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From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of CCP4BB
automatic digest system
Sent: 27 September 2012 00:00
To: CCP4BB@JISCMAIL.AC.UK
Subject: CCP4BB Digest - 26 Sep 2012 (#2012-272)
There are 4 messages totaling 193 lines in this issue.
Topics of the day:
1. Maprot question.
2. map sharpening
3. Refmac- solvent mask (2)
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Date: Wed, 26 Sep 2012 15:21:44 +0100
From: Eleanor Dodson <eleanor.dod...@york.ac.uk>
Subject: Re: Maprot question.
You could use COOT to do the map rotation - then the parameters seem to work
The conventions should be the same. I thought but I can't really speak for COOT.
If you look at the CCP4 documentation for MAPROT, and use the Superpose
molecules GUI task to fit A to B using lsqkab - that gives you a matrix which
should be OK for MAPROT. Check it against the COOt output Eleanor
There is
On 26 Sep 2012, at 01:19, Niu Tou wrote:
> Dear Colleagues,
>
> Does anybody know if the definition of rotation parameters in Maprot are
> different from that of Coot? I used Coot to superimpose a model A to model B,
> to get a new model A* and rotation parameters (Euler angles and
> translations), howerver when I used these parameters to move the original map
> with Maprot, the new map did not fit with model A*. I tried the 3x3 matrix
> and translations, it did not work either. I wonder if there is any different
> from these two prgrams?
>
> Thanks!
> Niu
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Date: Wed, 26 Sep 2012 17:45:11 +0100
From: Andreas Förster <docandr...@gmail.com>
Subject: map sharpening
Dear all,
a follow-up to yesterday's question about map sharpening. The problem was that
the sharpened maps aren't displayed in coot, but this is not coot's fault, as
can be seen from the output:
regular map:
making conventional map from MTZ filename unsharp.mtz using FWT PHWT Number of
OBSERVED reflections: 34725
INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid
sampling...Nuvw = ( 128, 128, 384)
INFO:: 0.086 seconds to read MTZ file
INFO:: 0.002 seconds to initialize map
INFO:: 0.305 seconds for FFT
INFO:: 0.013 seconds for statistics
Map mean: ........ -1.4987e-06
Map sigma: ....... 0.0957995
Map maximum: ..... 0.629714
Map minimum: ..... -0.606727
INFO:: 0.026 seconds for contour map
INFO:: 0.432 seconds in total
sharpened map:
(as above, except:)
Map mean: ........ 0
Map sigma: ....... 0
Map maximum: ..... 0
Map minimum: ..... 0
These mtz files are generated identically, zero rounds of refinement in Refmac
5.7 (from ccp4 6.3.0) with sharpening disabled or enabled (B value = 5, 20, 60,
200). There are no features in the sharpened maps. Why?
When I don't specify a B value for map sharpening, it is calculated to
61 and the resulting map displays just fine.
Andreas
On 25/09/2012 11:52, Robert Nicholls wrote:
> Hi Andreas,
>
> In your case, it sounds like a reasonable strategy would be to use external
> restraints for a few rounds of refinement (as you have done), but then
> release them and instead use jelly-body restraints. This two-stage process
> will help to initially hold your model in a sensible conformation using
> external restraints, but then gently release the structure in order to reduce
> further bias in later rounds. The immediate subsequent use of jelly-body
> restraints after external restraints will ensure that the model won't deviate
> too far from that sensible conformation, unless the data suggests otherwise.
>
> Of course, if certain regions lose their sensible conformations in subsequent
> rounds of refinement, you can continue to use external restraints just in
> these regions.
>
>> I substantially rebuilt a surface loop that I don't want to restrain by the
>> model.
>
>
> In this case, I would recommend re-generating the external restraints, this
> time telling ProSMART not to generate restraints for these particular
> residues/regions. This can be done using the -restrain and -restrain_rm
> keywords, as described in the documentation (let me know off-board if you
> want help with this).
>
> If you enable map sharpening then the single output MTZ file should be the
> sharpened map… I'm not sure why you are finding that the map is not
> displayed… do you see any difference between enabling/disabling map
> sharpening?
>
> Cheers,
> Rob
>
>
--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk
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Date: Wed, 26 Sep 2012 11:45:52 -0700
From: Kiran Kulkarni <dr.kirankulka...@yahoo.com>
Subject: Refmac- solvent mask
Dear CCP4 users,
Is it possible to specify a solvent mask to the refmac ?
Many thanks in advance for your time and help.
Regards,
-Ki
------------------------------
Date: Wed, 26 Sep 2012 13:58:40 -0700
From: James Holton <jmhol...@lbl.gov>
Subject: Re: Refmac- solvent mask
Yes, it's called a "partial structure". You input the mask as
structure factors and call them "FPART" in the refmac LABIN input.
http://www.ysbl.york.ac.uk/refmac/docs/keywords/xray-principal.html#labin_fparti_phiparti
Then enable refining the scale and B factor of the partial structure:
http://www.ysbl.york.ac.uk/refmac/docs/keywords/xray-general.html#scpa
pay attention to the scale and B assigned to the partial structure in
the refmac log. If it blows up (or down) then something is wrong.
Also, don't forget to turn off the built-in solvent with "SOLVENT NO"
when you do this.
http://www.ysbl.york.ac.uk/refmac/docs/keywords/xray-principal.html#solv
You can actually add multiple partial structures and scale them
independently, but in my hands things start to get crazy if you have
more than 2.
-James Holton
MAD Scientist
On Wed, Sep 26, 2012 at 11:45 AM, Kiran Kulkarni
<dr.kirankulka...@yahoo.com> wrote:
> Dear CCP4 users,
>
> Is it possible to specify a solvent mask to the refmac ?
>
> Many thanks in advance for your time and help.
>
> Regards,
> -Kiran
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End of CCP4BB Digest - 26 Sep 2012 (#2012-272)
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