Re: [ccp4bb] REFERENCE_DATA_SET in XDS-CORRECT

Hi Wolfram, I don't know why the (seemingly) wrong choice was made; usually this works as expected, so it may be a bug. If you send me just enough to reproduce this (XDS.INP, INTEGRATE.HKL, plus the reference data set) I'll find this out, and fix the bug if there is one. I treat all data as con

Re: [ccp4bb] Combining MR and SIR phases

Thanks everyone for your suggestions, I have a lot to try! Luke On Tue, 23 Jul 2019 at 17:43, Eleanor Dodson wrote: > Well - there are lots of ways to proceed. It doesnt really matter for the > crystallography theory if the exptl phases are from SAD or SIR. Just harder > to handle in some softw

Re: [ccp4bb] challenges in structural biology

There are a bunch of people doing this – in the small molecule world. And a lot of work has been done on some very robust protein systems too. Can you guess which ones? The real issue (at the moment) is that all the pre-work needed to predict if or how a protein might crystallise takes more wor

Re: [ccp4bb] challenges in structural biology

Yes, but are we poets or scientists? Wax lyrical in your poetry, but maybe have some standards in our science? cheers, tom Tom Peat Proteins Group Biomedical Program, CSIRO 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From

Re: [ccp4bb] challenges in structural biology

..and responding in the same vein: my OED says that its etymology also comes from the Latin sulfur, sulphura in the plural. So there is an etymological basis for the ph, even if it doesn’t come from Greek. Plus, since when has etymological logic has _anything_ to do with English spelling? Fi

Re: [ccp4bb] challenges in structural biology

Hi Going off at a tangent... The accepted spelling by the Royal Society of Chemistry (i.e. the professional body representing chemists in the U.K.) since at least the early 1990s has been "sulfate" too. "Sulphur", etc, has been deprecated for quite some time. Why? Well, there's no good etymolo

Re: [ccp4bb] challenges in structural biology

A recent paper in my favourite journal :-) suggests there is no correlation in crystallisation conditions even for similar proteins: http://scripts.iucr.org/cgi-bin/paper?S2053230X19000141 As you write, surface loops are likely to be diffe

Re: [ccp4bb] challenges in structural biology

What about developing a theory of how crystallization happens, i.e., what does the microscopic “picture” look like when crystals are forming, then predicting based on that picture? I remember looking into these things about ten years ago, and there were some cool things being done with various s

[ccp4bb] REFERENCE_DATA_SET in XDS-CORRECT

Hi all, I have a dataset that looks like from (a) primitive hexagonal crystal(s), apparent (from merging stats) point group 32 or may be (twinned?) 3. During CORRECT, I am imposing space group number 143 and specify a REFERENCE_DATA_SET to determine the optimal reindexing operator between two wedge

Re: [ccp4bb] Combining MR and SIR phases

Nomenclature: pure SIR or MIR without anomalous has almost never been used, since the beginning of macromolecular crystallography (why would you?). So those of us who are lazy have often used SIR/MIR when we meant SIRAS/MIRAS: we should be more precise. Phil Sent from my iPhone > On 23 Jul 2

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] challenges in structural biology

Biophysical techniques used to screen samples (e.g. SEC, SEC-MALS, DLS, SAXS, CD...) before freezing are not as promising as many hope for. There are lots of examples where samples behave beautiful by multiple biophysics methods and then crash and burn on a cryo-EM grid. Consequently, screening

Re: [ccp4bb] challenges in structural biology

On a completely different tack, isn’t the most pressing requirement in current structural biology a really good method of characterizing macromolecular samples *before *they are put onto cryoEM grids – ie analysing *and screening them *in solution. For one thing I’m told those huge microscopes are

Re: [ccp4bb] challenges in structural biology

Hi James – thx for starting a riveting thread. (Of course) I agree with Dom, Janet, Artem and the cosmic cats that crystallization is key. I also agree with Artem a relatively modest investment in the fundamentals of crystallization could make a big difference – even a 10% improvement in producti

Re: [ccp4bb] challenges in structural biology

On 7/23/19 3:35 AM, melanie.voll...@diamond.ac.uk wrote: > No longer those 20 odd names for ammonium sulphate You mean ammonium *sulfate*. As it is called across the pond. :) On a related note on common nomenclature for recording crystallization experiments that Janet brought up: I find it odd

Re: [ccp4bb] higher older tNCS

Dear Jessica, There's a dedicated Phenix bulletin board, where it would be better to post Phenix-specific questions. Nonetheless, you can do this in both the CCP4 and Phenix interfaces to Phaser, so I'll explain how to do this in all the interfaces. First, I'm guessing that the order of the tN

[ccp4bb] higher older tNCS

Hello everyone, Does anyone know of a good phenix tutorial on how to deal with higher order translational non-crystallographic symmetry (tNCS) in a structure? Ultimately, I need to know how to set TNCS NMOL to 3 in phaser of Phenix. I am using the phenix GUI, and I am uncertain how to alter this

[ccp4bb] Postdoc position available in an enzymology laboratory at Florida State University

Dear all One postdoctoral position is available immediately in an enzymology laboratory to elucidate mechanisms of DNA/RNA synthesis, DNA lesion bypass, and base excision repair catalyzed by various human and viral DNA/RNA polymerases, and to mechanistically investigate gene editing enzymes inc

[ccp4bb] PhD Positions: structural biology in biomedical research

Dear Colleagues, The Medical University of Graz and the University of Graz, offer PhD positions in the international PhD programs including the framework of the Special Research Program (SFB) Lipid Hydrolysis. We are hiring motivated PhD candidates for positions and offer an in-depth, multi

Re: [ccp4bb] Combining MR and SIR phases

Oops George - you are correct.. I guess I never think of using either SIR or SAD phases without some investigation into hand, and then only work with the better result. The selection for SAD is rather straightforward - use SHELXE to do density modification and if your sites are correct it is usual

[ccp4bb] Rigaku system up for grabs

Dear CCP4bb We are going through a large lab refurbishment programme and that, along with space costings for facilities, mean that sadly we will not be able to keep our local generator & detector. If anybody can come to Leeds and take it all away (free!) then please do so! The system: Rigaku M

Re: [ccp4bb] Combining MR and SIR phases

I'm afraid that I have to disagree with Eleanor, a very rare event. Both pure SIR and pure SAD give you only half of the necessary phase information. The initial map will in both cases be a double image. One then tries to improve it by density modification. For pure SAD one image is positive an

Re: [ccp4bb] Combining MR and SIR phases

Well - there are lots of ways to proceed. It doesnt really matter for the crystallography theory if the exptl phases are from SAD or SIR. Just harder to handle in some software I think I would start to refine the poor MR model with the xptl phases as restraints. REFMAC will do this. Then see if the

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

Hi, I agree with Melanie and I think we should also go further... We could require reviewers to tick a box on a PDB reviewer page to confirm they have “checked” the structure. Whether this box has been ticked could then be displayed on the PDB page (of course the reviewer would remain anonymous

[ccp4bb] Combining MR and SIR phases

Hi all, I have collected native data and data on a bromide derivative of one of my crystals, but have struggled to get a second derivative. I went through the SIR pipeline as the anomalous signal from the Br was weak and have generated some not-so-great phases. I have also attempted MR with the cl

Re: [ccp4bb] challenges in structural biology

I don't think AI will do our job in future as it heavily relies on the crystal structures for training. However, as a community we should embrace this technology/method to help us solve our structures. And why not start with crystallisation? And again the PDB is in a good position here to enforc

Re: [ccp4bb] Density questionable?

Dear Peer, Engi, Have you looked at the symmetry mates in Coot? If you look at the packing of your molecules and it makes sense to place an additional molecule in the gap in order to create crystal contacts then you should do so. I would place the whole molecule there and start with an occupa

Re: [ccp4bb] challenges in structural biology

If you look at the nice figure at the top of the online article, do you believe that this (or rather, the correct) arrangement of domains/ molecules can be predicted from a couple of correlated mutations, and energy minimization? I think AI is a long way from that. Finding the correct fold of a

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

Dear John, Yes, I think the PDB should be stricter. The PDB is in the position to enforce compliance with rules and if they are not followed then one doesn't get a validation report and in turn it would be difficult to publish (most journals require a validation report). For years it has been

Re: [ccp4bb] Density questionable?

Hi Engi, I understand that you say that the 2nd molecule in your case is not real; it's just model bias? I would not come to this conclusion. B values of NCS-related chains being quite different is not that rare. In my experience, at 1.8A and with a reasonably refined model (Rfree less than 30