[ccp4bb] 'ERROR' in merging two data sets

2010-09-30 Thread jai mohan
Dear all crystallographers, Recently I have collected two data sets from two different crystals, first data at 2.6A and second is at 1.9A, the datasets were isomorphous. I tried to  merge the two dataset as a single MTZ file using CAD (CCP4i), but it is unsucces

[ccp4bb] how to switch off anamolous processing of data

2010-09-30 Thread atul kumar
Dear all I use scala 6.1 Even though I scale my native data, scala outputs anamolous data statistics in these columns: Nmeas Nref Ncent %poss C%poss Mlplct AnoCmp AnoFrc AnoMlt Rmeas Rmeas0 (Rsym) Rpim RpimO PCV PCV0 I use "anamolous off" for scala and "anamolous no" for ctruncate. My co

Re: [ccp4bb] how to switch off anamolous processing of data

2010-09-30 Thread Tim Gruene
Dear Atul, you mention the anomalous statistics in the log-file. Is this what bothers you? There is nothing wrong with it, and you should check whether or not your final data set has merged Friedel pairs or not. It probably has, and that's what you want, isn't it? Tim On Thu, Sep 30, 2010 at 0

Re: [ccp4bb] how to switch off anamolous processing of data

2010-09-30 Thread Phil Evans
You don't have to. The anomalous values (F+, F-, Dano) are included in the file in case you need them later. You can just ignore them Phil On 30 Sep 2010, at 08:33, atul kumar wrote: > > Dear all > > I use scala 6.1 > > Even though I scale my native data, scala outputs anamolous data > stat

Re: [ccp4bb] 'ERROR' in merging two data sets

2010-09-30 Thread Phil Evans
If you want to merge them into a single dataset, you need to go back to the unmerged intensities (ie the output of eg Mosflm), combine them together, best done with Pointless (ccp4i task "Find or match Laue group") and scale them together in eg Scala (task "Scale and merge intensities" ) Phil

Re: [ccp4bb] 'ERROR' in merging two data sets

2010-09-30 Thread Eleanor Dodson
Different numbers of columns wont stop CAD working, but if you have the any occurence of the same labels in either file this will produce an error mesage - eg Label FreeRflag found twice.. And if you have labelled both data sets as Fnew or some such uninformative label, then again you will hav

[ccp4bb] changing spacegroup

2010-09-30 Thread Tim Gruene
Hello, we are currently preparing a tutorial for a practical from lysozyme data. pointless picked the spacegroup P41212 and phaser should show the students that P43212 is the correct spacegroup. How do I best change the scala-mtz-file to that spacegroup? Can I tell pointless (and eventually rerun

Re: [ccp4bb] changing spacegroup

2010-09-30 Thread Graeme Winter
Hi Tim, Is it as easy as reindex hklin a.mtz hklout b.mtz << eof symm P43212 eof This will simply (and correctly) reassign the symmetry operations. Is this what you meant? Best wishes, Graeme On 30 September 2010 10:49, Tim Gruene wrote: > Hello, > > we are currently preparing a tutorial for

[ccp4bb] Lousy diffraction at home but fantastic at the synchrotron?

2010-09-30 Thread Marcus Winter
This recent discussion does tend towards the ideal scenario: of identifying ones best-diffracting crystals... before embarking on the synchrotron trip. The established Oxford Diffraction PX Scanner home laboratory instrument can therefore be most useful. This enables the direct X-ray scree

Re: [ccp4bb] Lousy diffraction at home but fantastic at the synchrotron?

2010-09-30 Thread Klaus Fütterer
Marcus, May I ask the following: assuming 8 A is obtained from a single crystal on the home source, what diffraction limit would one expect on the PX scanner? Best regards, Klaus === Klaus Fütterer,

Re: [ccp4bb] changing spacegroup

2010-09-30 Thread Eleanor Dodson
Or mtzutils hklin1 a.mtz hklout b.mtz < Hi Tim, Is it as easy as reindex hklin a.mtz hklout b.mtz << eof symm P43212 eof This will simply (and correctly) reassign the symmetry operations. Is this what you meant? Best wishes, Graeme On 30 September 2010 10:49, Tim Gruene wrote: Hello, we a

[ccp4bb] T N Bhat

2010-09-30 Thread Eleanor Dodson
Does any one have T H Bhats email - He was at RSCB I think but is probably retired. Eleanor

[ccp4bb] SUMMARY - [ccp4bb] changing spacegroup

2010-09-30 Thread Tim Gruene
Thanks for everyone who replied (and so quickly) The space group can be changed with PROG hklin in.mtz hklout out.mtz << eof symm P43212 eof where PROG is 'reindex' (Graeme Winter), 'mtzutils' (Eleanor Dodson), 'cad' (Phil Evans, Manfred Weiss), or 'sortmtz' (Manfred Weiss), all of which are also

Re: [ccp4bb] changing spacegroup

2010-09-30 Thread Vellieux Frederic
Another possibility is with sftools, set spacegroup option Fred. PS not in ccp4i Graeme Winter wrote: Hi Tim, Is it as easy as reindex hklin a.mtz hklout b.mtz << eof symm P43212 eof This will simply (and correctly) reassign the symmetry operations. Is this what you meant? Best wishes, Gr

Re: [ccp4bb] T N Bhat

2010-09-30 Thread Frances C. Bernstein
Here is the link to his home page at NIST http://www.nist.gov/cstl/biochemical/cell_systems/talapady_n_bhat.cfm Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster

[ccp4bb] difficult P1 crystal

2010-09-30 Thread Mario Milani
Dear all, i have a 30 kDa protein that crystallize so far in three different conditions but with the same space group. It initially looks like tetragonal (I4, a=141, b=141, c=208) and then results triclinic (P1, a=141, b=141 c=144, alpha=119, beta=119, gamma=90), hosting about 24 mol. in the uni

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Sebastiano Pasqualato
Mario, beside what you were mentioning, I would definitely try a quick soak (10-30 seconds) of the crystals in cryo conditions supplemented with halides such as NaBr, or NaI, at pretty high concentrations (say 0.5 M), then directly freezing without backsoak. If the crystals survive the treatment

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Tim Gruene
Dear Mario, what is the resolution of the data? Could you try SeMet-MAD/SAD or some other phasing method to overcome the MR-problem? Tim On Thu, Sep 30, 2010 at 12:54:36PM +0100, Mario Milani wrote: > Dear all, > i have a 30 kDa protein that crystallize so far in three different conditions > b

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Mario Milani
Thank you for the suggestions. The data resolution is 1.9 so i can try different heavy atoms techniques ... anyway i am really puzzled by the peculiar assembly in the crystal and on the possible causes... does anyone know about similar cases? mario > > Mario, > beside what you were mentioning, I w

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Francis E Reyes
What does this mean? You index what looks to be tetragonal, do your collection, and then it integrates/scales only in P1? F On Sep 30, 2010, at 5:54 AM, Mario Milani wrote: > It initially looks like tetragonal (I4, a=141, b=141, c=208) and then > results triclinic (P1, a=141, b=141 c=144, al

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Tim Gruene
Hello Mario, at 1.9A you might even give S-SAD a try, especially if you have access to an inhouse source with the flexibility to collect data with a (real) high multiplicity. Tim On Thu, Sep 30, 2010 at 02:40:26PM +0200, Mario Milani wrote: > Thank you for the suggestions. The data resolution is

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread James Holton
Yes, this sort of thing happens a lot more often than one might think, but people who have crystals with such "high-copy asymmetric units" tend to not solve them. Hence, they don't end up in the PDB. In cases where the structure is eventually solved, it is usually done by finding an alternati

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Sanishvili, Ruslan
Hi James, Can you, or anybody else, point me to a publication where "...not that uncommon for one or more crystal symmetry operators to "collapse" upon cryo-cooling..." Thanks, Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (63

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread elizabeth . duke
no publication springs to mind immediately (often apparently of non scientific relevance) but I have seen it on numerous occasions so fully support James' comment. All you need to do is read the IUCr tables (yes, boring, but occaisionally useful) to see how simple it actually is. Liz __

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Sanishvili, Ruslan
Folks, I am not questioning James - I just would like to see some papers if there are any so I can use them as reference. Cheers, N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov

Re: [ccp4bb] ? steps after detwinning

2010-09-30 Thread Seema Nath
@R.Brown Resolution 3.2A DENZO suggests P6. Angles are 90,90,120 Data completeness ~95% R-merge-0.06 Wilson B-factor 42.0

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Daniel Bonsor
There are a couple of papers... Acta Cryst. (2010). F66, 346-351 Crystallization and X-ray diffraction studies of cellobiose phosphorylase from Cellulomonas uda The space group was originally P21. During collection the crystal moved out of the beam (and possibly the cyrostream). Upon recenter

Re: [ccp4bb] 'ERROR' in merging two data sets

2010-09-30 Thread jai mohan
To Eleanor, I changed the column label for two data sets, FreeR_Flag for the first data and F_x for the second data. Now CAD compiled the data successfully. The merged MTZ file contains column label like this H K  L  FreeR_Flag   F_x I conclude to use this file fo

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread James Holton
Nukri poses a very good question. Fortunately for me, I think others are answering it: Daniel Bonsor has emailed me a couple of relevant references, which I reproduce here: - Acta Cryst. (2010). F66, 346-351=20 Crystallization and X-ray diffraction studies of cellobiose phos

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Jon Schuermann
Mario, As others have asked, why/how did you decide on P1? You mentioned pseudo-translation being present. Depending on the location in the Patterson map this could be a pseudo-centering operator showing an apparent I4 space group. If this is the case you may want to reindex in the P4 cell

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Mark J van Raaij
we had a P1 case with 12 mols/au, about 30% sequence id, 2.4A resolution, which was solved after a lot of trials with phaser. Other problems of these crystals were that they took months to grow and invariable presented multiple lattices (we did not try microbeam). See: Crystallization of t

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Daniel Picot
Here is an example that is is not cryocongelation but spacegroup change upon cooling : Garavito RM, Jenkins J, Jansonius JN, Karlsson R, Rosenbusch JP. X-ray diffraction analysis of matrix porin, an integral membrane protein from Escherichia coli outer membranes. J Mol Biol. 1983 Feb 25;164(2):31

Re: [ccp4bb] difficult P1 crystal

2010-09-30 Thread Goragot Wisedchaisri
We had a P1 case with 8 molecules/asu and the crystal diffracted to 2A resolution. Initial indexing showed that the data could be indexed in P212121 space group but the data could not be merged in this space group (Rsym 60%). P1 was the only space group that we could merge the data (Rsym 10%).