Extremely long optimization times -- September 04, 2007 - 14:45

Hi all,

I am using the full_analysis.py script with data a three magnetic fields.

After a first complete cycle (going through the final optimization), I
realized that a few residues had extremely high chi-squared values (>
1000) no matter the diffusion model or model-free model chosen...

So I removed those residues (7 out of 222) and started the full_analysis
protocole again.

However, the optimization times are now extremely long and I should get
the final results in weeks...


Here are the available times (for local_tm, sphere and ellipsoid) :


Diffusion_model    Round      Time-before_N=222  X2          
Time-now_N=215  X2
===============    =====      =================  =======     
==============  =======
local_tm           ---          12h30              45949       
14h30            5802    OK, X2 much smaller

sphere             init         ---              1154338        ---     
      249255
                   1             2h30              65654        36h00  
        10303    Long, but X2 much smaller
                   2             2h30              65654      > 30h00

ellipsoid          init         ---               753535       
---            177764
                   1             4h00              64592      >
67h00                    ??
                   2             2h30              64592       
not_there_yet

Is it possible that the algorithms get stuck somewhere during the
optimization..?

I thought that removing badly fit residues would, on the contrary, speed
up calculations...

Thanks for ideas !


Sébastien  :)

-- 
         ______________________________________    
     _______________________________________________
    |                                               |
   || Sebastien Morin                               ||
  ||| Etudiant au PhD en biochimie                  |||
 |||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne                             |||||
 |||| CREFSIP (Universite Laval, Quebec, CANADA)    ||||
  ||| 1-418-656-2131 #4530                          |||
   ||                                               ||
    |_______________________________________________|
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