[sharp-discuss] missing ISYM

[mark.vanraaij at usc.es]

Thanks all for the useful comments.
It turns out that the problem was a mistake in my ccp4 setup  
(/tmp/mark was not writable/readable by all) - I thought sharp was  
stopping because of the missing ISYM but this was not the case.
In any case, I will try both the new and old truncate to see which  
gives best results.
However, in trying to solve the problem I appear to have created  
another problem. Sharp was using /usr/local/ccp4-6.1.1/ rather than  
the /usr/local/ccp4-6.1.3/ I installed last week (and now works  
correctly, with the tmp directory "fixed").
In trying to troubleshoot I deleted the /usr/local/ccp4-6.1.1  
directory and now sharp stops because it looks for the ccp4 programs  
there.
How can I get sharp to use the new, correct directory without  
reinstalling sharp? I can't see where this variable is set...

Mark


Quoting Phil Evans <pre at mrc-lmb.cam.ac.uk>:

>
> I agree it should be fixed (one way would be to use F+ & F- instead   
> of <F> and DANO). The reason it is a bit marginal is that in most   
> datasets the number of reflections without both F+ and F-   
> measurements is small
>
> Phil
>
> On 18 May 2010, at 17:38, Gerard Bricogne wrote:
>
>> Dear Phil,
>>
>>     I don't quite agree that the loss of the ISYM column is "not a huge
>> loss". It may not make a difference at the moment, but it is actually
>> critical in exploiting AAS (the anisotropy of anomalous scattering) in the
>> development version of SHARP, since this phenomenon breaks the equivalence
>> between symmetry-related reflections, and ISYM is essential in keeping track
>> of the symmetry relations between the various (then inequivalent) unmerged
>> measurements. Losing track of ISYM is this context is just as bad as losing
>> the distinction between I+ and I- in relation to anomalous scattering.
>>
>>     See M. Schiltz & G. Bricogne (2008). "Exploiting the anisotropy of
>> anomalous scattering boosts the phasing power of SAD and MAD experiments",
>> Acta Cryst. D64, 711-729.
>>
>>     Also, in the recent special issue of Acta D containing the Proceedings
>> of the 2009 CCP4 Study Weekend: M. Schiltz & G. Bricogne (2010). "Broken
>> symmetries in macromolecular crystallography: phasing from unmerged data",
>> Acta Cryst. D66, 325-338.
>>
>>     I am "surprised and disappointed" that decisions to drop information
>> can be taken by CCP4 developers without at least some consultation to ensure
>> that a full and up-to-date scientific picture is taken into account. This
>> clearly needs to be fixed!
>>
>>
>>     With best wishes,
>>
>>          Gerard.
>>
>>
>> --
>> On Tue, May 18, 2010 at 04:20:55PM +0100, Phil Evans wrote:
>>>
>>> ctruncate does not generate the ISYM column, not a huge loss. In   
>>> [auto]sharp if you leave the ISYM assignment blank it works for   
>>> me, I think
>>
>>>
>>> Phil
>>>
>>> On 18 May 2010, at 15:54, mark.vanraaij at usc.es wrote:
>>>
>>>> Dear all,
>>>>
>>>> As a first-time use, I appear to get stumpe at one of the first
>>>> hurdles. My truncate output files do not have the ISYM column, and I
>>>> don't see how to "generate" or "keep" the ISYM column in CCP4i.
>>>>
>>>> Mark
>>>>
>>>> _______________________________________________
>>>> sharp-discuss mailing list
>>>> sharp-discuss at globalphasing.com
>>>> https://www.globalphasing.com/mailman/listinfo/sharp-discuss
>>>
>>> _______________________________________________
>>> sharp-discuss mailing list
>>> sharp-discuss at globalphasing.com
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>>
>> --
>>
>>     ===============================================================
>>     *                                                             *
>>     * Gerard Bricogne                     gb10 at GlobalPhasing.com  *
>>     *                                                             *
>>     * Global Phasing Ltd.                                         *
>>     * Sheraton House, Castle Park         Tel: +44-(0)1223-353033 *
>>     * Cambridge CB3 0AX, UK               Fax: +44-(0)1223-366889 *
>>     *                                                             *
>>     ===============================================================
>
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