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Re: [ccp4bb] just how bad can phases be and still help
 

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CCP4bb <-- 2007 <-- September 2007 <-- 07 September 2007
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Subject: Re: just how bad can phases be and still help
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-09-07 		Next message:
Subject: 2 postdoctoral positions at KI Stockholm
From: Andreas Kohl Andreas {- dot -} Kohl {- at -} KI {- dot -} SE
Date: 2007-09-07


Subject: Re: just how bad can phases be and still help
From: Boaz Shaanan bshaanan {- at -} BGU {- dot -} AC {- dot -} IL
Date: 2007-09-07
Hi,

This is a most fundamental yet tricky question. If you take FOM as a measure, it depends at what stage and it also doesn't necessarily tell you about the interpretability of the map. After solvent flattening. FOM are always high but maps can still be rubbish. I'm pretty sure the FOM of the maps with the left handed helices (Chang affair) were high. FOM before solvent flattening can be low but are quite often progam dependent. I tend to rely on those produced by SHARP. I've had FOM's as low as 0.3 which after solvent flattening gave nice maps and good structures (SAD or MAD). My rule of thumb therefore when using SHARP is that if the FOM before solvent flattening is below 0.3 I might be in trouble (I would still go ahead with solvent flattening and all the rest but I expect problems in such cases). It is the underlying correctness of the phases which matters and I don't know which number represents this best. I agree with Bill and with probably most other people's experience, as well as yours I'm sure, that it is the map that matters and not necessrily the measures used to quantify phases quality.

These are my thoughts.

Cheers,

Boaz

----- Original Message -----
From: "Bryan W. Lepore"
Date: Friday, September 7, 2007 0:27
Subject: [ccp4bb] just how bad can phases be and still help
To: CCP4BB@JISCMAIL.AC.UK

> general question - perhaps the fundamental question -
>
> for anyone who had "weak/poor/bad" phases from some source, that
> were
> later actually used to solve a structure when combined w/
> another source -
> HOW bad were the worst phases on their own, in terms of
> resolution, FOM,
> CC, e-density, (any other numbers)? what was MOST
> important in knowing
> the phases would help (presumably e-dens.).
>
> i.e, was it only when relatively "better" phases gave any
> interpretable
> density that it was known that the "bad" phases would help?
>
> -bryan
>

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan‎
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