Re: [ccp4bb] should the final model be refined against full datset

2011-10-15 Thread Nicholas M Glykos
Dear Ethan, List, > Surely someone must have done this! But I can't recall ever reading > an analysis of such a refinement protocol. > Does anyone know of relevant reports in the literature? Total statistical cross validation is indeed what we should be doing, but for large structures the com

Re: [ccp4bb] should the final model be refined against full datset

2011-10-15 Thread Anastassis Perrakis
> > > For structures with a small number of reflections, the statistical noise > in the 5% sets can be very significant indeed. We have seen differences > between Rfree values obtained from different sets reaching up to 4%. This is very intriguing indeed! Is there something specific in these

Re: [ccp4bb] should the final model be refined against full datset

2011-10-15 Thread Nicholas M Glykos
> > For structures with a small number of reflections, the statistical > > noise in the 5% sets can be very significant indeed. We have seen > > differences between Rfree values obtained from different sets reaching > > up to 4%. > > This is very intriguing indeed! Is there something specific i

Re: [ccp4bb] data processing problem with ice rings

2011-10-15 Thread Kay Diederichs
Hi ChenTiantian, the R-factors and I/sigma are bad even at low resolution where the first icering does not influence the results. Thus, the problem with your data processing has little to do with the icerings. I guess that the indexing is not correct. My suggestion: 1) using adxv or a similar

Re: [ccp4bb] "Insufficient virtual memory"

2011-10-15 Thread Kay Diederichs
Hi Ian, compiling on your 32bit machine gave you a 32bit binary, so your 12GB RAM cannot be used! HTH, Kay Am 20:59, schrieb Ian Tickle: Hello all, some Fortran developer out there must know the answer to this one. I'm getting a "forrtl: severe (41): insufficient virtual memory" error when

Re: [ccp4bb] data processing problem with ice rings

2011-10-15 Thread Harry
Hi I'd agree with Kay here - I would think that the original indexing is incorrect. One thing I notice on the original image as posted - there's a red cross on it - if that's supposed to mark the beam position, I think it's about 4mm or so away from the true position. So - (1) check th

Re: [ccp4bb] How to calculate energy?

2011-10-15 Thread Boaz Shaanan
This should all be in the CNS output file for each cycle.   Boaz     Boaz Shaanan, Ph.D. Dept. of Life Sciences  Ben-Gurion University of the Negev  Beer-Sheva 84105 

Re: [ccp4bb] Akta Prime

2011-10-15 Thread Mark Brooks
Dear Mike,                At Evotec (a UK site), we gave up using GE to service our GE instruments (!) due to problems with their bureaucracy. Agilent offer service contracts for Aktas that are competitively priced and are a work-alike in our experience. For call-outs, they sub-contract the usual

[ccp4bb] small 3ml Superdex column performance

2011-10-15 Thread Alexandra Deaconescu
Hi everyone: I was hoping I could get your opinion on the performance of the small approx. 3ml gel filtration columns from GE Healthcare. We currently have an Akta fplc and we would like to do small runs using small volumes of sample. As far as I know we have two options: 1. use the Superdex

Re: [ccp4bb] data processing problem with ice rings

2011-10-15 Thread Nian Huang
Hi, I agree with other people. You must have a wrong index here. Can you tell us what is the unit cell for this crystal from your determination? I can see very close spots in the high resolution shell from your image, which are overlapped into one spot in the low resolution shell. Try to use other

Re: [ccp4bb] small 3ml Superdex column performance

2011-10-15 Thread Artem Evdokimov
Hi, You're probably referring to the Superdex 5/150 Tricorn column, with working volume of 3ml, and not the 15/150? Those columns work quite nicely for small sample volumes. For analytical runs 15-25ul injection is pretty nice. The PC columns are originally designed to be used with the SMART syst