Re: [ccp4bb] twinned data refinement

If you have unmerged data try running it through pointless/aimless/ctruncate. That analyses twin fractions very carefully and with that twin law you should see some evidence of 6 fold symmetry but less pronounced than for the 3 and 2 fold symmetry operators.. Eleanor On 11 June 2015 at 01:03,

Re: [ccp4bb] twinned data refinement

On Wednesday, 10 June, 2015 17:35:25 Mengbin Chen wrote: Hello everyone, I am refining a 2.5 angstrom structure whose phase is solved by molecular replacement with a search probe determined by SAD with 3 angstrom resolution. While I am able to see densities of a bunch of water molecules and

[ccp4bb] twinned data refinement

Hello everyone, I am refining a 2.5 angstrom structure whose phase is solved by molecular replacement with a search probe determined by SAD with 3 angstrom resolution. While I am able to see densities of a bunch of water molecules and ligands in the MR solved structure, which means that the phase

Re: [ccp4bb] twinned data refinement

Thank you Jacob and Ethan! I haven't put water molecules into the density blob, which aren't many out there, but I fitted the ligands in already. Molbrobity statistics are not yet great, since there are 13.5% rotamer outliers. Will adjust the models manually, and try refmac and TLS refinement.

[ccp4bb] twinned data

Dear all Lately i have found my crystals to be pseudomerohedrally twinned with a twin fraction of 0.22..but on doing twin refinement nothing much is changing in terms of statistics as compared to the previously solved data which did not include twin refinement (in present case the data is solved

Re: [ccp4bb] Twinned Data - more information

Or put all files into pointless.. It will read XDS and do the indexing checks Eleanor On 19 Oct 2012, at 12:45, vellieux wrote: Well, the first thing I note is that P6(3) is a polar space group. Hence what I would do myself is the following: take your crystal 'number 1' (as a reference);

Re: [ccp4bb] Twinned Data - more information

Dear Iris, just to add to Fred's posting: since XDS Version June 2, 2008 re-indexing is no longer necessary if REFERENCE_DATA_SET is used - XDS then does the re-indexing automatically in the CORRECT step. This makes it very easy to avoid the problem of alternative indexing in space groups like

Re: [ccp4bb] Twinned Data

Hello, I am afraid that you aren't saying (writing) enough to describe the problem(s) you are facing... Twin fraction ? How many crystals were used to collect the diffraction data (remember that there are polar space groups, where c going up is different from c going down) etc etc. Without

[ccp4bb] Twinned Data - more information

Hello everybody, I collected datasets with a resolution to 2.8A from 3 crystal grown in the same condition. The space group seems to be P63. Statistic of XSCALE.LP SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS

Re: [ccp4bb] Twinned Data - more information

Well, the first thing I note is that P6(3) is a polar space group. Hence what I would do myself is the following: take your crystal 'number 1' (as a reference); take the results of XDS for crystal number 2 (XDS_ASCII.HKL) and reindex it; try to see which of the original XDS_ASCII or the

Re: [ccp4bb] Twinned data

: Friday, October 01, 2010 6:35 PM To: Clayton, Gina Martyn Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Twinned data If you really have the systematic absences for P41 or P43 then you must have (at least) four molecules in the cell, twinning cannot reduce this. Since a solvent content of 16

Re: [ccp4bb] Twinned data

: Clayton, Gina Martyn gina_clay...@merck.com Date: Friday, October 1, 2010 21:28 Subject: [ccp4bb] Twinned data To: CCP4BB@JISCMAIL.AC.UK Hi there Just wondering if anyone has any suggestions how I can deal, if possible, with the following situation -. My first encounter with twinned data

[ccp4bb] Twinned data

Hi there Just wondering if anyone has any suggestions how I can deal, if possible, with the following situation -. My first encounter with twinned data... which initially indexed as p43/p41 cell dimensions 58.4 58.4 61 90 90 90. Having seen the Matthews Coefficient for the solvent content of

Re: [ccp4bb] Twinned data

If you really have the systematic absences for P41 or P43 then you must have (at least) four molecules in the cell, twinning cannot reduce this. Since a solvent content of 16% is too low, the most likely explanation is that it is not twinned but that the protein is smaller than the one you are

[ccp4bb] Twinned data and maps

Hi again, Thanks for your insight into refinement tools for twinned data. I have a couple of twinned data sets that are nearly perfectly pseudomerohedrally twinned. I've begun to refine my data in Refmac5 (using the automated twin refinement), CNS (using the twin inputs) and Shelxl; I'm testing

Re: [ccp4bb] Twinned data and maps

I am not sure if there is any way of avoiding model bias if the coordinates are included regardless of whether there is twinning or not - my preferred method is to set the occupancies of suspect regions to 0.00 then do refinement of the better parts of the model and then check maps again and

[ccp4bb] AW: [ccp4bb] Twinned data and maps

...@jiscmail.ac.uk] Im Auftrag von Walter Kim Gesendet: Monday, March 16, 2009 7:22 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Twinned data and maps Hi again, Thanks for your insight into refinement tools for twinned data. I have a couple of twinned data sets that are nearly perfectly

Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps

... Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Walter Kim Gesendet: Monday, March 16, 2009 7:22 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Twinned data and maps Hi again, Thanks for your insight into refinement tools

Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps

to try more than one program, and also to try Phenix ... Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Walter Kim Gesendet: Monday, March 16, 2009 7:22 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Twinned data and maps

Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps

Phenix ... Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Walter Kim Gesendet: Monday, March 16, 2009 7:22 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Twinned data and maps Hi again, Thanks for your insight into refinement

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Twinned data and maps

: Monday, March 16, 2009 12:52 PM An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps But dont all twinned refinement programs output detwinned terms for a map? Certainly REFMAC and SHELX do. Eleanor Clemens Steegborn wrote: Hi Walter, You should definitely detwin

Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps

, 2009 7:22 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Twinned data and maps Hi again, Thanks for your insight into refinement tools for twinned data. I have a couple of twinned data sets that are nearly perfectly pseudomerohedrally twinned. I've begun to refine my data in Refmac5 (using