Re: [ccp4bb] vector and scalars

2010-10-16 Thread Tim Gruene
Dear Ian, maybe you should switch from Fortran to C++. Then you would not be forced to make nature follow the semantics of your programming language but can adjust your code to the problem you are tackling. The question you post would nicely fit into a first year's course on C++ (and of course can

Re: [ccp4bb] molecule on symmetry axis

2010-10-16 Thread Tim Gruene
Hello Jackie Vitali, What happens if you model the tartaric acid as if it were not on a symmetry axis and then let phenix deal with the symmetry? I once had a water of which refmac stubbornly lowered the occupancy to 0.5 even though i kept on bringing it back to 1.0 until I realised that it was on

Re: [ccp4bb] molecule on symmetry axis

2010-10-16 Thread Robbie Joosten
Hi Tim, I'm all for automation and 'smart' software but it should not be a substitute for common sense. In the case of occupancies, not all software seems to be smart. There are about 1100 structures in the PDB that have problems with wrong occupancies at special positions and a good part of th

Re: [ccp4bb] update REFMAC

2010-10-16 Thread Boaz Shaanan
Hi, If I may add to that (straight from Garib's mouth) an option that I have not been aware of: adding external keywords (it's in the gui as I discovered. I have not tried it yet). Adding external keywords: Please have a look the presentation: http://www.ysbl.york.ac.uk/refmac/Presentations/Re

[ccp4bb] How to add water molecules..??

2010-10-16 Thread Hussain Bhukyagps
Dear All, How to add water molecules in the structure (PDB) after all the refinements..?? Thank You, Hussey.

Re: [ccp4bb] How to add water molecules..??

2010-10-16 Thread Frederic VELLIEUX
I am not sure that I understand your question perfectly... You can add/remove waters "automatically" during refinement using the proper options. After refinement, then you can also (i.e. you should also) take the output mtz file and use a graphics program (with PDB and MTW file) for modelling (i

Re: [ccp4bb] quantum diffraction

2010-10-16 Thread Bernhard Rupp
> The wave function doesn't collapse to a single outcome > until the detector measures something Reference: Tronrud D, Entanglement-phasing in Quantumcryptocrystallography, Nature epub, doi:0101010.

Re: [ccp4bb] quantum diffraction

2010-10-16 Thread Jürgen Bosch
Can't find your reference unless you are referring to this one: JOURNAL OF MODERN OPTICS, 1994, VOL .41, NO .12, 2413-2423 In case I'm wrong, could you post the direct link for download of Dale's paper ? Thanks, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of

Re: [ccp4bb] molecule on symmetry axis

2010-10-16 Thread Nicholas K. Sauter
Phenix can refine a tartaric acid on the twofold if you set the occupancy to 0.5 AND set the custom-nonbonded-symmetry-exclusion selection to the tartaric acid. It's a new feature. Nick Sent from my iPhone Nicholas K. Sauter (510)847-1592 cell (510)486-5713 desk On Oct 16, 2010, at 1:25 AM, T

Re: [ccp4bb] vector and scalars

2010-10-16 Thread Ian Tickle
Hi Tim As I indicated previously, the Fortran code was only meant to define my statement of the problem so that there can be absolutely no ambiguity as to the question: the answer to the problem (if it exists) has nothing whatsoever to do with the programming language used and I don't see how it c

Re: [ccp4bb] vector and scalars

2010-10-16 Thread James Stroud
On Oct 16, 2010, at 12:32 PM, Ian Tickle wrote: I have not yet come across a purely algebraic problem which possesses semantics that couldn't be expressed in Fortran. That doesn't mean there aren't any, If it can't be expressed in FORTRAN, it probably can't be solved in any other language e

Re: [ccp4bb] vector and scalars

2010-10-16 Thread Douglas Theobald
On Oct 16, 2010, at 3:32 PM, Ian Tickle wrote: > Hi Tim > > As I indicated previously, the Fortran code was only meant to define > my statement of the problem so that there can be absolutely no > ambiguity as to the question: the answer to the problem (if it exists) > has nothing whatsoever to do

Re: [ccp4bb] vector and scalars

2010-10-16 Thread Ian Tickle
Tim, PS perhaps you should ask George Sheldrick whether he has ever found himself constrained as to the algorithms he is able to program by the semantics of Fortran. I suspect his answer will be the same as mine! Cheers -- Ian On Sat, Oct 16, 2010 at 8:50 AM, Tim Gruene wrote: > Dear Ian, > >

Re: [ccp4bb] molecule on symmetry axis

2010-10-16 Thread George M. Sheldrick
It is nice to see that another old SHELX feature has now found its way into Phenix-refine: 'PART -N' = 'custom-nonbonded-symmetry-exclusion selection' ?! PART -N is indeed rather useful for the refinement of (solvent) molecules disordered about special positions, for example it allows hydrogens

Re: [ccp4bb] [QUAR] Re: [ccp4bb] embarrassingly simple MAD phasing question (another)

2010-10-16 Thread Kay Diederichs
Am 20:59, schrieb James Holton: ... The loss of the 1/r^2 term arises because diffraction from a crystal is "compressed" into very sharp peaks. That is, as the crystal gets larger, the interference fringes (spots) get smaller, but the total number of scattered photons must remain constant. The p

[ccp4bb] Pseudo-symmetry/refinement

2010-10-16 Thread Mike John
Hi all, The data is 2.2A, p41212, unit cell has c axis twice longer than a or b. Data processed by HKL2000, the diffraction pattern shows Strong-weak-weak in C direction, indicating translational pseudo-symmetry. Xtriage analysis confirmed the pseudo-symmetry (large Patterson off-origin pe