at a close homolog, we realized that our first protein residue is already involved in a beta sheet. From peoples' experience - how FEW residues can we add between the cleav

Re: [ccp4bb] further inconsistencies (was: tcltkblt and python distributions)

OK, thanks for your comments. The most important statement was that BINARY.install just does not work any more without manual intervention on Linux systems! I recommend placing this information in an obvious location! *BUT* Again trying with a fresh download (this time without python since I wan

Re: [ccp4bb] further inconsistencies (was: tcltkblt and python distributions)

Hi, Actually, cctbx on linux has two different built, because different linuxes use different python unicode convention (ucs and utf) therefore, since ccbtx and phaser got some python modules built. They originally are in $CCP4/lib-ucs and $CCP4/lib-utf, but they are not inside $CCP4/lib. The same

Re: [ccp4bb] further inconsistencies (was: tcltkblt and python distributions)

Hello Oliver, if by 'conventional' you mean - download the source code - ./configure OS && make && make install I did not share your experience a couple of days ago when I did that. I used both the ftp and the download interface and nothing was missing. However from from your mentioning of 'BINA

[ccp4bb] further inconsistencies (was: tcltkblt and python distributions)

Dear ccp4 developers, when trying to do a conventional install of ccp4 (i.e. avoiding the install.sh script), I ran across additional problems/inconsistencies with the package: 1. In the tarball I freshly downloaded this morning, the cctbx tree under ccp4-6.0.2/lib was completely missing!!! 2.

Re: [ccp4bb] recommendation for heavy atoms used in lithium sulfate and ammonium sulfate

Hi Tiancen, I can recommend using a Halide soak (bromide or iodine). You could try to "exchange" part your salt with sodium bromide. Always use a bad looking crystal for the first soak though to see that it doesn't get damaged by the soak. See for further reference: Novel approach to phas