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CCP4BB  March 2010

CCP4BB March 2010

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Subject:

Re: self rotation education

From:

Ian Tickle <[log in to unmask]>

Reply-To:

Ian Tickle <[log in to unmask]>

Date:

Fri, 19 Mar 2010 16:01:26 +0000

Content-Type:

text/plain

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Parts/Attachments

text/plain (159 lines)

Francis, I would at least compute all the maps to the same resolution,
and as I suggested earlier use all the Fobs data you have, and finally
try using E's.  The differences could be due to the solvent model (or
lack of it) in the Fcalc's, though I concede that doesn't explain the
difference between Molrep & Polarrfn for the Fobs data.  Using E's
down-weights the low-res solvent contribution, so it might help here.

Sorry can't help with Molrep, I've never tried doing comparisons with
Polarrfn.  It could be that Molrep is applying some default sharpening
factor.

Cheers

-- Ian

On Fri, Mar 19, 2010 at 2:41 PM, Francis E Reyes
<[log in to unmask]> wrote:
> All,
>
> I recalculated in molrep_srfn, using F and SIGF of the original data (foo_30_rf.pdf) and FCalc/SIGF on the refined model (foo_29_rf.pdf). Note that foo_29_rf.pdf ( calculated phases using 50A to ~2.5A ) is extremely different than the original self rf functions I sent (which was the calculated phases from 50A-3A calculated in polarrfn).  In both cases, molrep_srfn greatly diminishes the psuedo peaks on the 180 slice independent of whether I use the original F's or calculated Fs.
>
> This is a little disconcerning as the purpose of this exercise is to determine whether I can properly interpret the self rotation peaks with a known model so that I can extend what I learned to a much more difficult present case where I have NCS but quite poor phases. Now I don't know which program to use.
>
> Does molrep_srfn do some fancy scaling to the data that polarrfn does not?
>
> F
>
>
>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>
> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>
>
>
> On Mar 19, 2010, at 8:12 AM, Ian Tickle wrote:
>
>> Dirk, I'm not sure this is right, the NCS 2-folds clearly occur at phi
>> = 45, 135 ..., not at phi = 30, 150 ... as required by your
>> explanation.  Also you haven't explained the very clear peaks near
>> theta = 45, phi = 0. 90 ... .  I won't be convinced until I see the
>> results from RFCORR!
>>
>> Cheers
>>
>> -- Ian
>>
>> On Fri, Mar 19, 2010 at 9:47 AM, Dirk Kostrewa
>> <[log in to unmask]> wrote:
>>> ... and here a slightly clearer version where I numbered the NCS-related
>>> positions 1,2,3 and their crystallographic equivalent positions 1',2',3',
>>> which makes the NCS dyads a bit easier to understand ...
>>>
>>> Sorry for sending two pictures.
>>>
>>> Best regards,
>>>
>>> Dirk.
>>>
>>> Am 19.03.10 10:31, schrieb Dirk Kostrewa:
>>>
>>> Dear Francis Reyes,
>>>
>>> from the self-rotation function at kappa=120 degrees, you can see that one
>>> threefold NCS axis is perpendicular to a crystallographic twofold axis. I
>>> haven't worked this out for your particular case, but the combination of a
>>> threefold (n-fold) NCS axis perpendicular to a crystallographic twofold axis
>>> creates three (n) NCS twofold axes (that can be viewed from both directions
>>> and in case of an uneven NCS axis appear "twice"). I've appended a schematic
>>> stereographic projection to make this a bit clearer (full dyad symbol
>>> crystallographic, open dyad and triangle symbols NCS, green circles
>>> positions above plane, red circles positions below plane created by
>>> crystallographic dyad, dashed lines help to visualize the NCS threefold,
>>> thick solid line crystallographic twofold, thin solid lines NCS twofolds).
>>>
>>> Good luck,
>>>
>>> Dirk.
>>>
>>> Am 18.03.10 16:03, schrieb Francis E Reyes:
>>>
>>> Hi all
>>>
>>> I have a solved structure that crystallizes as a trimer to a reasonable
>>> R/Rfree, but I'm trying to rationalize the peaks in my self rotation. The
>>> space group is P212121, calculating my self rotations from 50-3A,
>>> integration radius of 22 (the radius of my molecule is about 44). I can see
>>> the three fold NCS from my structure on the 120 slice, but I'm trying to
>>> rationalize apparent two folds in my kappa=180. A picture of both slices is
>>> enclosed. The non crystallographic peaks for kappa=180, P222 begin to appear
>>> at kappa=150 and are strongest on the 180 slice.
>>>
>>> My molecule looks close to a bagel (44A wide and 28A tall). The three fold
>>> NCS is down the axis of looking down on the bagel hole. I'm trying to find
>>> the two fold. I imagine it could be slicing the bagel in half (like to eat
>>> it for yourself) or slicing it vertically (like to share amongst kids) but
>>> I'm not exactly sure what's the best way to visualize this. Is there
>>> something easier than correlation maps with getax (since I have the rotation
>>> (polarrfn) and translation?). If you have an eye for spotting symmetry, Ill
>>> send the pdb in confidence.
>>> Thanks!
>>>
>>> FR
>>>
>>>
>>>
>>>
>>> ---------------------------------------------
>>> Francis Reyes M.Sc.
>>> 215 UCB
>>> University of Colorado at Boulder
>>>
>>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>>
>>> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>>>
>>>
>>>
>>>
>>>
>>> --
>>>
>>> *******************************************************
>>> Dirk Kostrewa
>>> Gene Center, A 5.07
>>> Ludwig-Maximilians-University
>>> Feodor-Lynen-Str. 25
>>> 81377 Munich
>>> Germany
>>> Phone:       +49-89-2180-76845
>>> Fax:         +49-89-2180-76999
>>> E-mail:      [log in to unmask]
>>> WWW: www.genzentrum.lmu.de
>>> *******************************************************
>>>
>>>
>>> --
>>>
>>> *******************************************************
>>> Dirk Kostrewa
>>> Gene Center, A 5.07
>>> Ludwig-Maximilians-University
>>> Feodor-Lynen-Str. 25
>>> 81377 Munich
>>> Germany
>>> Phone:       +49-89-2180-76845
>>> Fax:         +49-89-2180-76999
>>> E-mail:      [log in to unmask]
>>> WWW: www.genzentrum.lmu.de
>>> *******************************************************
>>>
>
>
>

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