[ccp4bb] Coot: changing scroll map keybinding

Hi, I believe, I have seen somewhere a keybinding, which cycle through maps attached to scroll wheel (basicaly moving the radio button "Scroll" in Display Manager). However, I can't find anywhere what key does that... Any ideas? Or do you know a coot function which does that? Best regards,

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Re: [ccp4bb] crystallization optimization

Dear Frank, I may see in the attached pic several nucleation points and a considerable amount of microcrystals. Based to my knowledge decreasing the concentration of the precipitant and/or the protein concentration would be a reasonable approach to refine the initial hits. By checking the diagram

Re: [ccp4bb] Problem with a cell content

Dear all, Thank you for all suggestions – I will try to go higher with the resolution and compare the maps. Thanks again! Best regards, Anna From: CCP4 bulletin board on behalf of Eleanor Dodson Reply-To: Eleanor Dodson

Re: [ccp4bb] crystallization optimization

The point I was failing to make: reducing either protein or precipitant concentration will indeed reduce nucleation, but often won't get you bigger or more single crystals: it will just make the appearance of crystals less reliable. The way to get big single reliable crystals is to

Re: [ccp4bb] crystallization optimization

Dear Patrick, Of course this is the best-first choice! I got confused with the names in my previous email. I was reffering to Chen when I mentioned the screens. Kindly, On Wed, Jul 12, 2017 at 12:48 PM, Olga Moroz wrote: > MMS (microseed matrix screening) into several

Re: [ccp4bb] crystallization optimization

MMS (microseed matrix screening) into several screens, as Patrick suggested earlier, would be the first choice for me. Works very often. Good luck! Olga > On 12 Jul 2017, at 08:48, Frank von Delft wrote: > > The point I was failing to make: reducing either

Re: [ccp4bb] crystallization optimization

Vicky, streak seeding is a very good method, but it can be quite a lot of work. Before he tries that, why wouldn't we suggest to Liuqing that he should try MMS - that is, adding a liquid seed stock to random screens? That way he is likely to end up with seeds in wells with similar conditions that

Re: [ccp4bb] Stable Refinement as Low(ish) resolution

Besides empirically adjusting the weighting factor for X-ray data to increase the geometric constraints, have you tried jelly-body refinement or refinement with external constraints? The latter two methods can be helpful when refining low resolution data. Roger Rowlett On Jul 12, 2017 7:33 PM,

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Re: [ccp4bb] crystallization optimization

Hi Everyone, Franks point is really interesting. We routinely reduce the protein concentration when we see too many precipitated wells, but we never dilute the screen. Has anyone tried this? All the best, Alun On 12/07/17 08:48, Frank von Delft wrote: The point I was failing to make:

Re: [ccp4bb] crystallization optimization

Dear All, Fine-tuning protein and precipitant concentration is of course the first line of approach, followed by both rMMS and streak-seeding. I would like to remind you of a far less popular but often successful in my hands, optimisation technique: It consists in incubating the trial at the

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Re: [ccp4bb] Stable Refinement as Low(ish) resolution

Dear Rhys, I second Roger on the use of jelly-body refinement. In addition, give Buster a try. It sometimes does magic at lowish resolution. All best. Andreas On Thu, Jul 13, 2017 at 1:17 AM, Rhys Grinter wrote: > Dear All, > > I'm currently in the process of

Re: [ccp4bb] Stable Refinement as Low(ish) resolution

Pretty much what the others have said, but there is a low resolution refinement pipeline in CCP4 called LORESTR (LOw-REsolution STructure Refinement). Several people I know have had good results with this. It automates the process of finding homologues, generating restraints, trying different

Re: [ccp4bb] Stable Refinement as Low(ish) resolution

Hi Rhys, Along with what others have suggested, you can always try prosmart refinement. I found it really helpful in my cases. Best of luck, Sudipta. Sudipta Bhattacharyya Postdoctoral research fellow University of Texas at Austin Texas, USA. On Jul 12, 2017 6:20 PM, "Rhys Grinter"

Re: [ccp4bb] crystallization optimization

All great suggestions and a few new ones I haven't used before (thanks Emmanuel and Frank). I agree with Emmanuel, a fine screen should definitely be first port of call, change the precipitant to go higher and lower than the initial hit (I normally vary the PEG in 2% jumps, in a 24 or 48 well

Re: [ccp4bb] crystallization optimization

It’s been my anecdotal experience that the phase diagram for proteins is nowhere near as uniform as is presented in most textbooks. So while in the presented diagram, I would definitely support the proposed experiment, knowing you are in that region of the phase diagram is many many many

Re: [ccp4bb] crystallization optimization

Yes, exactly. Thanks for doing the Right Thing and posting the actual diagram. On 12/07/2017 16:26, Patrick Shaw Stewart wrote: Alun I agree Frank's point is very interesting - and he intriguingly refers us to the phase diagram. Is the point that Line A is longer than Line B ? Best

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Re: [ccp4bb] crystallization optimization

So, if we have a commercial 96 well screen where more than around 60% of the drops precipitate. It may be worth diluting the whole screen say (30ul screen and 20ul water in each well) and repeating . rather than diluting the protein. Has anyone ever tried this? All the best, Alun On

Re: [ccp4bb] crystallization optimization

Yes, we have our screenmaking robot programmed to set 50% diluted screens and frequently employ this when a large fraction of the undiluted screens result in precipitation. We have found quite a few productive hits this way, as some previously grungy wells often present crystals when diluted.

Re: [ccp4bb] crystallization optimization

Yes, we have done this (addition of water to dilute screen reagents in the well) and also try it now in some cases and in fact, this is also the rationale behind Hampton's Crystal Screen Lite. Best, Debanu -- Debanu Das > On Jul 12, 2017, at 9:01 AM, Alun R Coker wrote: >

[ccp4bb] Stable Refinement as Low(ish) resolution

Dear All, I'm currently in the process of refining a low(ish) resolution structure at 3.2 Ang, with a fair level of anisotropy. I processed the data through the anisotropy server (https://services.mbi.ucla.edu/anisoscale/), which elliptically truncated the data to 4.0, 3.8 and 3.2 Ang. This

Re: [ccp4bb] Stable Refinement as Low(ish) resolution

Hi Rhys, In Refmac, you can change the weighting of the Xray terms vs the geometry restraints rather than use what is automatically assigned. Have you tried this? In Phenix you can use secondary structure restraints (probably you can do this in Refmac too, but I haven't tried) and try checking