Of Andrey
Nascimento
Sent: Thursday, March 28, 2013 12:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
Dear all,
As I said in the latest topic, I could not model the third molecule. But when I
superpose the two trimmers found in P1 MR solution
Dear Appu,
I am sorry, I do not have the script file. I ran it basically from default
parameters in CCP4 GUI. I just ran the sfcheck for 'check experimental data
only' and I got the twin law and twin fraction from the output (post script
file). So, I put these information on the detwin and ran it.
Dear Herman,
I would like to mention one more information, maybe I have forgotten. When
a process the data in P21212 and run the sfcheck it do not appear to have
twinning (even when a ran phenix Xtriage with older process data in
P21212). I will send direct to your e-mail the .pdf file with
Dear all,
As I said in the latest topic, I could not model the third molecule. But
when I superpose the two trimmers found in P1 MR solution (link below), I
get the first two molecules perfect aligned and the third molecule
inverted! (It is also possible to see the 2-fold axis and the third
Seems reasonable: P21 with beta=90 is pretty common, and it often ends
up twinned as well.
Most importantly, your R-factors support the hypothesis.
(Only keep in mind that R-factors are lower in twinned refinement - look
on Garib's webpage for the presentation where he describes that --
First - I dont think you have a 3rd molecule where you have put it - or at
least not one with full occupancy. Those maps are a clear indication that
something is wrong. What is the Matthews coefficient for the numbers in the
asymmetric unit?
Presumably your processing gave you a lattice which
Dear all,
I have tried the procedure recommended by Zbyszek, expanding data from a
higher symmetry and keeping the R-free set. But the map for third molecule
(new molecule placed) are still very bad, even when a tried to reprocess
data in P1 or P2 (P 1 21 1). The previous placed molecule (present
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
Maybe this thread still needs some more pedagogy/explanation for those newbies
and for biologist/ wanna-be crystallographers like me. My original reaction
was- if the true space group is P21 you wouldn't want to expand from
Dear Zbyszek,
I am concerned that the unmerged data would be bypassed and not preserved in
your recommendation. I also find it counter intuitive that the merged data
would then be unmerged into a lower symmetry and be better than the unmerged
data; there is I imagine some useful reference or
Dear all,
We have solved the problem. Data processing in P1 looks better (six
molecules in ASU), and Zanuda shows a P 1 21 1 symmetry (three molecules in
ASU), Rfactor/Rfree drops to 0.20978/0.25719 in the first round
of refinement (without put waters, ligands, etc.).
Indeed, there were one more
It is a clear-cut case of crystal packing disorder. The tell-tale sign is
that data can be merged in the higher-symmetry lattice, while the number
of molecules in the asymmetric unit (3 in P21) is not divisible by the
higher symmetry factor (2, by going from P21 to P21212).
From my experience,
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Zbyszek
Otwinowski [zbys...@work.swmed.edu]
Sent: Tuesday, March 19, 2013 9:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
It is a clear-cut case of crystal
Otwinowski [zbys...@work.swmed.edu]
Sent: Tuesday, March 19, 2013 9:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
It is a clear-cut case of crystal packing disorder. The tell-tale sign is
that data can be merged in the higher-symmetry lattice
A. Rice
[pr...@uchicago.edu]
Sent: Tuesday, March 19, 2013 10:34 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
Hi Zbyszek,
If the issue is perfect twinning, I agree - good point!
But you don't want to confuse people who simply have nearly
@JISCMAIL.AC.UK] On Behalf Of Phoebe A.
Rice
Sent: Tuesday, March 19, 2013 4:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
oops, I should have expanded my comments to include the sort of funky lattice
order-disorder Zbyszek so cleverly diagnosed
@JISCMAIL.AC.UK] on behalf of Phoebe A. Rice
[pr...@uchicago.edu]
Sent: Tuesday, March 19, 2013 10:34 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
Hi Zbyszek,
If the issue is perfect twinning, I agree - good point!
But you don't want to confuse
Check for translational NCS
And you are way too conservative with resolution. Even those holding
onto the Rmerge-dictated past would probably acquiesce to lower I/sig
cutoff. If you are using aimless, follow its recommendations based on
CC1/2, it's good for you.
Cheers,
Ed.
On Fri,
Wow, Usually on the default settings of adxv, I can see spots at this I/sig!
I suspect your data goes higher than 1.77.
Include more of the high resolution data. You very likely don't have the
correct space group.
F
On Mar 15, 2013, at 11:39 AM, Andrey Nascimento
What happens if you solvent-flatten/flip/massage that map, but tell the
software the solvent content much lower than what you think it is now? Maybe
you'll find another copy of the molecule?
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
Hi Andrey,
I am taking a risky guess:
From your slide #2, it looks like a termini (unless this correspond to the
beginning or end of disordered a loop) of the protein chain(s) is (are)
extending toward(s) the solvent channel. Are the density features shown in
slides #3,4, and 5 extend from this
Or give it to arp/warp, either with the current model to improve or with phases
from the current model to build new model?
Phoebe A. Rice wrote:
What happens if you solvent-flatten/flip/massage that map, but tell the
software the solvent content much lower than
what you think it is now? Maybe
I second Phoebe's suggestion. Looks like another molecule to me. If you are
doing molecular replacement you may need to get creative about trimming. When
we had a case like that it wasn't until the third person worked on it that we
go a solution because he trimmed the model differently than the
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