Re: [ccp4bb] refmac problem in running arp/warp

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: PDB format survey?
From: Joe Krahn krahn {- at -} NIEHS {- dot -} NIH {- dot -} GOV
Date: 2007-08-09

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Subject: adjustable loops, other cryo mounting methods
From: "Bryan W {- dot -} Lepore" bryanlepore {- at -} MAIL {- dot -} UTEXAS {- dot -} EDU
Date: 2007-08-09

Subject: Re: refmac problem in running arp/warp
From: Roberto Steiner roberto {- dot -} steiner {- at -} KCL {- dot -} AC {- dot -} UK
Date: 2007-08-09

Dear Tommi,

a) WHAT IS GAMMA??

Gamma is a factor used in the Refmac minimization procedure.
In most cases Refmac achieves convergence with gamma = 0.0.
In case the program fails to reach convergence with gamma = 0.0, gamma
is increased stepwise. This generally facilitates convergence.

Regards,
Roberto

> dear all (well experts i suppose),
> can someone explain what this means (REFMAC):
>
> Resolution limits = 19.944 2.600
> Number of used reflections = 12652
> Percentage observed = 100.0000
> Percentage of free reflections = .0000
> Overall R factor = .3922
> Overall weighted R factor = .3737
> Overall correlation coefficient = .8399
> Cruickshanks DPI for coordinate error= 3.4923
> Overall figure of merit = .6952
> ML based su of positional parameters = .6421
> ML based su of thermal parameters = 29.9144
> -----------------------------------------------------------------------------
> Trying gamma equal 0.0000000000E+00
> Not converging with gamma equal 0.0000000000E+00
> Trying gamma equal 0.5500000343E-01
> Not converging with gamma equal 0.5500000343E-01
> Trying gamma equal 0.1155000031
> Not converging with gamma equal 0.1155000031
> Trying gamma equal 0.1820500046
> Not converging with gamma equal 0.1820500046
> Trying gamma equal 0.2552550137
> Not converging with gamma equal 0.2552550137
> Trying gamma equal 0.3357805014
> Not converging with gamma equal 0.3357805014
> Trying gamma equal 0.4243585467
> Not converging with gamma equal 0.4243585467
> Trying gamma equal 0.5217944384
> Not converging with gamma equal 0.5217944384
> Trying gamma equal 0.6289739013
> Gamma decreased to 0.6075379848
>
>
>
> I am runing this on a mac --two different mac platroms, powerpc does
> this and goes on intel mac pro (or whatever it was) gamma shoots up and
> the program gets stuck in a loop...
>
> so, a) WHAT IS GAMMA??
>
> b) why the difference between the machines??, is this a bug, or diagnostic
> of some problem...?
> (with my refiment.. which isnt really working...)
>
>
> related to that, any opinions whether it is a good idea to include HL
> restraints in arp/warp buidling/refinment at 2.6Å and poor starting phases..
> (starting from exp. phases, i recall Tassos suggested this but for which
> case??? i am running vs 7)
> (i still have the partial model but little success to go beyond it by any
> means....tweaking parameters in arpwarp now.... suggestions??)
>
> many thanks...,
> tommi
>
>
>
>
> --
> Tommi Kajander, Ph.D.
> Macromolecular X-ray Crystallography
> Research Program in Structural Biology and Biophysics
> Institute of Biotechnology
> PO box 65 (Street address: Viikinkaari 1, 4th floor)
> University of Helsinki
> FIN-00014 Helsinki, Finland
> Tel. +358-9-191 58903
> Fax +358-9-191 59940
>

--
Dr. Roberto Steiner
Randall Division of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Phone +44 (0)20-7848-8216
Fax +44 (0)20-7848-6435
e-mail roberto.steiner@kcl.ac.uk

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: PDB format survey?
From: Joe Krahn krahn {- at -} NIEHS {- dot -} NIH {- dot -} GOV
Date: 2007-08-09

Next message:
Subject: adjustable loops, other cryo mounting methods
From: "Bryan W {- dot -} Lepore" bryanlepore {- at -} MAIL {- dot -} UTEXAS {- dot -} EDU
Date: 2007-08-09