Re: [ccp4bb] Problem with Coot on Mountain Lion
I have had success with the standalone Coot, found here: http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot It doesn't use the Fink package, which seems to be part of your problem. Try completely uninstalling your version and reinstalling this one. I've had no problems at all, though it did take Coot a minute or two to start once I upgraded to Mountain Lion.
Re: [ccp4bb] .cv to .mtz conversion
We recently had this problem in our lab. No matter what we tried, we could not get convert2mtz (or any other program) to work properly. We were probably doing something wrong with the fortran? Depending on how far along you are, you can try using phenix.refine. Just input your model and the .cv file and phenix will export a new .cv file with Free-R flags intact. If you aren't to the model building stage yet, this won't work however.
Re: [ccp4bb] Help needed in solving a MAD dataset
I second autoSHARP/SHARP. It makes great initial maps, and once you get it running, it is totally worth it.
[ccp4bb] Using SHARP to phase multiple different Sulphur-SAD datasets
Hello all, Does anyone know of an example where SHARP was used to phase multiple sulphur-SAD datasets and combine all of the data into one map? I have multiple crystals of the same protein, but each crystal form has a different LtoM mutation (the sulfur content of the native construct is too low for phasing without the mutations). The crystals are sensitive to oxidaton, so I cannot make one construct with all of the mutations, and selenomethionine incorporation is out due to the oxidaton issues. Each crystal form from all mutants is isomorphous. I would like to collect highly redundant datasets of each form, and then use SHARP to find all the Sulphurs, and combine the initial phases from all datasets with the native data and build the model. The protein has two domains, and I know the structure of one of them (~40% of the total), so I should be able to use the intial MR phases to help with finding the sulphurs Is this feasible? Are there any examples like this out there? Could something like ths also be done in MLPHARE or CRANK, etc? I want to make sure this is sound before I head off to a synchrotron with a million crystals! Thanks everyone!
Re: [ccp4bb] Difficult MR structures
Hi, If I were you, I would collect a redundant dataset (~15-20 or even higher if possible) at home and use the anomalous flag in Scalepack/Denzo. You should be able to pick up the anomalous differences (especially with data to 2.0A) for Se, even at CuKa wavelength at home! Good luck! Se.png
[ccp4bb] Solvent content of crystals vs. resolution?
Hello all, Does anyone know of some relevant literature (or a general idea really) that discusses protein crystal solvent content vs. average resolution? I am under the impression that the higher the solvent content, the lower the average resolutionbut I'd like to see some sort of data to back this up. Thanks!
[ccp4bb] Reducing Agent Tips?
Hello all, Anyone have any tips for reducing agents for use with the following crystallization conditions: 100 mM hepes, pH 7.5, 24% PEG 1500 or 100 mM Tris, pH 8.0, 24% PEG 1500 I've tried BME and DTT (1 mM). Currently trying out TCEP. The protein seems to be sensitive to oxidation, with a selenomet-derivative even more so. Thanks!
Re: [ccp4bb] How to get rid of the skin in the screening drop
This happened to me previously, and the only thing that worked for me was to lower the protein concentration. I was setting my protein up at 10 mg/mL, only to find skins on nearly all the drops. I would damage the crystals trying to get them out of the drops... I lowered my protein concentration to 7.5 mg/mL... the crystals still grew, and the skin didn't. This seems to happen a lot when you set up crystals with PEGs, so you might be able to lower the concentration of PEG as well.
