Re: [ccp4bb] Instrument help: any comments on bench-top SPR

Bioptix is another option you may consider for your needs. if they still have the Bioptix Innovators program running you may also be able to have the instrument placed for a free timed trial with training to see if fits your needs. contact them to see. the sensor chips, one for amine-coupling is

Re: [ccp4bb] small lysozyme crystals?

i wonder if crushing with a hammer maybe a good first step. does streak seeding after that give smaller crystals amongst the range of different size crystals possible. perhaps? either way would be good for the summer student to try out. -- Karthik On Tue, Jul 26, 2011 at 10:55 AM, James Holton

[ccp4bb] program to display space group symmetry in three dimensions

Hi, I was looking around for programs that display space group symmetry information and could not find any but perhaps i am lost for valuable or relevant keywords. I found two references TABLES and CRYST, but are there other alternatives that are more recent, or that can run on more common

Re: [ccp4bb] where I have been going wrong in crystallization?

It makes slight sense if the word 'respect' can be correlated with whether the drop is mixed (protein+ppt). i have heard some protein may indeed crystallize if it were not mixed or vice-versa (do not expect it with lysozyme though). it would make sense if diffusion played a role but with few ul

[ccp4bb] overexpression of unintended protein

Hi, I apologize immediately that this question is not directly related to crystallography but the protein i am trying to overexpress is eventually for that purpose. i understand the huge knowledge-base of people here experienced in protein expression/purification and would appreciate any insight

Re: [ccp4bb] overexpression of unintended protein

your story may be different, but I agree that overexpression can indeed do weird things to the guts of E. coli. -James Holton MAD Scientist Karthik S wrote: Hi, I apologize immediately that this question is not directly related to crystallography but the protein i am trying

Re: [ccp4bb] AW: [ccp4bb] off-topic: crystal optimization without buffer

Hi Katja, If your protein preparation did have salt, you could try lowering that salt (if your protein tolerates) and grid search with varying (increasing) PEG concentrations. Seeding and Additives should really help. the effect/outcome is difficult to predict but these two techniques are helpful

Re: [ccp4bb] how to find missing density or fill gap

You know the sequence of the target so the missing residues can be built by looking at the difference density. if the protein is phased right by MR then the extra residues if they were actually present (and not clipped off in crystallization) you should see them. coot can be used to visualize and

Re: [ccp4bb] Peak wavelength of SeMet and the corresponding f_prime and f_doubleprime.

This link was posted earlier, perhaps it is the one you were looking for: http://skuld.bmsc.washington.edu/scatter/AS_form.html http://skuld.bmsc.washington.edu/scatter/AS_form.html-- Karthik Graduate Student University of Michigan On Sat, Oct 31, 2009 at 10:44 AM, james09 pruza

Re: [ccp4bb] Help me!!

I have been there, and like most things that we want to learn the best way is to practice them. suggest joining a lab that solves structures using crystallography would be your best way to learn. there are introductory textbooks that will also give you a feel for the subject (like crystallography

Re: [ccp4bb] Test of cryoconditions without X-rays or cryostream

I have not heard of anyone checking for suitable cryo in that fashion how fast can you do it before it is affected by room temp and how would you know about the ice rings, but when you have crystal(s) and not crystal you can freeze different ones in several different cryos (sugars, glycerol etc)

[ccp4bb] Solvent mask in refinement programs

How is the solvent mask handled for zero occupancy atoms? In general is it justified that i fear some of the electron density belonging to the protein in the periphery of the molecule can be solvent flattened and i never see them thereafter in my electron density maps or is this just not going to

Re: [ccp4bb] Solvent mask in refinement programs

...@umich.edu _ On Thu, Sep 17, 2009 at 2:28 PM, Karthik S biokart...@gmail.com wrote: How is the solvent mask handled for zero occupancy atoms? In general is it justified that i fear some of the electron density belonging to the protein in the periphery of the molecule  can

Re: [ccp4bb] Stacked Plate Like Crystals

You may be able to optimize them but that is still a step further, with recent advances in microbeam at the synchrotron, you *may* be able to scan through different regions of your crystal (especially if the stacking is not exactly one on top and is little oblique) and collect data! -- Karthik