Dear Eugene

plz find the merging statics over this link

https://www.dropbox.com/sh/3155bp0c8axo7tx/0P1RWTTD8z?n=21758536

I have tried different subset of images for indexing, only cell edges are
changing very marginal ( < 1 ) but no change in space group.



Dear Manfred

I have collected my data over mar345 detector, not present in detector type
dropdown, how can I add.


regards and thanks to all

pramod

On Mon, Jun 24, 2013 at 10:31 PM, Eugene Valkov <eugene.val...@gmail.com>wrote:

> Hi Pramod,
>
> Can you post your merging statistics in different space groups, not just
> log files from scaling? These are summarised nicely by Scala or Aimless.
>
> Also, have you tried indexing from different subsets of images? Perhaps
> there is a substantial contribution from a 'satellite' crystal in one
> orientation or crystal will be less split? I've had cases where I could not
> index properly if I had just used 0 and 90, but when I tried different
> subsets of images it worked. This is very easy to do in iMosflm.
>
> Andrew Leslie or other Mosflm developers, if they are reading this, might
> well be interested in looking at your images as they are currently
> interested in these kinds of problems with multiple lattices (see *Acta
> Cryst.* (2013). D*69*, 1195-1203)
>
> Eugene
>
>
> On 21 June 2013 21:58, Pramod Kumar <pramod...@gmail.com> wrote:
>
>> Dear ...
>>
>> Francis
>>
>> Last I remember, HKL2000 bases its indexing on the 'strongest' spots on
>> an image (though you could manually select spots). It could result in a
>> misindex if the strongest spots come from separate lattices..
>>
>> I have used both HKL2000 and mosflm giving the same results (although I
>> have used manual selection of spots as a trial but results are identical).
>>
>> Try a program that uses all spots for indexing, across all images (XDS
>> for example) and you might get the true space group..
>>
>> I have given several efforts to the XDS but its giving error  "data image
>> of particular no. does not exist (initially it was saying 11th image than i
>> change image range then it says 21st and so on) *kindly check my data
>> collection profile and XDS.INP* file in attachment'
>>
>>
>> Or if the crystal is big enough, you could try shooting it in different
>> areas and 'searching' for a better spot to collect data.
>> Or 'grow a better crystal'.
>>
>> raising the crystals and struggle is on the peak...
>>
>>
>> Dear Eugene
>>
>> plz find the attached scale log file, scaling table of mosflm
>>
>>
>> When you index spots in Mosflm, do your predictions agree with the spots?
>>
>> plz see the snapshot of predicted spots..
>>
>>
>>
>> Dear Eleanor
>> Yes both the molecule are visible in the ASU.
>>
>>
>>
>> Dear Pozharski
>>
>> Balbes pipeline hitting extremely high marks when fed into Phaser while
>> being complete nonsense (it's a 150kDa multi-domain protein and resulting
>> domain arrangement made absolutely no sense).  Refinement was stuck with
>> high R-values and I sadly gave up on it for now.  I suspected that refmac
>> step included in the pipeline artificially shifts the model so that it
>> conforms to Patterson map better, which results in high score in Phaser.
>>
>> My domain arrangement is as expected, two molecules in ASU.
>>
>>
>> thanks and regards
>>
>> pramod
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Thu, Jun 20, 2013 at 3:50 PM, Eleanor Dodson <
>> eleanor.dod...@york.ac.uk> wrote:
>>
>>> As others say - the Rfactors look pretty good for MR, mine usually start
>>> over 50% even with a better model and one hopes they then decrease..
>>> But you say you took the Balbes model into phaser? and I think Balbes
>>> automatically runs cycles of refinement so any comment on R factors may not
>>> mean much.
>>>
>>> Have you found both molecules in the asymmetric unit? You only give LLG
>>> for one?
>>> Eleanor
>>>
>>>
>>>
>>>
>>> On 19 June 2013 17:44, Eugene Valkov <eugene.val...@gmail.com> wrote:
>>>
>>>> Yes, I would agree with Francis that diffraction shows contribution
>>>> from several lattices, which could lead to misindexing. However, it should
>>>> be feasible to get a model that refines from this sort of data.
>>>>
>>>> Pramod - could you please post your data processing statistics from
>>>> your scaling program? Better if you have several for different spacegroups.
>>>>
>>>> Also, I have no idea how HKL200 does this, but could you please provide
>>>> an indexing solution table from Mosflm that shows penalties associated with
>>>> each type of space group? Was there a sharp penalty drop at some point or
>>>> was it more gradual?
>>>>
>>>> When you index spots in Mosflm, do your predictions agree with the
>>>> spots? Or is there a substantial portion that are missed?
>>>>
>>>> I would consider altering thresholds in Mosflm for indexing (see the
>>>> manual).
>>>>
>>>> Eugene
>>>>
>>>>
>>>>
>>>>
>>>> On 19 June 2013 17:34, Francis E. Reyes <francis.re...@colorado.edu>wrote:
>>>>
>>>>> On Jun 17, 2013, at 12:36 PM, Pramod Kumar <pramod...@gmail.com>
>>>>> wrote:
>>>>>
>>>>> >> I have a crystal data diffracted  around 2.9 A*,
>>>>> >> during the data reduction HKL2000 not convincingly showed the space
>>>>> group (indexed in lower symmetry p1), while the mosflm given C-centered
>>>>> Orthorhombic, and again with little play around HKL2000 given CO
>>>>> >
>>>>>
>>>>>
>>>>>
>>>>> > no ice ring is appeared, diffraction pattern looks ok, misindexing
>>>>> in any direction is not conclusive to me (plz see the imj attachment)
>>>>>
>>>>> The diffraction does not look ok... there's hints of multiple
>>>>> lattices... which is not a problem if the two lattice orientations do not
>>>>> perfectly overlap (i.e. their spots are separable).
>>>>>
>>>>> Last I remember, HKL2000 bases its indexing on the 'strongest' spots
>>>>> on an image (though you could manually select spots). It could result in a
>>>>> misindex if the strongest spots come from separate lattices (and even 
>>>>> worse
>>>>> if you have twinning/pseudosymmetry issues).
>>>>>
>>>>> Try a program that uses all spots for indexing, across all images (XDS
>>>>> for example) and you might get the true space group.
>>>>>
>>>>> Or if the crystal is big enough, you could try shooting it in
>>>>> different areas and 'searching' for a better spot to collect data.
>>>>>
>>>>> Or 'grow a better crystal'.
>>>>>
>>>>> F
>>>>>
>>>>>
>>>>>
>>>>> ---------------------------------------------
>>>>> Francis E. Reyes PhD
>>>>> 215 UCB
>>>>> University of Colorado at Boulder
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Dr Eugene Valkov
>>>> MRC Laboratory of Molecular Biology
>>>> Francis Crick Avenue
>>>> Cambridge Biomedical Campus
>>>> Cambridge CB2 0QH, U.K.
>>>>
>>>> Email: eval...@mrc-lmb.cam.ac.uk
>>>> Tel: +44 (0) 1223 407840
>>>>
>>>
>>>
>>
>>
>> --
>> ************************************************
>> Pramod Kumar.
>> Graduate Student.
>> Crystallography lab.
>> Department Of Biotechnology.
>> Indian Institute Of Technology Roorkee
>> Uttranchal.247667
>> India
>> +919359189657.
>> ************************************************
>>
>
>
>
> --
> Dr Eugene Valkov
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue
> Cambridge Biomedical Campus
> Cambridge CB2 0QH, U.K.
>
> Email: eval...@mrc-lmb.cam.ac.uk
> Tel: +44 (0) 1223 407840
>



-- 
************************************************
Pramod Kumar.
Graduate Student.
Crystallography lab.
Department Of Biotechnology.
Indian Institute Of Technology Roorkee
Uttranchal.247667
India
+919359189657.
************************************************

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