[ccp4bb] Shear number of beta-barrel proteins

[Iris Gawarzewski]

Hello everybody,

I need some pratical advice for determination of the shear number of my 
beta-barrel protein. Is there any software tool, which I can use or do I have 
to determine it by hand?


Thanks in advance,

Iris
___
Dipl-Biol. Iris Gawarzewski
PhD student
Workgroup of Prof. Dr. Schmitt
Institute of Biochemistry
Building 26.32.03.21
Heinrich-Heine University Düsseldorf
Universitätsstr. 1
40225 Düsseldorf
-Germany-
Tel: 0049-211-81-13577

Re: [ccp4bb] Shear number of beta-barrel proteins

[Noinaj, Nicholas (NIH/NIDDK) [F]]

Iris,

Having tackled this question myself recently, I was unable to find any software 
to do this analysis for me.  So, unless someone has personal scripts or 
software that isn't openly available or something that I may have missed, I 
think you will have to do the analysis manually.  While the analysis itself 
isn't hard once you understand how it is performed, I was hoping to use some 
software/tool to verify the accuracy of my results.

If needed, I am happy to provide you with the references that I used for this, 
good luck!




Cheers,
Nick





[ Nicholas Noinaj ]
the Buchanan Lab
Laboratory of Molecular Biology
LMB-NIDDK, NIH
50 South Drive, Room 4505
Bethesda, MD  20892-8030
1-301-594-9230 (lab)
1-859-893-4789 (cell)
noin...@niddk.nih.gov

[ the Buchanan Lab ]
http://www-mslmb.niddk.nih.gov/buchanan/





From: Iris Gawarzewski [mailto:iris.gawarzew...@uni-duesseldorf.de]
Sent: Tuesday, July 30, 2013 4:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Shear number of beta-barrel proteins

Hello everybody,

I need some pratical advice for determination of the shear number of my 
beta-barrel protein. Is there any software tool, which I can use or do I have 
to determine it by hand?


Thanks in advance,

Iris
___
Dipl-Biol. Iris Gawarzewski
PhD student
Workgroup of Prof. Dr. Schmitt
Institute of Biochemistry
Building 26.32.03.21
Heinrich-Heine University Düsseldorf
Universitätsstr. 1
40225 Düsseldorf
-Germany-
Tel: 0049-211-81-13577

Re: [ccp4bb] Twin or underestimation of symmetry

[Eleanor Dodson]

This is a bit puzzling.
Sticking to point groups:
P3 &  P6 are sub groups of P6/mmm so data which merges in P6/mmm will
always satisfy P3 and P6.
And twinning in P3 or P6 will make the data seem to have higher symmetry.
Four way twinning is unusual, but possible of course.

But if you really have twinning, you should see it indicated in the
pointless/aimless plots, or via Xtriage.. If those tests do not show it and
you dont have a non-crystallographic translation twinning is unlikely.

Your choice of SGs seem puzzling too.
 If the data is P31 (or P32) then you should see intensities for l=3n, and
absences for l=3n+-1
If the data is P61 (or P65) then you should only see intensities for l=6n.
If the data is P6322 you should only see intensities for l=2n.
What are the absences along 00l?

Eleanor






On 29 July 2013 18:37, Jeffrey D Brodin  wrote:

>  Hi everyone,
>
> I have a dataset that's been giving me some trouble and wanted to get your
> ideas on the best way to proceed. The data extend to ~2.6 Å and scale
> integrate/scale well in P622. According to Pointless, the symmetry is
> either P622 or P6322, however, neither Molrep norm Phaser finds molecular
> replacement solutions in these space groups. If I run Phaser and let it
> check all other space groups it finds a solution in P6122, but I can only
> refine it to an Rfree value of ~35%. The data also scales well in P3 and P6
> and I get molecular replacement solutions in space groups of either P31 or
> P61. However, the Refinement again stalls at an Rfree value of ~35%. I
> tried adding twin refinement in Refmac and it seems to be helping; The
> R/Rfree values dropped to 20.9/27.3 and the map appears much better
> compared to the previous refinements. The refined twin fractions are 0.26,
> 0.24, 0.24 and 0.25. Am I doing something wrong with the refinement or is
> this a legitimate way to treat the data. Thank you in advance for your help.
> *
> *
>

Re: [ccp4bb] Twin or underestimation of symmetry

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jeffrey,

how complete is you model, i.e. what is the ratio between  the number
of atoms in the PDB file (without solvent/ ligands) and the expected
number of atoms as calculated from the sequence?
If a substantial part of the molecule is disordered you may not be
able to get a much better model.

What is the R-value and Rfree? If you have placed many water atoms you
may have hovered out the difference density allowing you to further
improve your model.

Regards,
Tim

On 07/29/2013 07:37 PM, Jeffrey D Brodin wrote:
> Hi everyone,
> 
> I have a dataset that's been giving me some trouble and wanted to
> get your ideas on the best way to proceed. The data extend to ~2.6
> Å and scale integrate/scale well in P622. According to Pointless,
> the symmetry is either P622 or P6322, however, neither Molrep norm
> Phaser finds molecular replacement solutions in these space groups.
> If I run Phaser and let it check all other space groups it finds a
> solution in P6122, but I can only refine it to an Rfree value of
> ~35%. The data also scales well in P3 and P6 and I get molecular
> replacement solutions in space groups of either P31 or P61.
> However, the Refinement again stalls at an Rfree value of ~35%. I
> tried adding twin refinement in Refmac and it seems to be helping;
> The R/Rfree values dropped to 20.9/27.3 and the map appears much
> better compared to the previous refinements. The refined twin
> fractions are 0.26, 0.24, 0.24 and 0.25. Am I doing something wrong
> with the refinement or is this a legitimate way to treat the data.
> Thank you in advance for your help.
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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[ccp4bb] Placing coordinates and mtz reflections file on a common new origin

[Mo Wong]

Hi all,

I am trying to get multiple molecular replacement solutions on the same
origin. I know this has been asked before, however, in my case I want to
stick to CCP4 programmes (I am aware PHENIX can do this).

I have tried to get this to work using csymmatch which outputs the
origin-shifted coordinates, but this gives me a solution which I can't
apply to the reflections file (I am using phasechange to calculate the
shifted mtz file), i.e:

Change of origin: uvw = ( 0.08333, 0.5, 0.5 )

reforigin can bail due to cell dimension differences (I could recompile
with a greater tolerance, but I'd rather not start messing with code).
cphasematch obviously produces a sensible map with uvw=0.0,0.5,0.5, but I'd
like to calculate the matching origin-shifted coordinates without having to
write a fortran programme (is there a programme out there which can do
this?).

I'm guessing I can use clipper to do this in one easy step (preferably
without having to merge the 2 mtz files in CAD), but I'd rather not have to
re-invent the wheel if someone's done this already.

Thanks for any help!

[ccp4bb]

[Kraatz Sebastian]

Dear all,
does anyone of you has any experience in adapting ARCIMBOLDO for other
clusters than Condor, e.g. grid engine? Does anyone know of a case of
success where ARCIMBOLDO was used to solve a coiled coil structure?
 
Best regards,
Sebastian Kraatz

Re: [ccp4bb] ARCIMBOLDO

[Claudia Millán Nebot]

Dear Sebastian,

our new release, planned around the ECM in Warwick, runs on a single
workstation having access to a local or remote grid, supporting either
condor or SGE/Opengrid.

Coiled coils should be particularly suitable and we have solved a number of
them, including twinned structures. Depends on the data, often they are
very anisotropic and more difficult than one would anticipate.

Best wishes,

Claudia Millán (cmn...@ibmb.csic.es)

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain


2013/7/30 Kraatz Sebastian 

> **
> Dear all,
> does anyone of you has any experience in adapting ARCIMBOLDO for other
> clusters than Condor, e.g. grid engine? Does anyone know of a case of
> success where ARCIMBOLDO was used to solve a coiled coil structure?
>
> Best regards,
> Sebastian Kraatz
>

Re: [ccp4bb] Advise on setting up/ maintaining a Ubuntu cluster

[Adam Ralph]

Dear Sergei,

 Second point is probably easier to do. An alternative to NFS is sshfs. The 
advantage is that it uses SSH which is installed by default and configured the 
same way. If you generate key pairs you can use ssh or sshfs without a password.
Check this page below;

http://www.howtoforge.com/mounting-remote-directories-with-sshfs-on-ubuntu-11.10


Typically LDAP is being used for centralised authentication but NIS is 
probably
just as good. Page below is about the client setup.

https://help.ubuntu.com/community/LDAPClientAuthentication


Both of the above are more likely to survive upgrades.

Adam

Re: [ccp4bb] Twin or underestimation of symmetry

[Phoebe A. Rice]

Check the pseudo-precession pics (0kl plane, etc).  A rhombohedral crystal that 
is indexed as P6xx may have seemingly-bizarre systematic absences that could 
trick one into thinking its P63xx.  

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene 
[t...@shelx.uni-ac.gwdg.de]
Sent: Tuesday, July 30, 2013 7:26 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Twin or underestimation of symmetry

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jeffrey,

how complete is you model, i.e. what is the ratio between  the number
of atoms in the PDB file (without solvent/ ligands) and the expected
number of atoms as calculated from the sequence?
If a substantial part of the molecule is disordered you may not be
able to get a much better model.

What is the R-value and Rfree? If you have placed many water atoms you
may have hovered out the difference density allowing you to further
improve your model.

Regards,
Tim

On 07/29/2013 07:37 PM, Jeffrey D Brodin wrote:
> Hi everyone,
>
> I have a dataset that's been giving me some trouble and wanted to
> get your ideas on the best way to proceed. The data extend to ~2.6
> Å and scale integrate/scale well in P622. According to Pointless,
> the symmetry is either P622 or P6322, however, neither Molrep norm
> Phaser finds molecular replacement solutions in these space groups.
> If I run Phaser and let it check all other space groups it finds a
> solution in P6122, but I can only refine it to an Rfree value of
> ~35%. The data also scales well in P3 and P6 and I get molecular
> replacement solutions in space groups of either P31 or P61.
> However, the Refinement again stalls at an Rfree value of ~35%. I
> tried adding twin refinement in Refmac and it seems to be helping;
> The R/Rfree values dropped to 20.9/27.3 and the map appears much
> better compared to the previous refinements. The refined twin
> fractions are 0.26, 0.24, 0.24 and 0.25. Am I doing something wrong
> with the refinement or is this a legitimate way to treat the data.
> Thank you in advance for your help.
>

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.14 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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=q8Ki
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Re: [ccp4bb] Twin or underestimation of symmetry

[Jeffrey D Brodin]

The model is essentially 100% identical. The structure is of a point mutant 
that has already been solved.


From: Tim Gruene [t...@shelx.uni-ac.gwdg.de]
Sent: Tuesday, July 30, 2013 5:26 AM
To: Jeffrey D Brodin
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Twin or underestimation of symmetry

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jeffrey,

how complete is you model, i.e. what is the ratio between  the number
of atoms in the PDB file (without solvent/ ligands) and the expected
number of atoms as calculated from the sequence?
If a substantial part of the molecule is disordered you may not be
able to get a much better model.

What is the R-value and Rfree? If you have placed many water atoms you
may have hovered out the difference density allowing you to further
improve your model.

Regards,
Tim

On 07/29/2013 07:37 PM, Jeffrey D Brodin wrote:
> Hi everyone,
>
> I have a dataset that's been giving me some trouble and wanted to
> get your ideas on the best way to proceed. The data extend to ~2.6
> Å and scale integrate/scale well in P622. According to Pointless,
> the symmetry is either P622 or P6322, however, neither Molrep norm
> Phaser finds molecular replacement solutions in these space groups.
> If I run Phaser and let it check all other space groups it finds a
> solution in P6122, but I can only refine it to an Rfree value of
> ~35%. The data also scales well in P3 and P6 and I get molecular
> replacement solutions in space groups of either P31 or P61.
> However, the Refinement again stalls at an Rfree value of ~35%. I
> tried adding twin refinement in Refmac and it seems to be helping;
> The R/Rfree values dropped to 20.9/27.3 and the map appears much
> better compared to the previous refinements. The refined twin
> fractions are 0.26, 0.24, 0.24 and 0.25. Am I doing something wrong
> with the refinement or is this a legitimate way to treat the data.
> Thank you in advance for your help.
>

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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Re: [ccp4bb] ARCIMBOLDO

[Kraatz Sebastian]

Hi guys,
thanks for the quick response. For two of our coiled coils we tried AMPLE, but 
it proved to be a rather tricky case. We are definitely going to try 
ARCIMBOLDO. We already forwarded the case to the persons in charge of the beam 
lines and the clusters to arrange for an installation.

Many thanks,
Sebastian  

-Original Message-
From: clmil...@gmail.com on behalf of Claudia Millán Nebot
Sent: Tue 7/30/2013 4:24 PM
To: Kraatz Sebastian
Subject: Re: [ccp4bb] ARCIMBOLDO
 
Hi Sebastian,

we have to hold the new ARCIMBOLDO release until publication, the paper is
in press and should appear next month or latest september. There will be a
talk and a tutorial at the Software Fayre in Warwick. In the meantime, we
have installed beta versions at some places (MRC, Uni. Konstanz, Australian
Synchrotron). So it would be possible, if you have an urgent use case and
given synchrotrons are visited by many users, to have a beta version at the
SLS. In that case, your system manager is welcome to contact us.

Best wishes,



Claudia Millán (cmn...@ibmb.csic.es)

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain


2013/7/30 Claudia Millán Nebot 

> Dear Sebastian,
>
> our new release, planned around the ECM in Warwick, runs on a single
> workstation having access to a local or remote grid, supporting either
> condor or SGE/Opengrid.
>
> Coiled coils should be particularly suitable and we have solved a number
> of them, including twinned structures. Depends on the data, often they are
> very anisotropic and more difficult than one would anticipate.
>
> Best wishes,
>
> Claudia Millán (cmn...@ibmb.csic.es)
>
> Institut de Biologia Molecular de Barcelona (IBMB-CSIC)
>
> Barcelona, Spain
>
>


> Hi,

 

> Hopefully Isabel Uson will reply to you – she is normally very helpful with 
> Arcimboldo.

 

> As an alternative approach, we have recently been looking specifically at 
> coiled-coil structures with AMPLE (in the CCP4 suite, although it continues 
> to evolve). We have had _some_ success, but these are difficult for MR as I 
> am > sure you know. If you wish, we’d be happy to have a look.

 

> Cheers

> Martyn

> 2013/7/30 Kraatz Sebastian 
>
>> **
>> Dear all,
>> does anyone of you has any experience in adapting ARCIMBOLDO for other
>> clusters than Condor, e.g. grid engine? Does anyone know of a case of
>> success where ARCIMBOLDO was used to solve a coiled coil structure?
>>
>> Best regards,
>> Sebastian Kraatz
>>
>
>

Re: [ccp4bb] Advise on setting up/ maintaining a Ubuntu cluster

[Francois Berenger]

Be careful that running data intensive jobs over NFS
is super slow (at least an order of magnitude compared
to writing things on a local disk).
Not only the computation is slow, but you may be slowing down
all other users of the cluster too...

F.

On 07/30/2013 11:28 PM, Adam Ralph wrote:

Dear Sergei,

  Second point is probably easier to do. An alternative to NFS is
sshfs. The
advantage is that it uses SSH which is installed by default and
configured the
same way. If you generate key pairs you can use ssh or sshfs without a
password.
Check this page below;

http://www.howtoforge.com/mounting-remote-directories-with-sshfs-on-ubuntu-11.10


 Typically LDAP is being used for centralised authentication but NIS
is probably
just as good. Page below is about the client setup.

https://help.ubuntu.com/community/LDAPClientAuthentication


 Both of the above are more likely to survive upgrades.

Adam

[ccp4bb] Output of Phaser

[Chen Zhao]

Dear all,

I am sorry for my new-comer question, but I am not clear what the multiple
RFZ, TFZ, PAK and LLG scores belong to after each solution set in the
phaser output (eg. .sol) file. My bet is that each of them corresponds to
each of the solutions listed below, but I am not sure. Also I know that
TFZ== represents the TFZ score based on the refined orientation, but why
does it sometimes appear in the middle instead of at the end?

One example could look like this:

SOLU SET *RFZ=5.4 TFZ=3.6 PAK=0 LLG=67* TFZ==1.8 *RFZ=2.2 TFZ=5.1 PAK=3
LLG=91* LLG=102
SOLU SPAC XXX
SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X
SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X
SOLU ENSE ensemble1 VRMS X
SOLU ENSE ensemble2 VRMS X

SOLU SET* RFZ=4.2 TFZ=2.8 PAK=0 LLG=51* *RFZ=3.1 TFZ=5.1 PAK=1 LLG=71
LLG=86 *TFZ==5.3
SOLU SPAC XXX
SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X
SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X
SOLU ENSE ensemble1 VRMS X
SOLU ENSE ensemble2 VRMS X

Thank you so much!

Sincerely,
Chen

[ccp4bb] delete reflections with negative peak profile correlation

Hi All,
Inspired by the "micro diffraction assembly" methods (see 
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12357.html), I 
checked one XDS_ASCII.HKL file and found many reflections has negative peak 
profile correlation. After deleted them and rerun XSCALE, I/sigma is higher and 
Rmeas is lower in the same high resolution shell than without deletion. 
I am wondering why it's not a common practice to delete those reflections?
Thanks!