[buster-discuss] problem with buster (release 20240710) on MacM4 / Sequoia 15.2

[Laurent Maveyraud]

Hi Clemens,

thanks for your help.

crossec runs fine when used directly from the command line, but is stuck 
when using refine...

However, disabling the check about form factor seems to be working!

If I can help to  identify the source of the problem, don't hesitate to 
get in touch,

kind regards

laurent

Le 13/01/2025 à 10:44, Clemens Vonrhein a écrit :
> Hi Laurent,
>
> On Wed, Jan 08, 2025 at 09:26:31AM +0100, Laurent Maveyraud via buster-discuss wrote:
>> I just upgraded my MacBookPro to the latest M4 chip, and have problems while
>> running buster (snapshot 20240710) with CCP4 9.
>>
>> It seems that it get stuck at crossec step at the first cycle : crossec
>> keeps running (I stopped it after 15 minutes....).
> That suggests a problem with the CCP4 "crossec" program. Can you try
> running e.g.
>
>    crossec <<e
>    ATOM S
>    NWAV 1 1.0
>    e
>
> This should be VERY fast and return you something like
>
>    ...
>     $TABLE:Wave length v F' and F"-  S    :
>     $GRAPHS:Lambda v F' and F" S    :A:2,3,4: $$
>     Atom_type Lambda  F'  F" $$
>     Lambda  F'  F" $$
>
>    S           1.0000     0.1886     0.2439
>    ...
>
>> Are there any known problems with M4 / Sequoia ?
> Not from our (Global Phasing software) side (yet) - but we have only
> access to a M1 system running 15.1 (where the above command works
> fine).
>
> You can switch off the check about formfactors (which is the part that
> runs CROSSEC) via the
>
>    AutomaticFormfactorCorrectionAnalyse=no
>
> parameter (until there is a better understanding where the problem
> comes from).
>
> Does that help here?
>
> Cheers
>
> Clemens
>
>> have a nice day,
>>
>> laurent
>>
>> this is the command I used :
>>
>> refine -p ./refine_02/refine-coot-0.pdb -Gelly ./refine_02/occ.gelly -l
>> ../../my.restraints.cif -m ./scale_01/staraniso_alldata-unique.mtz -WAT 3 -d
>> refine_03 -nthreads 6 > refine_03.log &
>>
>> here are the last lines of the logfile :
>>
>>   ################################ BIG cycle 1
>> #################################
>>
>>
>>   ESC[1mNOTEESC[m : (controllable) refinement parameters = XYZ B OCC
>>
>>   running BUSTER (187.01405 - 1.48565 A) in refine_03/01-BUSTER/Cycle-1
>> [extra library /tmp/maveyrau-BUSTER/maveyrau-1736324017-refine__22844.elib]:
>>
>>   ESC[1mNOTEESC[m : created file for BABSLV by removing 165 atom(s)
-- 
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  Laurent Maveyraud


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Doctoral School Biology - Health - Biotechnologies

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