Sorry forgot to mention, if you go down the impurities route, there is SAUC to
check for similar unit cells in the PDB
http://iterate.sourceforge.net/sauc/
And there used to be Nearest Cell but my phone can't find that one anymore ;-
Sent from Yahoo Mail on Android
On Thu, 29 Aug 2019 at 18:41, Jonathan Cooper<bogba...@yahoo.co.uk> wrote:
It would be useful to know the number of molecules per asymmetric unit and the
sequence similarity of the search model and target. There is always Molrep to
try which is good at NCS ;-
Sent from Yahoo Mail on Android
On Thu, 29 Aug 2019 at 18:30, David Briggs<david.bri...@crick.ac.uk> wrote:
#yiv8743831735 #yiv8743831735 -- .yiv8743831735EmailQuote
{margin-left:1pt;padding-left:4pt;border-left:#800000 2px solid;}#yiv8743831735
Following on from Ivan's suggestion, SIMBAD might he worth a shot.
https://journals.iucr.org/d/issues/2018/07/00/rr5159/
The other thing you might try is handing the MR phases to the density modifying
and autobuilding program of your choice, increasing the number of cycles by
$arbitarylargenumber and then leaving it to run for a few hours/over night.
This has worked for me in the past when resolution was decent, phaser had found
an obviously correct MR solution, but the domain placed was only ~30-40% of the
total scattering mass of the ASU, and more conventional refinement was not
yielding decent maps outside the aforementioned domain.
Good luck!
Dave
--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Phil Jeffrey
<pjeff...@princeton.edu>
Sent: Thursday, August 29, 2019 5:24:48 PM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Another difficult MR case Are you *sure* there's no
translational NCS ?
For example your first molecular replacement solution out of Phenix shows
EULER 293.6 27.7 288.7
FRAC -0.02 0.02 0.02
(that's "first molecule at origin in P1")
and
EULER 294.0 27.9 288.8
FRAC -0.37 0.02 0.02
which is essentially the same orientation, and a translation down one
crystallographic axis (a*)
And this suggests to me that either Xtriage or Phaser is missing
something here. Does Phaser find translational NCS in its initial data
analysis ? Unmodeled translational NCS could cause significant problems
with the molecular replacement search.
Phil Jeffrey
Princeton
On 8/29/19 11:28 AM, Napoleão wrote:
> Deal all,
> Sorry for the long post.
> I have a data set obtained from a crystal produced after incubating a
> protease with a protein which is mostly composed by an antiparallel beta
> sheet. I have tried numerous approaches to solve it, and failed.
> Molecular replacement using Phaser, and the protease or the protein as a
> template yields no solution. However, molecular replacement using only
> part of the beta sheet yields LLG=320 TFZ==28.0 (see below).
>
> The apparently good data extends to 1.9 A, as processed by XDS, and the
> space group is P1 (pointless agree). XDS info below:
>
> SPACE_GROUP_NUMBER= 1
> UNIT_CELL_CONSTANTS= 44.43 72.29 77.30 97.802 89.939 101.576
>
> a b ISa
> 9.647E-01 3.176E-03 18.07
>
> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR
> R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano
> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed
> expected Corr
> 1.90 24890 19149 23814 80.4% 58.1%
> 63.7% 11482 0.77 82.2% 63.8* 3 0.694 492
> total 163756 125884 146938 85.7% 10.6%
> 10.8% 75744 3.78 15.0% 99.0* -3 0.761 5834
>
>
> Xtriage in Phenix 1.16-3549 gives me all green lights (print below),
> suggesting the data presents no twinning, no translational NCS, no ice
> rings and is not anisotropic.
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffullonline.org%2Fscience%2Fphenix_xtriage_green.png&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=RMV8abo87ybMyxaqD%2FHgOakRhGvzGgsQXzkuzC4c8HI%3D&reserved=0
>
> Molecular replacement in Phaser yields single solutions like:
>
> Solution annotation (history):
> SOLU SET RFZ=3.0 TFZ=* PAK=0 LLG=29 RFZ=2.8 TFZ=8.8 PAK=1 LLG=310
> TFZ==27.6
> LLG=320 TFZ==28.0
> SOLU SPAC P 1
> SOLU 6DIM ENSE ensemble1 EULER 293.6 27.7 288.7 FRAC -0.02
> 0.02 0.02 BFAC
> -6.03
> SOLU 6DIM ENSE ensemble1 EULER 294.0 27.9 288.8 FRAC -0.37
> 0.02 0.02 BFAC
> -6.52
> SOLU ENSEMBLE ensemble1 VRMS DELTA -0.1983 RMSD 0.49 #VRMS 0.21
>
> or partial solutions like:
>
> Partial Solution #1 annotation (history):
> SOLU SET RFZ=3.7 TFZ=* PAK=0 LLG=32 RFZ=2.8 TFZ=13.0 PAK=0 LLG=317
> TFZ==30.2
> LLG=331 TFZ==30.5 RFZ=2.4 TFZ=7.2 PAK=0 LLG=464 TFZ==18.5 RFZ=2.7
> TFZ=5.7 PAK=1
> LLG=501 TFZ==6.8 LLG=509 TFZ==6.6
> SOLU SPAC P 1
> SOLU 6DIM ENSE ensemble1 EULER 85.4 153.0 138.5 FRAC -0.01 -0.00
> -0.00 BFAC
> -12.30
> SOLU 6DIM ENSE ensemble1 EULER 86.2 153.2 139.5 FRAC -0.36 -0.01
> -0.01 BFAC
> -9.16
> SOLU 6DIM ENSE ensemble1 EULER 83.8 152.3 135.9 FRAC -0.00 0.00
> -0.25 BFAC
> 1.52
> SOLU 6DIM ENSE ensemble1 EULER 191.2 109.1 39.3 FRAC -0.27
> -0.01 0.22 BFAC
> 10.18
> SOLU ENSEMBLE ensemble1 VRMS DELTA -0.0447 RMSD 0.49 #VRMS 0.44
>
>
> However, after 1 refinement round in Phenix_Refine (Final: r_work =
> 0.4881 r_free = 0.5009) I got densities that are part good and part bad,
> and if I delete the bad parts and refine again, the good parts become
> bad. Please check the prints:
>
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffullonline.org%2Fscience%2Fgood_part_of_density.png&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=TZ69yTqXL1Kr%2FsAlUYJbxuCM1RQH0hDa9quwlz3Hueo%3D&reserved=0
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffullonline.org%2Fscience%2Fbad_part_of_density.png&data=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543&sdata=F%2B07eOV%2FziEwrhISIkbbRaWM8pdP3md94r%2FIgSZ9gWc%3D&reserved=0
>
> What is the explanation for these molecular replacement results?
> What else should I try? Arcimboldo takes 2 days+ to run and yields no
> good solution.
>
> Thank you!
> Regards,
> Napo
>
>
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