[ccp4bb] ctruncate bug?

2014-08-15 Thread Huw Jenkins
Hi I seem to be getting a lot of outliers rejected by Phaser with data processed with the latest ctruncate which are not present when data is processed with the older version (or old truncate) - has something been changed in the code that would cause this? With CCP4 6.4: ctruncate

Re: [ccp4bb] dynapro DLS cuvettes

2014-08-15 Thread Andreas Förster
Here's another one, catalog number 105-250-15-40: http://www.hellma-analytics.com/kuevetten/136/en/pg_id,41$g_id,24$item_id,63/fluorescence-cells.html#63 We use that for light scattering on a Zetasizer Nano. Andreas On 14/08/2014 10:35, Gloria Borgstahl wrote: Does any one know of a

[ccp4bb] cc1/2 value in hkl2000

2014-08-15 Thread Faisal Tarique
Hello everyone Can anybody please tell me where to locate the Corelation value between half sets (CC1/2) of a data processed through HKL2000 ?? -- Regards Faisal School of Life Sciences JNU

Re: [ccp4bb] cc1/2 value in hkl2000

2014-08-15 Thread Ed Pozharski
Probably the only way is to take unmerged scalepack output to aimless. Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Faisal Tarique faisaltari...@gmail.com /divdivDate:08/15/2014 9:40 AM (GMT-05:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject:

Re: [ccp4bb] cc1/2 value in hkl2000

2014-08-15 Thread Edward A. Berry
On 08/15/2014 09:40 AM, Faisal Tarique wrote: Hello everyone Can anybody please tell me where to locate the Corelation value between half sets (CC1/2) of a data processed through HKL2000 ?? First of all you must have a recent version of the suite- it didn't exist in earlier versions. Then,

Re: [ccp4bb] cc1/2 value in hkl2000

2014-08-15 Thread Philip Kiser
If you are using newer versions of HKL2000 it is printed in the scale.log file. On Fri, Aug 15, 2014 at 9:40 AM, Faisal Tarique faisaltari...@gmail.com wrote: Hello everyone Can anybody please tell me where to locate the Corelation value between half sets (CC1/2) of a data processed through

[ccp4bb] FW: [ccp4bb] dynapro DLS cuvettes

2014-08-15 Thread Prince, D Bryan
Some memories from the dark recesses of my mind… Hope it helps! Bryan From: Prince, D Bryan Sent: Thursday, August 14, 2014 6:07 PM To: 'Gloria Borgstahl' Subject: RE: [ccp4bb] dynapro DLS cuvettes Dear Gloria, I seem to remember that we had a DynaPro DLS system and used disposable plastic

Re: [ccp4bb] CC-half value ??

2014-08-15 Thread Ed Pozharski
Same here.  Ultimately, the KD test must be used in the end to finalize the resolution (keeping in mind recently discussed issues of effective resolution given data completeness).  I just want to add that at least some versions of aimless report overestimated resolution based on CC1/2 cutoff

[ccp4bb] Zinc binding protein expressed from insect cells

2014-08-15 Thread Harvey Rodriguez
Dear all, Sorry for the non-crystallographic question. Currently I am working on a zinc binding protein which is expressed in insect cells and may contain 4-6 zinc ions. As we know, so many zinc binding proteins can absorb the iron ions from the culture medium and the protein looks from yellow to

Re: [ccp4bb] CC-half value ??

2014-08-15 Thread Phil Evans
I should make the estimation in Aimless more robust, and curve fitting sounds like a good idea (but what function?). Outliers are a difficult problem, but anyway I think you should look at the curve and not just the number estimated. I would look at I/sigI as well, and anisotropy to decide the

Re: [ccp4bb] Zinc binding protein expressed from insect cells

2014-08-15 Thread Pascal Egea
Hi Heng, DTT can react with metal cations such as Zinc or Iron. This is why people to tend to use little DTT or no DTT at all on metal affinity columns or replace it b-mercaptoethanol or TCEP that do not interfere. Regarding the incorporation of Zinc into the culture media. I recall that Zinc

Re: [ccp4bb] CC-half value ??

2014-08-15 Thread Faisal Tarique
Thank you for your valuable suggestions..it really helped me a lot.. On Fri, Aug 15, 2014 at 8:38 PM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: I should make the estimation in Aimless more robust, and curve fitting sounds like a good idea (but what function?). Outliers are a difficult

Re: [ccp4bb] Zinc binding protein expressed from insect cells

2014-08-15 Thread Roger Rowlett
Harvey, Depending on the zinc-binding site, it may not bind Fe(II) at all. Zn(II) and Fe(II) have very different preferred ligand binding environments. For many zinc-metalloenzymes, substitution with Fe(II) would be difficult to impossible. In general, you will find it very difficult to make

Re: [ccp4bb] ctruncate bug?

2014-08-15 Thread Eleanor Dodson
Hmm - Phaser doesn't usually use such high resolution data? Surprised you are getting any stuff from resolutions higher that 2A. Whether the intensity at that resolution is meaningful would need careful inspection of the truncate logs - is the wilson plot reasonable? Are the 4th moments linear,

Re: [ccp4bb] desiring untouched ligand

2014-08-15 Thread Remie Fawaz-Touma
Hi all and thanks for your input. I am trying to fix a sugar chain that has consecutive glucoses and I need the angle C-O-C to be as close to 104 degrees as possible keeping alpha bonds between the sugars, so when I do a Real Space Refinement in Coot, the structure gives angles close enough to