Re: [ccp4bb] refmac5 vs phenix refine mixed up

2013-01-25 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Pavel, dear Garib, how do you figure out automatically the correct flag? (I hope both phenix and refmac will allow to manual overwrite the software's decision) Cheers, Tim On 01/24/2013 07:47 PM, Pavel Afonine wrote: Hi, It would be nice

Re: [ccp4bb] off topic - legacy hardware help needed

2013-01-25 Thread Adam Ralph
You can just connect two machines together with an ethernet cable, no switches or routers. However you need a crossover cable to do this. Most likely you have standard cables only in the lab. Adam 

Re: [ccp4bb] refmac5 vs phenix refine mixed up

2013-01-25 Thread Garib N Murshudov
Dear Tim In principle if a user defines freer flag then refmac knows about that (unless freer flag is 0 then refmac assumes that it is default). In this case (if freer defined by user) then it is not altered. regards Garib On 25 Jan 2013, at 09:14, Tim Gruene wrote: -BEGIN PGP SIGNED

Re: [ccp4bb] off topic - legacy hardware help needed

2013-01-25 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Adam, cross-over cables are only required for really old machines. For a few years, RJ-45 plugs have been able to figure out automatically whether they are connected to a switch or directly to another machine. Best, Tim On 01/25/2013 10:40 AM,

Re: [ccp4bb] refmac5 vs phenix refine mixed up

2013-01-25 Thread Robbie Joosten
I noticed that Refmac has done the 1vs0 thing correct for ages, which is very useful because mix-ups between the work set and test set used to be quite common in the reflection files at the pdb (Refmac saved me a lot of extra work with this). Dealing with this problem is very simple as the

Re: [ccp4bb] A question about FFT

2013-01-25 Thread Eleanor Dodson
The FFT software tries to limit the volume to the asymmetric unit for the spacegroup. This has to be a 3-D box, so cubic spacegroups give more peaks than expected, but not a full list of 1260 .. However there may not be a complete list - these S are in di-sulphide bonds, and at limited resoluton

Re: [ccp4bb] A question about FFT

2013-01-25 Thread Ian Tickle
Hi Wei Are you saying that the highest 9 peaks in your list that you highlighted correspond to disulphide-disulphide vectors and the rest don't? Actually of the 9 only 3 are independent, the other 6 are related by the 3-fold so you need to take that into account in your calculation of the no of

Re: [ccp4bb] refmac5 vs phenix refine mixed up

2013-01-25 Thread Nat Echols
On Fri, Jan 25, 2013 at 2:24 AM, Robbie Joosten robbie_joos...@hotmail.com wrote: Phenix however needs to deal with the CCP4 type reflection binning. Now the size of the sets cannot be used which means that you have find a smarter solution. So I wonder how this is implemented. Does Phenix use

[ccp4bb] RapiData: Seats are available - the deadline is in 10 days for our course on Data Collection and Structure Solving at the NSLS.

2013-01-25 Thread Robert Sweet
We will present RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/.

Re: [ccp4bb] A question about FFT

2013-01-25 Thread Ian Tickle
Hi Wei The explanation from looking at your FFT log file would appear to be that what you have calculated is not a Patterson at all but an anomalous difference Fourier, which would of course explain the lack of peaks! The evidence for this is that the FFT run 1) has the phase FOM assigned, 2)