[phenixbb] Pb LocalResolutionMap calculation

[Tom Terwilliger]

Hi Philippe,

Yes, certainly the number of boxes affects the resulting local_resolution
map.  The 2400 boxes correspond to 14x14x14 boxes for a cubic map which
means that you have only a gradual sampling along any axis of your map.

You can adjust the number of boxes with the parameter n_boxes=2400.  In the
GUI, search under "All parameters" for "box" and you'll get the entry
form.   I will move this to the front page in tomorrow's nightly build of
Phenix so it is easier to set.

All the best,
Tom T


On Sun, Oct 29, 2023 at 3:42 AM CUNIASSE Philippe <Philippe.CUNIASSE at cea.fr>
wrote:

> Hi Tom,
>
> thank so much you for your answer. I uploaded the nigthtly build and it
> worked far better (a couple of hours) and ended correctly.
>
> I noticed that the gain was due to the fact the only about 2400 boxes were
> calculated (in place of more than 40000 in my slow previous
> calculation, likely explaining the gain of a factor 20). As i have a very
> large map, i wonder how this affects the quality of the LocalResolutionMap.
> And i also wonder if there is a mean to define this parameter to study this
> effect.
>
> Thank you so much for your help.
>
> Best regards.
>
> Philippe.
>
>
> -----------------------------------------------
>
> Philippe Cuniasse, PhD/HDR.
>
> Institut de Biologie Integrative de la cellule.
>
> UMR 9198 CNRS-CEA-Univ Paris Sud
>
> Bat 144 CE-Saclay
>
> 91191 Gif-sur-Yvette Cedex
>
> France
>
> Tel:      (33) 1 69 08 56 35
>
> Fax:      (33) 1 69 08 47 12
>
> Email: philippe.cuniasse at cea.fr
>
> Web: http://biodev.cea.fr/rasmot3d/
>
> -----------------------------------------------
>
> ------------------------------
> *De :* Tom Terwilliger <tterwilliger at newmexicoconsortium.org>
> *Envoyé :* vendredi 27 octobre 2023 11:04:52
> *À :* CUNIASSE Philippe
> *Cc :* phenixbb at phenix-online.org; Tom Terwilliger
> *Objet :* Re: [phenixbb] Pb LocalResolutionMap calculation
>
> Hi Philippe,
>
> I'm sorry for the slow calculation...the problem is the number of boxes is
> too high.  If you download a nightly build like this one:
>
> https://phenix-online.org/download/phenix/nightly/?version=1.21rc1-5130
>
> then it should be a lot faster (still not quick, but in your case should
> be 20x faster).
> All the best,
> Tom T
>
>
> On Fri, Oct 27, 2023 at 2:16 AM CUNIASSE Philippe <
> Philippe.CUNIASSE at cea.fr> wrote:
>
>> Dear all,
>>
>>
>> i try to calculate local resolution maps with phenix since a couple of
>> days. It turns out that the calculation seems very slow and i suspect
>> that there is a problem because i even cannot stop the calculation with the
>> abort button in the gui. In my last run (still running), i use 2 half-maps
>> and the program can read them correctly, start the calculation by returning
>> that 42875 boxes are considered. I run it on my MacBook pro  (M1 running
>> OSX 13.4 with 32Gb RAM) on 4 cpu. The calculation actually runs on 4 CPUs.
>> However, with this calculation (and also a smaller map with about 17000
>> boxes on 1CPU), the calculations run more than 24 hours without finishing.
>> I wonder if there coud be a problem and if no, what could be the duration
>> of such calculation.
>>
>> Thanks in advance for your help.
>>
>> Best regards.
>>
>> Philippe Cuniasse.
>>
>>
>>
>> -----------------------------------------------
>>
>> Philippe Cuniasse, PhD/HDR.
>>
>> Institute for Integrative Biology of the Cell (I2BC)
>>
>> UMR 9198 CNRS-CEA-Univ Paris Sud
>>
>> Bat 144 CE-Saclay
>>
>> 91191 Gif-sur-Yvette Cedex, France
>>
>>
>>
>> Tel:      (33) 1 69 08 56 35
>>
>> Fax:      (33) 1 69 08 47 12
>>
>> Email: philippe.cuniasse at cea.fr
>>
>> Web: http://biodev.cea.fr/rasmot3d/
>>
>> Web: https://www.i2bc.paris-saclay.fr
>>
>> [image: signature_2661676233]
>>
>> -----------------------------------------------
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>>
>
>
> --
> Thomas C Terwilliger
> Laboratory Fellow, Los Alamos National Laboratory
> Senior Scientist, New Mexico Consortium
> 100 Entrada Dr, Los Alamos, NM 87544
> Email: tterwilliger at newmexicoconsortium.org
> Tel: 505-431-0010
>
>

-- 
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20231029/9add62f6/attachment.htm>