Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

On 11/30/2016 10:16 PM, Keller, Jacob wrote: If you fine slice and everything is then a partial, isn't that *more* sensitive to lack of synchronization between the shutter and rotation axis than the wide-frame method where there's a larger proportion of fulls that don't approach the frame

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

I am wondering whether part of the benefit of fine slicing is really increased multiplicity in disguise. I have seen in papers that empirically things do not improve much (or can even get slightly worse) past 0.5*SigPhi, which is the XDS-defined version of mosaicity; according to MOSFLM’s

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

>If you fine slice and everything is then a partial, isn't that *more* >sensitive to lack of synchronization between the shutter and rotation axis >than the wide-frame method where there's a larger proportion of fulls that >don't approach the frame edges (in rotation space) ? Especially if

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

There is a very nice paper by Colin Nave on Matching X-ray beam and detector properties to protein crystals of different perfection​,J Synchrotron Radiat. 2014 21, 537–546. Due to the spectral and geometric properties of in house sources there is probably no advantage with an oscillation below

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

Jacob, If you fine slice and everything is then a partial, isn't that *more* sensitive to lack of synchronization between the shutter and rotation axis than the wide-frame method where there's a larger proportion of fulls that don't approach the frame edges (in rotation space) ? Especially if

[ccp4bb] advice on screen dispensing?

Dear All, It looks like our old Hydra died of old age, and new Hydras seem quite expensive. We are now looking for an optimal way to transfer crystallisation screens from the deep well blocks into crystallisation plates. We were told Liquidator96 from Rainin, 5-200mkl worked well and was very

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

If the mosaicity is, say, 0.5 deg, and one is measuring 1 deg frames, about half the time is spent measuring non-spot background noise under spots in phi, which is all lumped into the intensity measurement. Fine slicing reduces this. But I am conjecturing that there is also

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

Hi Jacob, I may have missed completely your point but as far as my memory goes, the main argument in favour of fine slicing has always been reduction of the noise arising from incoherent scattering, which in the old days arose from the capillary, solvent, air, you name it. The noise

[ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

Dear Crystallographers, I am curious whether the observed effects of fine phi slicing might in part or in toto be due to simply higher "pseudo-multiplicity." In other words, under normal experimental conditions, does simply increasing the number of measurements increase the signal and improve

Re: [ccp4bb] RapiData at SSRL 2017

Please ignore, wrong email thread Leonard M. Thomas Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology Department of Chemistry and Biochemistry University of Oklahoma Stephenson Life Sciences Research Center

Re: [ccp4bb] RapiData at SSRL 2017

Hi Clyde, We have a crystal collecting now. If it does not finish by the time our time is up you can remove it. It is sort of a lets take some frames and see if we can do anything with it. Overall the run was okay, ended up with some useful information, not sure about publishable data but we

Re: [ccp4bb] Unfilled electron density for structure with tNCS

There are reasons why MR might fail to find additional copies; perhaps a surface loop in the search model interferes with packing. You should probably take a look at solvent content. On 11/30/2016 12:20 PM, Matthew Bratkowski wrote: Hello all, I am working on a structure in space group P4

[ccp4bb] Unfilled electron density for structure with tNCS

Hello all, I am working on a structure in space group P4 at a resolution of about 4 angstrom. Xtriage indicates that translational NCS is present. I am able to solve the structure by molecular replacement with four copies in the asymmetric unit, and there are two sets of identical copies.

Re: [ccp4bb] To win or not twinning?

First - there is a useful document about possible twin laws in the CCP4 documentation. It references the SHELX description of twinning for small molecules. http://www.ccp4.ac.uk/html/twinning.html It is possible in a trigonal system that you could have two twin operators but the twinning stats

Re: [ccp4bb] structure determination from a hollow crystal

Hi Eike, I wouldn't necessarily let the morphology deter you. While working on my PhD, a colleague collected beautiful data from hollow crystals. If the crystals collapse while looping, is it possible for you to perform "micro-surgery" on the crystal so that you only have a single face?

Re: [ccp4bb] To win or not twinning?

What about spacegroups in PG 32, e.g., p3212? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Napoleao Fonseca Valadares Sent: Wednesday, November 30, 2016 2:01 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] To win or not twinning? Dear CCP4ers, I'd like to kindly

Re: [ccp4bb] How to merge two cif files of ligands.

Dear Peng, The CCP4 interface for this task can be found in the menu Refinement -> Restraint Preparation -> Merge monomer libraries. Cheers, Wouter 2016-11-30 13:33 GMT+01:00 Peng : > Hello, > I was wondering how to merge two cif files of ligands for refinement. > Thanks, >

[ccp4bb] How to merge two cif files of ligands.

Hello, I was wondering how to merge two cif files of ligands for refinement. Thanks, Peng

Re: [ccp4bb] To win or not twinning?

Hi, The significant difference of refinement R values of the two models, single vs twinned crystal, indicates that the later is a far superior model of your crystal, corroborated its lower difference in Rfree-Rwork. However, I am curious about the refined twinning fraction, did it

[ccp4bb] AW: structure determination from a hollow crystal

Dear Eike, The fact that the crystal is hollow, won’t ruin your diffraction, as long as the crystal remains rigid. However, when the crystal is flexible and collapses during mounting and freezing, you are in trouble. Against the good practice, I would in this case try a big loop and scoop the

[ccp4bb] AW: [ccp4bb] To win or not twinning?

Dear Napo, For me this looks like a correct treatment of a twinned crystal. What more do you want/expect? Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Napoleao Fonseca Valadares Gesendet: Mittwoch, 30. November 2016 08:01 An: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

Dear all, I had this experience: going pedantically to the individual points the RSRZ and other validation statistics in the form were reporting - in a vast majority of the cases nothing was wrong at all. So it seems to be somewhat overdoing its job - not that this is bad on its own - but we are