JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for CCP4BB Archives


CCP4BB Archives

CCP4BB Archives


CCP4BB@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

CCP4BB Home

CCP4BB Home

CCP4BB  September 2007

CCP4BB September 2007

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: just how bad can phases be and still help

From:

"Dunten, Pete W." <[log in to unmask]>

Reply-To:

Dunten, Pete W.

Date:

Sat, 8 Sep 2007 13:23:33 -0700

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (111 lines)

Here's one - FOM > 0.5 after shelxe, SAD phases, not traceable

Lots of weak data, as truncate shows . . . 

 Analysis of mean intensity by parity for reflection classes

  For each class, Mn(I/sig(I)) is given for even and odd parity with respect to the condition,
eg group 1: h even & odd; group 7 h+k+l even & odd; group 8 h+k=2n & h+l=2n & k+l=2n or not

            1           2           3           4           5           6           7           8
            h           k           l          h+k         h+l         k+l        h+k+l    h+k,h+l,k+l

Totals: 22.0 22.9   21.9 23.0   39.4  5.3   39.4  5.3   21.9 23.0   22.0 22.9   22.4  0.0   37.9 17.0

The stats from shelxe for an incorrect solution

 Mean weight and estimated mapCC as a function of resolution
 d    inf - 2.43 - 1.93 - 1.68 - 1.52 - 1.41 - 1.33 - 1.26 - 1.21 - 1.15 - 1.06
 <wt>    0.581  0.625  0.614  0.610  0.603  0.594  0.600  0.583  0.574  0.547
 <mapCC> 0.988  0.981  0.979  0.980  0.978  0.979  0.978  0.975  0.969  0.955
 N        4117   4037   4172   4272   4177   3923   4338   3632   4456   3638

 Pseudo-free CC = 75.58 %

and the other hand

 Mean weight and estimated mapCC as a function of resolution
 d    inf - 2.43 - 1.93 - 1.68 - 1.52 - 1.41 - 1.33 - 1.26 - 1.21 - 1.15 - 1.06
 <wt>    0.589  0.635  0.617  0.622  0.623  0.621  0.625  0.610  0.602  0.579
 <mapCC> 0.987  0.982  0.981  0.982  0.980  0.983  0.982  0.978  0.976  0.968
 N        4117   4037   4172   4272   4177   3923   4338   3632   4456   3638

 Pseudo-free CC = 78.72 %

and the correct solution, which was traceable

 Mean weight and estimated mapCC as a function of resolution
 d    inf - 2.43 - 1.93 - 1.68 - 1.52 - 1.41 - 1.33 - 1.26 - 1.21 - 1.15 - 1.06
 <wt>    0.571  0.623  0.612  0.621  0.623  0.618  0.623  0.608  0.615  0.605
 <mapCC> 0.987  0.984  0.983  0.984  0.982  0.984  0.983  0.980  0.980  0.975
 N        4117   4037   4172   4272   4177   3923   4338   3632   4456   3638

 Pseudo-free CC = 85.42 %

Pete


-----Original Message-----
From: CCP4 bulletin board on behalf of James Holton
Sent: Sat 9/8/2007 8:57 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] just how bad can phases be and still help
 
In my experience, the "threshold of interpretability" for electron 
density maps is when the FOM is ~0.5 or higher.  I am basing this on 
anecdotal responses to this movie:
http://bl831.als.lbl.gov/~jamesh/movies/index.html#phase
In this case, the displayed value for FOM is exact.  Depending on how 
you are estimating FOM, your mileage may vary. 

As noted on another thread, different programs do indeed report 
different values for the same statistic.  The reason why different 
programs give different FOMs is because the definition of FOM is the 
cosine of the difference between the reported phase (output by the 
program) and the "true" phase.  Since you obviously don't know the 
"true" phase, this is a hard number to figure out.  Every phasing 
technique has a different method of estimating the FOM, but all of them 
are just that: estimates.  In fact, it is somewhat preposterous to try 
to compute the deviation from some unknown "correct" value, which is why 
we have so many other phase quality statistics like phasing power, lack 
of closure, RCullis etc.  These are at least well-defined for a given 
data set, but unfortunately don't have much more than an empirical 
correlation to the number you really want to know: FOM.

Map interpretability depends on the "true" FOM, but unfortunately, all 
we have to work with is the FOMs we can estimate.  There are sometimes 
practical reasons for underestimating the FOM (see the mlphare manual), 
and a solvent-flattening job that is allowed to run for far too many 
cycles will get phase bias and overestimate the FOM.    I can say that 
in controlled tests I have done, the FOM reported by dm (if you have a 
modern version and let it decide when to stop cycling) tends to be 
fairly accurate.  Yes, it does depend on resolution, but if you have 
high-res data with very low FOM, then you basically don't have any 
high-res data in an FOM-weighted map.  I tend to predict map 
interpretability by asking the question "to what resolution limit is the 
average FOM > 0.5?"  If that is 10A, then I generally don't bother 
looking at the map.

Perhaps the best way to settle this is to put it out to a challenge: 
does anybody have a map calculated with an average FOM(fromsomeprogram) 
< 0.5 that they were able to trace?  Does anyone have a map calculated 
with FOM(fromsomeprogram) > 0.5 that was total garbage?

-James Holton
MAD Scientist


Bryan W. Lepore wrote:
> 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

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

May 2024
April 2024
March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager