Re: [ccp4bb] reindexing mtz

Sorry - my bad memory and mis-reading the manual... Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) > On 10 Jan 2018, at 21:30, Phil Evans wrote: > > I don’t think Pointless can (or should) read .x files -

Re: [ccp4bb] reindexing mtz

I don’t think Pointless can (or should) read .x files - they have to go into scalepack as that sorts out various things in the data. Pointless can read unmerged .sca files from scalepack, but they can’t be (properly) scaled in Aimless Phil > On 10 Jan 2018, at 21:11, CCP4BB >

Re: [ccp4bb] reindexing mtz

Hi Peter No, don't bother scaling in hkl2000. Just take the .x files and read them into Pointless directly - it should auto-detect the file type and any output reflection file from it will be in MTZ format. Then Aimless can do the scaling. See the manual, e.g.

Re: [ccp4bb] reindexing mtz

Just to be absolutely clear about my approach to doing this, I should scale in HKL2000 as an unmerged set, and then take the unmerged scalepack, convert to mtz and run through pointless? Also, would taking my current mtz (which is a merged dataset) work using the reindex program in CCP4? Are

Re: [ccp4bb] reindexing mtz

Thanks Paul - Peter, in that case I think you can just read the data into pointless and it will suggest possible spacegroups and the appropriate reindexing. eleanor On 10 January 2018 at 11:07, Paul Emsley wrote: > On 10/01/2018 10:58, Eleanor Dodson wrote: > >> Yes

Re: [ccp4bb] reindexing mtz

Yes - that is possible, but need more information. Are the files unmerged data? Eleanor On 10 January 2018 at 03:34, Peter Hsu wrote: > Dear all, > > Looking to get some advice on reindexing an old dataset. I recently solved > a structure of reasonable resolution at

[ccp4bb] reindexing mtz

Dear all, Looking to get some advice on reindexing an old dataset. I recently solved a structure of reasonable resolution at ~3A in C2. I had an old dataset at 4A in P213 that I never got a MR solution with until I solved the structure of it at 3A. I've recently gone back to to this and

[ccp4bb] Reindexing of lattice

Hi, I am trying to reindex a P212121 lattice to change the axis order from 32.62, 64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I can't find how to reindex the lattice. Does anyone know how I should do this and an example of the execute script that I should use?

[ccp4bb] Reindexing lattice

Hi, I am trying to reindex a P212121 lattice to change the axis order from 32.62, 64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I can't find how to reindex the lattice. Does anyone know how I should do this and an example of the execute script that I should use?

Re: [ccp4bb] Reindexing lattice

reindex k, l, h you can use Pointless or Reindex Phil On 1 Jul 2015, at 16:04, D Bonsor dbon...@ihv.umaryland.edu wrote: Hi, I am trying to reindex a P212121 lattice to change the axis order from 32.62, 64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I can't

Re: [ccp4bb] Reindexing of lattice

of Bonsor, Daniel [dbon...@som.umaryland.edu] Sent: Wednesday, July 01, 2015 10:14 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Reindexing of lattice Hi, I am trying to reindex a P212121 lattice to change the axis order from 32.62, 64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING

Re: [ccp4bb] Reindexing of lattice

@JISCMAIL.AC.UK Subject: [ccp4bb] Reindexing of lattice Hi, I am trying to reindex a P212121 lattice to change the axis order from 32.62, 64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I can't find how to reindex the lattice. Does anyone know how I should do

Re: [ccp4bb] reindexing monoclinic data

Gregory Bowman wrote: Yes, but I don't actually want to swap a and c (convention that a is shorter than c), but instead flip k and keep h and l the same. Incidentally, it is not immediately obvious to me why in matrix I cited below that the new l is h+l: -1 0 0 0 -1 0 1 0 1 Greg Because -a

Re: [ccp4bb] reindexing monoclinic data

Sorry for adding confusion- of course in reciprocal space beta* should be acute. The figures should have been labeled a, c not h,L. Edward A. Berry wrote: Gregory Bowman wrote: Yes, but I don't actually want to swap a and c (convention that a is shorter than c), but instead flip k and keep h

[ccp4bb] reindexing monoclinic data

Hi all, We have several primitive monoclinic datasets for the same protein with various ligands, with essentially the same unit cell parameters. We would like to have these with the molecules/density oriented the same way for easy comparison, but as chance would have it, some have effectively

Re: [ccp4bb] reindexing monoclinic data

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Greg, with XDS I normally set REFERENCE_DATA_SET to the first one indexed / integrated in order to maintain consistent indexing between data sets. Not sure whether similar options are available in other integration programs, but if I remember

Re: [ccp4bb] reindexing monoclinic data

Hi Yes, in the CCP4 world, pointless is the program for you. On 26 Aug 2011, at 17:00, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Greg, with XDS I normally set REFERENCE_DATA_SET to the first one indexed / integrated in order to maintain consistent indexing

Re: [ccp4bb] reindexing monoclinic data

Gregory Bowman wrote: Hi all, We have several primitive monoclinic datasets for the same protein with various ligands, with essentially the same unit cell parameters. We would like to have these with the molecules/density oriented the same way for easy comparison, but as chance would have

Re: [ccp4bb] reindexing monoclinic data

Hi Greg, you could also CAD them into one huge mtzfile with different labels e.g. FP_Lig1, FP_Lig2 etc. Then they would be the way you need them for direct comparison in Coot, Pymol or whatever program you wish to use. Jürgen On Aug 26, 2011, at 11:55 AM, Gregory Bowman wrote: Hi all, We

[ccp4bb] reindexing

Hi everyone, We collected several derivative data sets which have different cell parameters: (1) 50.48074.140 149.51090.00094.16090.000 p2 (2) 96.79274.052 154.27190.00090.06090.000 p2 For one of data sets, HKL2000 and Mosflm gave (1) and (2) as autoindex

Re: [ccp4bb] reindexing

No On 11 Feb 2011, at 14:03, Wang, Xiaoqiang wrote: Hi everyone, We collected several derivative data sets which have different cell parameters: (1) 50.48074.140 149.51090.00094.16090.000 p2 (2) 96.79274.052 154.27190.00090.06090.000 p2 For one of

Re: [ccp4bb] reindexing

Dear Xiaoqiang, both HKL2000 and Mosflm allow you to enter the cell and space group explicitly, so you can check yourself on screen whether the data from crystal (2) are indexed by the cell from crystal (1) and vice versa. Tim On Fri, Feb 11, 2011 at 08:03:52AM -0600, Wang, Xiaoqiang wrote:

Re: [ccp4bb] reindexing

] On Behalf Of Wang, Xiaoqiang Sent: Friday, February 11, 2011 6:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] reindexing Hi everyone, We collected several derivative data sets which have different cell parameters: (1) 50.480    74.140   149.510    90.000    94.160    90.000 p2 (2) 96.792    74.052

Re: [ccp4bb] reindexing

@JISCMAIL.AC.UK Subject: [ccp4bb] reindexing Hi everyone, We collected several derivative data sets which have different cell parameters: (1) 50.48074.140 149.51090.00094.16090.000 p2 (2) 96.79274.052 154.27190.00090.06090.000 p2 For one of data sets, HKL2000

Re: [ccp4bb] Reindexing scaled data

You dont need to reprocess - just reindex k,l,h or whatever you want to do.. Reprocessing is not necessary if you are keeping the same pointgroup. There is no change in the expected geometry of the diffraction.If for example you were changing from pontgroup P222 where all angles are restrained

[ccp4bb] Reindexing scaled data

Hi all, This maybe a simple/stupid question. I collected data at the synchrotron, integrated and scaled the data in P222 using HKL2000, though I should of scaled the data as P212121. When I try to reindex using Reindex I get a message of You are changing the symmetry of merged data are

Re: [ccp4bb] Reindexing P21.. the process?

Francis E Reyes wrote: Hi all I have data integrated and scaled to P21 via denzo/scalepack. I'm concerned about the workflow to obtain the alternate indexing arrangement (h,k,l) - (h,-k,-h-l). I was thinking .sca ( not specifying NO MERGE) - .mtz - reindex but the documentation for reindex

Re: [ccp4bb] Reindexing P21.. the process?

Negating the DANO columns is the correct thing to do if the reindex operator changes hkl to h,-k,-h-l which will then be put back into the asymmetric unit with Friedel's law + symmetry eg hkl (1,2,3) - (1,-2,-4) -Operator[-h,-k,-l] - -1,+2, +4 The Friedel's law operator -h,-k,-l interchanges

Re: [ccp4bb] Reindexing P21.. the process?

+1 phenix FTW FR On Jan 13, 2010, at 3:28 PM, Peter Zwart phzw...@lbl.gov wrote: try using phenix.reflection_file_converter data.sca --change_of_basis=h,-k,-h-l --sca=reindex.sca or something like that HTH Peter 2010/1/13 Francis E Reyes francis.re...@colorado.edu: Hi all I have

Re: [ccp4bb] Reindexing Orthorhombic

Mo;lecular replacement can choose any suitable origin so you cant predict. The easiest way is to run superpose molecules Match all residues to each other. You should get a rotation matrix -1 0 0 0 0 1 / 0 1 0 with some translation which sjould be very c;lose tpo components of 0, or 1/2 along

Re: [ccp4bb] Reindexing Orthorhombic

James Stroud wrote: ... What is the operation to reindex such that real space is rotated 180 about z? These are in P212121. Isn't that the 21 along z in your orthorhomic space group? Just apply it to your MR solution instead, and add an affine normaliser if needed to superpose the

Re: [ccp4bb] Reindexing Orthorhombic

If you were lazy you'd just run phaser ;-) -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 17 Apr 2009, James Stroud wrote: Update: The pounding I am beginning to feel in my head is reminiscent of a pounding I felt while

Re: [ccp4bb] Reindexing Orthorhombic

Update: The pounding I am beginning to feel in my head is reminiscent of a pounding I felt while working in p43212 a while ago. I think this is an alternate origin issue. Now I just need to figure out how to redefine the origin. James On Apr 16, 2009, at 9:38 PM, James Stroud wrote:

Re: [ccp4bb] Reindexing Orthorhombic

Dear James, yes, this reminds me of a problem long time ago: since the origin in P212121 is defined as the midpoint of non-intersecting screw axes (I hope that's right - I don't have the tables at hand), you have to add (1/4*a,1/4*c,1/4*b) after re-indexing, if I'm not mistaken. Best

Re: [ccp4bb] Reindexing Orthorhombic

when reindexing p212121 with -h,l,k, you get P 21 21 21 (a+1/4,b-1/4,c-1/4) so you should subtract 1/4 from x and add a quarter to y and z. some tools in the cctbx are available that make this go easy (reindexing and moving things back to a standard setting). Reruning phaser might be the least

Re: [ccp4bb] Reindexing Orthorhombic

James, If you still have the raw images on line, you can use a new feature in LABELIT to take care of matching the 2nd dataset indexing solution against the isomorphous atomic model from data set 1, and then re-integrate. Usage: labelit.index data set 2 first image data set 2 90-degree

Re: [ccp4bb] Reindexing Orthorhombic

For the sake of completeness I also thought that the REFERENCE_DATA_SET card in XDS does the same thing. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 17 Apr 2009, Nicholas K. Sauter wrote: James, If you still have the

[ccp4bb] Reindexing Orthorhombic

Hello All, I have two crystals (that I'll call data set 1 and data set 2) that seem to be isomorphic, but y and z are transposed between the two data sets. Reindexing data set 2 with the operators h = -h k = l l = k makes the axes match data set 1, but running MR with the previous

Re: [ccp4bb] Reindexing data from P23 to I23

The most useful tool for sorting this out is the program Pointless, which you download from the CCP4 pre-release pages if you haven't got it already Phil On 17 Jun 2008, at 13:00, Ajit Basak wrote: Dear all, I am writing to get some help and advice - Recently one of my data which I