Re: [ccp4bb] possible solution with Phaser

[Marc Graille]

Dear Luca,

few possibilities:
1) Consider that you may have only 3 monomers in the asymmetric unit and not 4 
as suggested from Matthew’s coefficient. Which are the R and Rfree values if 
you refine this model with only 3 molecules? 
2) When you look at the crystal packing on the correctly placed monomers (let’s 
call them A, B and C), is one of them (imagine C) forming a similar homodimer 
as AB with another monomer C according to the crystal symmetry?
3) Following up on Ethan’s suggestion, if you see extra-density that could 
correspond to part of the 4th monomer, you can try to use the 2Fo-Fc electron 
density map to locate the 4th molecule using MolRep and its option “Search in a 
map”. In this case, feed MolRep with the coordinates of the 3 correctly placed 
monomers as fixed model. It worked many times in my case. 

Hope this helps. 

Marc
—
Marc GRAILLE, PhD
DR1-CNRS
Laboratoire de Biologie Structurale de la Cellule  (BIOC; Ex-Laboratoire de 
Biochimie)
UMR7654 du CNRS

Head of the team: “Translation and degradation of eukaryotic mRNAs”

ÉCOLE POLYTECHNIQUE 
91128 PALAISEAU CEDEX
FRANCE 
📞: +33 (0)1 69 33 48 90

 : marc.grai...@polytechnique.edu  / : 
@GrailleLab 
https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes
—



> Le 6 janv. 2021 à 08:38, Luca Mazzei  a écrit :
> 
> Hi all,
> 
> I am struggling with the MR of a homo-dimer using Phaser. Matt_coeff strongly 
> suggests the presence of 4 mol per asym unit (space group P6222). The results 
> after a search of 4 mol per asymmetric unit of my monomer are the following:
> 
> ** SINGLE solution
> 
> ** Solution written to SOL file:  phaser_3f6v_A1_MOLREP.sol
> 
> ** Solution written to PDB file:  phaser_3f6v_A1_MOLREP.1.pdb
> ** Solution written to MTZ file:  phaser_3f6v_A1_MOLREP.1.mtz
>Solution annotation (history):
>SOLU SET  RFZ=3.9 TFZ=8.5 PAK=3 LLG=65 TFZ==10.0 RFZ=2.6 TFZ=17.0 PAK=3 
> LLG=326 TFZ==29.8 (& TFZ==22.5 & TFZ==19.7)
> LLG+=(326 & 529 & 593) LLG=795 TFZ==5.4 PAK=5 LLG=795 TFZ==5.4 PAK=5 
> LLG=795 TFZ==5.4
>SOLU SPAC P 62 2 2
>SOLU 6DIM ENSE autoMR EULER  125.3   60.8  300.2 FRAC  0.17 -0.13  0.08 
> BFAC -9.34 #TFZ==10.0
>SOLU 6DIM ENSE autoMR EULER  305.4   60.8  300.2 FRAC  0.27 -0.16  0.08 
> BFAC -5.29 #TFZ==29.8
>SOLU 6DIM ENSE autoMR EULER  294.7  119.1  120.3 FRAC  0.45  0.01  0.26 
> BFAC  0.34 #TFZ==22.5
>SOLU 6DIM ENSE autoMR EULER  305.5   61.6  300.1 FRAC  0.11 -0.16  0.08 
> BFAC 29.19 #TFZ==5.4
>SOLU ENSEMBLE autoMR VRMS DELTA -0.2463 #RMSD  0.93 #VRMS  0.79
> 
> It seems (also looking at the maps) that it correctly places three monomers 
> out of four. How can I use this information to improve the search of the 
> fourth monomer using the same template model?
> 
> Thanks in advance for your help,
> 
> Best regards
> 
> Luca Mazzei
> 
> Luca Mazzei - PhD
> Laboratory of Bioinorganic Chemistry
> Department of Pharmacy and Biotechnology (FaBiT)
> Alma Mater Studiorum - University of Bologna
> Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy
> Tel: +39 0512096235
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 
> 



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Re: [ccp4bb] possible solution with Phaser

[Randy John Read]

Dear Luca,

I think all of those orientations are symmetry-related copies of the same 
orientation.  This would imply that there is tNCS, but it doesn’t look like 
Phaser is applying tNCS.  The second and fourth molecules are in the same 
orientation, but differing by 1/6 of the a-axis cell translation.  Is there a 
large off-origin native Patterson peak, perhaps at 1/6,0,0?

Also, when there is tNCS it can be difficult to disentangle crystallographic 
and non-crystallographic symmetry.  Did you try all the space groups in the 
same point group?

Marc makes a good point about the number of copies.  The Matthews volume only 
gives you a rough estimate of the true number of copies, and the signal in 
placing the fourth molecule is very unconvincing compared to the first three.

Best wishes,

Randy Read

> On 6 Jan 2021, at 07:38, Luca Mazzei  wrote:
> 
> Hi all,
> 
> I am struggling with the MR of a homo-dimer using Phaser. Matt_coeff strongly 
> suggests the presence of 4 mol per asym unit (space group P6222). The results 
> after a search of 4 mol per asymmetric unit of my monomer are the following:
> 
> ** SINGLE solution
> 
> ** Solution written to SOL file:  phaser_3f6v_A1_MOLREP.sol
> 
> ** Solution written to PDB file:  phaser_3f6v_A1_MOLREP.1.pdb
> ** Solution written to MTZ file:  phaser_3f6v_A1_MOLREP.1.mtz
>Solution annotation (history):
>SOLU SET  RFZ=3.9 TFZ=8.5 PAK=3 LLG=65 TFZ==10.0 RFZ=2.6 TFZ=17.0 PAK=3 
> LLG=326 TFZ==29.8 (& TFZ==22.5 & TFZ==19.7)
> LLG+=(326 & 529 & 593) LLG=795 TFZ==5.4 PAK=5 LLG=795 TFZ==5.4 PAK=5 
> LLG=795 TFZ==5.4
>SOLU SPAC P 62 2 2
>SOLU 6DIM ENSE autoMR EULER  125.3   60.8  300.2 FRAC  0.17 -0.13  0.08 
> BFAC -9.34 #TFZ==10.0
>SOLU 6DIM ENSE autoMR EULER  305.4   60.8  300.2 FRAC  0.27 -0.16  0.08 
> BFAC -5.29 #TFZ==29.8
>SOLU 6DIM ENSE autoMR EULER  294.7  119.1  120.3 FRAC  0.45  0.01  0.26 
> BFAC  0.34 #TFZ==22.5
>SOLU 6DIM ENSE autoMR EULER  305.5   61.6  300.1 FRAC  0.11 -0.16  0.08 
> BFAC 29.19 #TFZ==5.4
>SOLU ENSEMBLE autoMR VRMS DELTA -0.2463 #RMSD  0.93 #VRMS  0.79
> 
> It seems (also looking at the maps) that it correctly places three monomers 
> out of four. How can I use this information to improve the search of the 
> fourth monomer using the same template model?
> 
> Thanks in advance for your help,
> 
> Best regards
> 
> Luca Mazzei
> 
> Luca Mazzei - PhD
> Laboratory of Bioinorganic Chemistry
> Department of Pharmacy and Biotechnology (FaBiT)
> Alma Mater Studiorum - University of Bologna
> Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy
> Tel: +39 0512096235
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk




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Re: [ccp4bb] possible solution with Phaser

[Eleanor Dodson]

First - test other spacegroups - your solutions have lots of 60
degree angles - and the space group is hexagonal - there can be confusion
between cryst symmetry and homo-dimer symmetries.

If you go back to the data processing and read the pointless output
carefully for point group clues- Qs to check.
Are the CCS for all crystal symops approximately equal? Could it be lower
symmetry? trigonal ? or the two fold axis generated from the dimer??
Then are there absences along c indicative of P61 ? :P 62?
or is there a non-cryst translation which could also generate absences?
Then I always run the MOLREP self-rotation to see in this case is there a
dimer two-fold somewhere different from the crystallographic ones?

These cases with lots of model symmetry in high symmetry spacegroups are
often tricky but neat fun when you get it sorted!
Eleanor

On Wed, 6 Jan 2021 at 08:56, Randy John Read  wrote:

> Dear Luca,
>
> I think all of those orientations are symmetry-related copies of the same
> orientation.  This would imply that there is tNCS, but it doesn’t look like
> Phaser is applying tNCS.  The second and fourth molecules are in the same
> orientation, but differing by 1/6 of the a-axis cell translation.  Is there
> a large off-origin native Patterson peak, perhaps at 1/6,0,0?
>
> Also, when there is tNCS it can be difficult to disentangle
> crystallographic and non-crystallographic symmetry.  Did you try all the
> space groups in the same point group?
>
> Marc makes a good point about the number of copies.  The Matthews volume
> only gives you a rough estimate of the true number of copies, and the
> signal in placing the fourth molecule is very unconvincing compared to the
> first three.
>
> Best wishes,
>
> Randy Read
>
> > On 6 Jan 2021, at 07:38, Luca Mazzei  wrote:
> >
> > Hi all,
> >
> > I am struggling with the MR of a homo-dimer using Phaser. Matt_coeff
> strongly suggests the presence of 4 mol per asym unit (space group P6222).
> The results after a search of 4 mol per asymmetric unit of my monomer are
> the following:
> >
> > ** SINGLE solution
> >
> > ** Solution written to SOL file:  phaser_3f6v_A1_MOLREP.sol
> >
> > ** Solution written to PDB file:  phaser_3f6v_A1_MOLREP.1.pdb
> > ** Solution written to MTZ file:  phaser_3f6v_A1_MOLREP.1.mtz
> >Solution annotation (history):
> >SOLU SET  RFZ=3.9 TFZ=8.5 PAK=3 LLG=65 TFZ==10.0 RFZ=2.6 TFZ=17.0
> PAK=3 LLG=326 TFZ==29.8 (& TFZ==22.5 & TFZ==19.7)
> > LLG+=(326 & 529 & 593) LLG=795 TFZ==5.4 PAK=5 LLG=795 TFZ==5.4 PAK=5
> LLG=795 TFZ==5.4
> >SOLU SPAC P 62 2 2
> >SOLU 6DIM ENSE autoMR EULER  125.3   60.8  300.2 FRAC  0.17 -0.13
> 0.08 BFAC -9.34 #TFZ==10.0
> >SOLU 6DIM ENSE autoMR EULER  305.4   60.8  300.2 FRAC  0.27 -0.16
> 0.08 BFAC -5.29 #TFZ==29.8
> >SOLU 6DIM ENSE autoMR EULER  294.7  119.1  120.3 FRAC  0.45  0.01
> 0.26 BFAC  0.34 #TFZ==22.5
> >SOLU 6DIM ENSE autoMR EULER  305.5   61.6  300.1 FRAC  0.11 -0.16
> 0.08 BFAC 29.19 #TFZ==5.4
> >SOLU ENSEMBLE autoMR VRMS DELTA -0.2463 #RMSD  0.93 #VRMS  0.79
> >
> > It seems (also looking at the maps) that it correctly places three
> monomers out of four. How can I use this information to improve the search
> of the fourth monomer using the same template model?
> >
> > Thanks in advance for your help,
> >
> > Best regards
> >
> > Luca Mazzei
> >
> > Luca Mazzei - PhD
> > Laboratory of Bioinorganic Chemistry
> > Department of Pharmacy and Biotechnology (FaBiT)
> > Alma Mater Studiorum - University of Bologna
> > Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy
> > Tel: +39 0512096235
> >
> >
> >
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
>
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> The Keith Peters Building   Fax: +44 1223
> 336827
> Hills Road   E-mail:
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
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[ccp4bb] Call open for BAG beamtime at DESY beamline P11, PETRA III

[Hakanpää , Johanna]

Dear all,

Please note the approaching deadline for submission of Block Allocation Group 
(BAG) proposals for DESY beamline P11 at the PETRA III synchrotron in Hamburg.

Proposals are to be submitted via https://door.desy.de
The deadline for submission is
--
Monday, 18 January 2021 (until midnight local Hamburg time, UTC+2)
--
This call for BAG proposals relates to beamtime to be allocated during 2021 
(second half) - 2023 (first half).

Detailed information, preparation guidelines and a template for BAG proposals 
are provided here:
https://photon-science.desy.de/users_area/user_guide/select_the_proposal_type

Beamline P11 is a versatile beamline dedicated to protein crystallography with 
a sample changer in unipuck format.

We offer various focusing modes with beam size from 5 x 10 um (flux 1 × 10^13 
ph/s at 12 keV at the sample position) to 300 x 300 um. Broad energy range from 
5.5 - 28 keV and Pilatus 6M/Eiger2 16M detectors. Fast sample changer cycle (20 
s) with storage capacity for 23 unipucks (368 samples) and remote access.

For further information please see 
http://photon-science.desy.de/facilities/petra_iii/beamlines/p11_bio_imaging_and_diffraction

On behalf of the P11 team,
Johanna


Johanna Hakanpää, PhD

Scientist, Beamline P11 (PETRA III)
Deutsches Elektronen-Synchrotron DESY
Notkestrasse 85
22607 Hamburg
Germany

Phone: +49 40 8998 5756
Email: johanna.hakan...@desy.de



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[ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

[Bernhard Rupp]

Dear Developers,

 

running cif2mtz in ccp4i (or from the console) in the case of non-standard
settings of space group 18 (which should be discouraged, to phrase it
mildly) 

on the mmcif from the PDB

_symmetry.space_group_name_H-M   "P 21 2 21" <--

_symmetry.Int_Tables_number  18 

#

 

leads to a problem because the resulting mtz file has the standard 18 symbol

 

Type  Merged MTZ

Space group   P 21 21 2 <-- 

Space group confidenceX  (confidence flag is not set)

Cell 88.578  44.416  71.56490  90  90  

 

Not sure if this is a loss of information when generating the mmcif upon
submission,

or the SG is retrieved solely by SG number not symbol (the latter can give
rise to a few more such situations).

 

Best, BR

 

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

[Marcin Wojdyr]

Dear Bernhard,

CCP4 has an alternative command-line tool for this; less tested but
happens to preserve P 21 2 21:
gemmi cif2mtz input.cif output.mtz

Marcin

On Wed, 6 Jan 2021 at 20:39, Bernhard Rupp  wrote:
>
> Dear Developers,
>
>
>
> running cif2mtz in ccp4i (or from the console) in the case of non-standard 
> settings of space group 18 (which should be discouraged, to phrase it mildly)
>
> on the mmcif from the PDB
>
> _symmetry.space_group_name_H-M   "P 21 2 21" ß
>
> _symmetry.Int_Tables_number  18
>
> #
>
>
>
> leads to a problem because the resulting mtz file has the standard 18 symbol
>
>
>
> Type  Merged MTZ
>
> Space group   P 21 21 2 ß
>
> Space group confidenceX  (confidence flag is not set)
>
> Cell 88.578  44.416  71.56490  90  90
>
>
>
> Not sure if this is a loss of information when generating the mmcif upon 
> submission,
>
> or the SG is retrieved solely by SG number not symbol (the latter can give 
> rise to a few more such situations).
>
>
>
> Best, BR
>
>
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

[Ian Tickle]

Hi  Bernhard

I gave up trying to use CIF2MTZ in the STARANISO server over a year ago.  I
agree with Marcin that his GEMMI program is the way to go.  It does
everything you need and Marcin is very quick to respond to any issues.

The problem is that there are alternate settings in the PDB so the software
just has to be able to handle them.  The space group number should not be
used for anything other than information, for the obvious reason that it's
not unique.  AFAIK all software uses either the full H-M symbol or the
general equivalent positions themselves (e.g. Shel-X).

>From your description the axes in the SG symbol have been permuted but the
cell axes remain in the original order?  If so that's plainly a bug which
should be fixed (or CIF2MTZ put in retirement).

Cheers

-- Ian


On Wed, 6 Jan 2021 at 19:38, Bernhard Rupp  wrote:

> Dear Developers,
>
>
>
> running cif2mtz in ccp4i (or from the console) in the case of non-standard
> settings of space group 18 (which should be discouraged, to phrase it
> mildly)
>
> on the mmcif from the PDB
>
> _symmetry.space_group_name_H-M   "P 21 2 21" ß
>
> _symmetry.Int_Tables_number  18
>
> #
>
>
>
> leads to a problem because the resulting mtz file has the standard 18
> symbol
>
>
>
> Type  Merged MTZ
>
> Space group   P 21 21 2 ß
>
> Space group confidenceX  (confidence flag is not set)
>
> Cell 88.578  44.416  71.56490  90  90
>
>
>
> Not sure if this is a loss of information when generating the mmcif upon
> submission,
>
> or the SG is retrieved solely by SG number not symbol (the latter can give
> rise to a few more such situations).
>
>
>
> Best, BR
>
>
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

[Bernhard Rupp]

Thanks Fellows,

 

> I agree with Marcin that his GEMMI program is the way to go.  It does 
> everything you need and Marcin is very quick to respond to any issues.

 

Yes, found it also in the windows distribution will try

 

> From your description the axes in the SG symbol have been permuted but the 
> cell axes remain in the original order?  If so that's plainly a bug which 
> should be fixed (or CIF2MTZ put in retirement).

 

Bug. No swap of indices -> chaos if you run Refmac thereafter. Will retire 
cif2mtz in my hacks. 

 

Robbie suggested eliminating the SG number in the CIF as a workaround.

 

Many thx, BR

 

 

On Wed, 6 Jan 2021 at 19:38, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

Dear Developers,

 

running cif2mtz in ccp4i (or from the console) in the case of non-standard 
settings of space group 18 (which should be discouraged, to phrase it mildly) 

on the mmcif from the PDB

_symmetry.space_group_name_H-M   "P 21 2 21" <--

_symmetry.Int_Tables_number  18 

#

 

leads to a problem because the resulting mtz file has the standard 18 symbol

 

Type  Merged MTZ

Space group   P 21 21 2 <-- 

Space group confidenceX  (confidence flag is not set)

Cell 88.578  44.416  71.56490  90  90  

 

Not sure if this is a loss of information when generating the mmcif upon 
submission,

or the SG is retrieved solely by SG number not symbol (the latter can give rise 
to a few more such situations).

 

Best, BR

 

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

  _  

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 &A=1 

 

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