Re: [ccp4bb] problem with 'generate' (cns_solve)

Hi Mareike, Did you also use Coot to fit the small molecule into the structure? If so, there might be some glitch at the stage of writing out the remodeled ligand... Do the coordinates for the small molecule look different within the input and output pdb files for the ligand when you look at

Re: [ccp4bb] Ni-NTA purifications contaminated with E coli Glucosamine-fructose-6-phosphate aminotransferase

How about trying two opposite ion-exchange columns??!! Namely, monitoring co-elution behaviour on anion exchange and cation exchange. For example, we have a case where the contaminant and protein of interest will both bind and co-elute from monoQ but only protein of interest or contaminant

Re: [ccp4bb] Molecular replacement

The answer to your question is called Phaser. Using Phaser, you can input multiple search models in one search routine to look for solutions. You should read the online manual and tutorials, if you are not already familiar with Phaser. You can also 'modify' or appropriately 'trim' your

Re: [ccp4bb] Strange diffraction images

Very dumb question perhaps: If there were two interpenetrating lattices of slightly different cell dimensions, would we not expect that the indexing program would leave out a lot of the spots as unpredicted or uncovered? Could someone clarify with respect to the diffraction pattern that has

Re: [ccp4bb] Crystallography short courses?

The Rapidata course held at Brookhaven every year is a five-day course precisely for what you are talking about. I benefited much from attending the course. Check the link: http://www.px.nsls.bnl.gov/courses/rr_course_2007/ Hope that helps. Raji -Included Message-- I am

Re: [ccp4bb] High Wilson B

Hi Mike, To my limited understanding, it is hard to get an accurate Wilson estimate for data below 3Ang (am I right??!). To me, the B-factor you list doesn't sound bad although some folks might holler 'Bloody Murder' when I say so. I have a structure to 3.7Ang (I'd have liked higher resolution

Re: [ccp4bb] questions about CNS

Well, I guess you can mess with the overall B-factor correction in the anneal.inp and rigid.inp files and say, turn them off. NOT a good way to proceed. That is just to let you know where to find it. If you haven't already done so, do the following after the simulated annealing step. After

Re: [ccp4bb] Protein-DNA complex for crystallization

Hi Kumar, 1) While you contemplate other ideas, have you tried the following already? - microseeding or macroseeding with the tiny crystals you have? - crystallization using sitting drop vapour diffusion under oil? Often, one gets a burst of nucleation with several tiny crystals. Not sure if

Re: [ccp4bb] Help with reducing crystal mosaicity

You can also try to use the micromount loops (look like ink-pen nibs) sold by Mitegen. They are a much easier alternative to capillary mounts; they are easy to handle and work well for room temperature data collection. Good luck. Raji -Included Message-- At the risk of

Re: [ccp4bb] How to remove nucleic acid contamination for crystallizing zinc finger protein

Yes, I have seen colleagues get rid of tons of DNA contamination in bacterial RNA polymerase preps by PolyminP (PEI) precipitation. Seemed like it was the only method that worked (among several tried) to remove all the non-specific DNA. Worked very well. As painful as it appeared, PEI

Re: [ccp4bb] heavyatom soaking problem

In one case, co-crystallization with heavy atom (Au) was one of the few approaches that worked. Not sure if you've also tried short soaks with Hg, Pt, Au. Helped for one of my former colleagues while long soaks messed things up. You have not mentioned if Selenomethionine derivatization has

Re: [ccp4bb] parameter and topology files in CNS

Hi Jae, Try resetting the MAXJNT parameter (increase the set value). I had problems with MAXA and other parameters and I suspect your problem has the same solution. You might need root access for the same. Also, make sure that you are specifically asking to read the topology and parameter

[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] Multiple nucleation

I've found that crystallization in sitting drops under oil dramatically reduces the no. of nucleation events and increases the overall crystal size. Now, if the increased crystal size helps improve diffraction is something to be tested. Among the many other suggestions... Raji

Re: [ccp4bb] mtz to hkl conversion

Hi Vineet, Try using TEXTAL for model building at your resolution. I heard that this is optimized for 2.8Ang or so resolution. For MTZ to HKL with HL's intact, read the Tutorial section on the CNS webpage with example scripts. Go to section 'Data Conversion' and look at 'Converting a CCP4 MTZ

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