Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

[Kay Diederichs]

Wladek Minor runs proteindiffraction.org . This also has E.g. JCSG data sets.
BR,
Kay

On Thu, 29 Nov 2018 23:35:55 +, Diana Tomchick 
 wrote:

>I hope you are compressing your images, typically that makes them 1/4 the 
>original size.
>
>SBGrid and Wladek Minor also have image archival services. As I am replying 
>from my cell phone while on vacation, the links to those services are not 
>handy to me. But they have been mentioned many times on this bulletin board, 
>and should be easily findable by an Internet search.
>
>Diana
>
>**
>Diana R. Tomchick
>Department of Biophysics, Rm. ND10.214A
>University of Texas Southwestern Medical Center
>5323 Harry Hines Blvd.
>Dallas, TX 75061 USA
>214-645-6383 (office)
>



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Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

[Tim Grüne]

Hi Jacob,
The idea of a scientific service being restricted by nationality is so strange 
to me that this possibility for misunderstanding did not occur to me.
Best,
Tim

On November 29, 2018 10:24:49 PM GMT+01:00, "Keller, Jacob" 
 wrote:
>I saw explicitly that it is not limited to EU.
>
>JPK
>
>+
>Jacob Pearson Keller
>Research Scientist / Looger Lab
>HHMI Janelia Research Campus
>19700 Helix Dr, Ashburn, VA 20147
>Desk: (571)209-4000 x3159
>Cell: (301)592-7004
>+
>
>The content of this email is confidential and intended for the
>recipient specified in message only. It is strictly forbidden to share
>any part of this message with any third party, without a written
>consent of the sender. If you received this message by mistake, please
>reply to this message and follow with its deletion, so that we can
>ensure such a mistake does not occur in the future.
>
>-Original Message-
>From: CCP4 bulletin board  On Behalf Of
>graeme.win...@diamond.ac.uk
>Sent: Thursday, November 29, 2018 4:22 PM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: Re: [ccp4bb] Long term storage for raw images/
>crystallographic data sets
>
>Dear Tim,
>
>I do not think Zenodo is limited to Europeans - at least I could not
>find this on their policy page:
>
>http://about.zenodo.org/policies/
>
>I know of plenty of uploads from Japan for example
>
>Best wishes Graeme
>
>On 29 Nov 2018, at 21:16, Tim Gruene
>mailto:tim.gru...@psi.ch>> wrote:
>
>Dear Raquel,
>
>when they are associated with a publication, you can publish them on
>data.sbgrid.org in the US or at
>zenodo.org in Europe.
>
>Best regards,
>Tim
>
>On Thursday, November 29, 2018 9:54:02 PM CET Lieberman, Raquel L
>wrote:
>Dear All,
>
>How do your labs handle long-term raw data backups? My lab is maxing
>out our 6TB RAID backup (with two off-site mirrors) so I am
>investigating our next long term solution. The vast majority of the
>data sets are published structures (i.e. processed data deposited in
>PDB) or redundant/unusable so immediate access is not anticipated, but
>the size of data sets is increasing quickly with time, so I am looking
>for a scalable-yet-affordable solution.
>
>Would be grateful for input into various options, e.g. bigger HD/RAIDs,
>cloud backup, tape, anything else.
>
>I will compile.
>
>Thank you,
>
>Raquel
>--
>Raquel L. Lieberman, Ph.D.
>Professor
>School of Chemistry and Biochemistry
>Georgia Institute of Technology
>
>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>--
>--
>Paul Scherrer Institut
>Tim Gruene
>- persoenlich -
>OSUA/204
>Forschungsstrasse 111
>CH-5232 Villigen PSI
>phone: +41 (0)56 310 5297
>
>GPG Key ID = A46BEE1A
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
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>
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>and do not use, copy, retain, distribute or disclose the information in
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>and not necessarily of Diamond Light Source Ltd. 
>Diamond Light Source Ltd. cannot guarantee that this e-mail or any
>attachments are free from viruses and we cannot accept liability for
>any damage which you may sustain as a result of software viruses which
>may be transmitted in or with the message.
>Diamond Light Source Limited (company no. 4375679). Registered in
>England and Wales with its registered office at Diamond House, Harwell
>Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United
>Kingdom
>
>
>
>
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Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

[Tim Grüne]

Hi Graeme,
I meant to say that the zenodo server sits in Europe, and the sbgrif server in 
the us. It was not meant to indicate any restrictions. 
Best,
Tim


On November 29, 2018 10:21:36 PM GMT+01:00, "graeme.win...@diamond.ac.uk" 
 wrote:
>Dear Tim,
>
>I do not think Zenodo is limited to Europeans - at least I could not
>find this on their policy page:
>
>http://about.zenodo.org/policies/
>
>I know of plenty of uploads from Japan for example
>
>Best wishes Graeme
>
>On 29 Nov 2018, at 21:16, Tim Gruene
>mailto:tim.gru...@psi.ch>> wrote:
>
>Dear Raquel,
>
>when they are associated with a publication, you can publish them on
>data.sbgrid.org in the US or at
>zenodo.org in Europe.
>
>Best regards,
>Tim
>
>On Thursday, November 29, 2018 9:54:02 PM CET Lieberman, Raquel L
>wrote:
>Dear All,
>
>How do your labs handle long-term raw data backups? My lab is maxing
>out our
>6TB RAID backup (with two off-site mirrors) so I am investigating our
>next
>long term solution. The vast majority of the data sets are published
>structures (i.e. processed data deposited in PDB) or redundant/unusable
>so
>immediate access is not anticipated, but the size of data sets is
>increasing quickly with time, so I am looking for a
>scalable-yet-affordable
>solution.
>
>Would be grateful for input into various options, e.g. bigger HD/RAIDs,
>cloud backup, tape, anything else.
>
>I will compile.
>
>Thank you,
>
>Raquel
>--
>Raquel L. Lieberman, Ph.D.
>Professor
>School of Chemistry and Biochemistry
>Georgia Institute of Technology
>
>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>--
>--
>Paul Scherrer Institut
>Tim Gruene
>- persoenlich -
>OSUA/204
>Forschungsstrasse 111
>CH-5232 Villigen PSI
>phone: +41 (0)56 310 5297
>
>GPG Key ID = A46BEE1A
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
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>
>-- 
>This e-mail and any attachments may contain confidential, copyright and
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>only. If you are not the intended addressee or an authorised recipient
>of the addressee please notify us of receipt by returning the e-mail
>and do not use, copy, retain, distribute or disclose the information in
>or attached to the e-mail.
>Any opinions expressed within this e-mail are those of the individual
>and not necessarily of Diamond Light Source Ltd. 
>Diamond Light Source Ltd. cannot guarantee that this e-mail or any
>attachments are free from viruses and we cannot accept liability for
>any damage which you may sustain as a result of software viruses which
>may be transmitted in or with the message.
>Diamond Light Source Limited (company no. 4375679). Registered in
>England and Wales with its registered office at Diamond House, Harwell
>Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United
>Kingdom

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Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

[Diana Tomchick]

I hope you are compressing your images, typically that makes them 1/4 the 
original size.

SBGrid and Wladek Minor also have image archival services. As I am replying 
from my cell phone while on vacation, the links to those services are not handy 
to me. But they have been mentioned many times on this bulletin board, and 
should be easily findable by an Internet search.

Diana

**
Diana R. Tomchick
Department of Biophysics, Rm. ND10.214A
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Dallas, TX 75061 USA
214-645-6383 (office)

On Nov 29, 2018, at 3:54 PM, Lieberman, Raquel L 
mailto:raquel.lieber...@chemistry.gatech.edu>>
 wrote:

Dear All,

How do your labs handle long-term raw data backups? My lab is maxing out our 
6TB RAID backup (with two off-site mirrors) so I am investigating our next long 
term solution. The vast majority of the data sets are published structures 
(i.e. processed data deposited in PDB) or redundant/unusable so immediate 
access is not anticipated, but the size of data sets is increasing quickly with 
time, so I am looking for a scalable-yet-affordable solution.

Would be grateful for input into various options, e.g. bigger HD/RAIDs, cloud 
backup, tape, anything else.

I will compile.

Thank you,

Raquel
--
Raquel L. Lieberman, Ph.D.
Professor
School of Chemistry and Biochemistry
Georgia Institute of Technology





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UT Southwestern


Medical Center



The future of medicine, today.




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[ccp4bb] Integrative Structural Biology Cluster (ISBUC) Coordinator

[Guillermo Montoya]

Dear All,

for those that like to work in a very multidisciplinary environment involving 
research and industry, please have a look at this opening

 https://employment.ku.dk/staff/?show=148511

as scientific coordinator in ISBUC

https://isbuc.ku.dk/



best regards


G.


Guillermo Montoya, Prof., Dr.
Research Director, Protein Structure and Function Programme
Novo Nordisk Foundation Center for Protein Research
Faculty of Health and Medical Sciences, University of Copenhagen,
Blegdamsvej 3A, DK-2200 Copenhagen, Denmark
web: www.cpr.ku.dk
PC: Lotta Avesson lotta.aves...@cpr.ku.dk








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Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

[Keller, Jacob]

I saw explicitly that it is not limited to EU.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board  On Behalf Of 
graeme.win...@diamond.ac.uk
Sent: Thursday, November 29, 2018 4:22 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Long term storage for raw images/ crystallographic data 
sets

Dear Tim,

I do not think Zenodo is limited to Europeans - at least I could not find this 
on their policy page:

http://about.zenodo.org/policies/

I know of plenty of uploads from Japan for example

Best wishes Graeme

On 29 Nov 2018, at 21:16, Tim Gruene 
mailto:tim.gru...@psi.ch>> wrote:

Dear Raquel,

when they are associated with a publication, you can publish them on 
data.sbgrid.org in the US or at 
zenodo.org in Europe.

Best regards,
Tim

On Thursday, November 29, 2018 9:54:02 PM CET Lieberman, Raquel L wrote:
Dear All,

How do your labs handle long-term raw data backups? My lab is maxing out our 
6TB RAID backup (with two off-site mirrors) so I am investigating our next long 
term solution. The vast majority of the data sets are published structures 
(i.e. processed data deposited in PDB) or redundant/unusable so immediate 
access is not anticipated, but the size of data sets is increasing quickly with 
time, so I am looking for a scalable-yet-affordable solution.

Would be grateful for input into various options, e.g. bigger HD/RAIDs, cloud 
backup, tape, anything else.

I will compile.

Thank you,

Raquel
--
Raquel L. Lieberman, Ph.D.
Professor
School of Chemistry and Biochemistry
Georgia Institute of Technology





To unsubscribe from the CCP4BB list, click the following link:
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--
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OSUA/204
Forschungsstrasse 111
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A



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are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

[graeme.win...@diamond.ac.uk]

Dear Tim,

I do not think Zenodo is limited to Europeans - at least I could not find this 
on their policy page:

http://about.zenodo.org/policies/

I know of plenty of uploads from Japan for example

Best wishes Graeme

On 29 Nov 2018, at 21:16, Tim Gruene 
mailto:tim.gru...@psi.ch>> wrote:

Dear Raquel,

when they are associated with a publication, you can publish them on
data.sbgrid.org in the US or at 
zenodo.org in Europe.

Best regards,
Tim

On Thursday, November 29, 2018 9:54:02 PM CET Lieberman, Raquel L wrote:
Dear All,

How do your labs handle long-term raw data backups? My lab is maxing out our
6TB RAID backup (with two off-site mirrors) so I am investigating our next
long term solution. The vast majority of the data sets are published
structures (i.e. processed data deposited in PDB) or redundant/unusable so
immediate access is not anticipated, but the size of data sets is
increasing quickly with time, so I am looking for a scalable-yet-affordable
solution.

Would be grateful for input into various options, e.g. bigger HD/RAIDs,
cloud backup, tape, anything else.

I will compile.

Thank you,

Raquel
--
Raquel L. Lieberman, Ph.D.
Professor
School of Chemistry and Biochemistry
Georgia Institute of Technology





To unsubscribe from the CCP4BB list, click the following link:
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--
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OSUA/204
Forschungsstrasse 111
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A



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are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
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Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

[Tim Gruene]

Dear Raquel,

when they are associated with a publication, you can publish them on 
data.sbgrid.org in the US or at zenodo.org in Europe.

Best regards,
Tim

On Thursday, November 29, 2018 9:54:02 PM CET Lieberman, Raquel L wrote:
> Dear All,
> 
> How do your labs handle long-term raw data backups? My lab is maxing out our
> 6TB RAID backup (with two off-site mirrors) so I am investigating our next
> long term solution. The vast majority of the data sets are published
> structures (i.e. processed data deposited in PDB) or redundant/unusable so
> immediate access is not anticipated, but the size of data sets is
> increasing quickly with time, so I am looking for a scalable-yet-affordable
> solution.
> 
> Would be grateful for input into various options, e.g. bigger HD/RAIDs,
> cloud backup, tape, anything else.
> 
> I will compile.
> 
> Thank you,
> 
> Raquel
> --
> Raquel L. Lieberman, Ph.D.
> Professor
> School of Chemistry and Biochemistry
> Georgia Institute of Technology
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OSUA/204
Forschungsstrasse 111
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A



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Description: This is a digitally signed message part.

Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

[graeme.win...@diamond.ac.uk]

Dear Raquel,

For published structures you can publish the raw data, which means that 
somebody else is looking after it - for this I would say that the current front 
runner is Zenodo - https://zenodo.org/ - which is paid for by CERN / EU etc. so 
someone else is (currently) picking up the tab.

This has the happy side effect that it is useful to others :-)

Best wishes Graeme

On 29 Nov 2018, at 20:54, Lieberman, Raquel L 
mailto:raquel.lieber...@chemistry.gatech.edu>>
 wrote:

Dear All,

How do your labs handle long-term raw data backups? My lab is maxing out our 
6TB RAID backup (with two off-site mirrors) so I am investigating our next long 
term solution. The vast majority of the data sets are published structures 
(i.e. processed data deposited in PDB) or redundant/unusable so immediate 
access is not anticipated, but the size of data sets is increasing quickly with 
time, so I am looking for a scalable-yet-affordable solution.

Would be grateful for input into various options, e.g. bigger HD/RAIDs, cloud 
backup, tape, anything else.

I will compile.

Thank you,

Raquel
--
Raquel L. Lieberman, Ph.D.
Professor
School of Chemistry and Biochemistry
Georgia Institute of Technology





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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


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are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
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[ccp4bb] Long term storage for raw images/ crystallographic data sets

[Lieberman, Raquel L]

Dear All,

How do your labs handle long-term raw data backups? My lab is maxing out our 
6TB RAID backup (with two off-site mirrors) so I am investigating our next long 
term solution. The vast majority of the data sets are published structures 
(i.e. processed data deposited in PDB) or redundant/unusable so immediate 
access is not anticipated, but the size of data sets is increasing quickly with 
time, so I am looking for a scalable-yet-affordable solution.

Would be grateful for input into various options, e.g. bigger HD/RAIDs, cloud 
backup, tape, anything else.

I will compile.

Thank you,

Raquel
--
Raquel L. Lieberman, Ph.D.
Professor
School of Chemistry and Biochemistry
Georgia Institute of Technology





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Re: [ccp4bb] Twinning in C 2 2 21

[Eleanor Dodson]

It is very common for a trigonal spacegroup H 32 to masquerade as C 2 2 21
Here is the log file for other cell.
Note that it is possible to reindex it with two cell dimensions equal and a
beta angle of 63 -
And the self rpotation shows a large rotation at 120 degrees

So go back to the data processing and see if you can reindex it
#CCP4I VERSION CCP4Interface 7.0.043
#CCP4I SCRIPT LOG hgen
#CCP4I DATE 29 Nov 2018  17:51:23
#CCP4I USER eleanor
#CCP4I PROJECT test
#CCP4I JOB_ID 50
#CCP4I SCRATCH /tmp/eleanor
#CCP4I HOSTNAME wombat
#CCP4I PID 55339

Type cell (--help for command line options) >>
Type lattice type >>
Type target cell, or eof (control/D) for no target >>


<<<

Input  cell:
 92.240148.780206.60090.000 90.000 90.000
 - Lattice Type C
Lattice point group: C 2 2 2
 within angular tolerance3.0 (reset with eg -tol[erance] 5)

  Lattice cell:   92.24 148.78 206.60 90.00  90.00
 90.00
Lattice unit cell after reindexing:   92.24 148.78 206.60 90.00  90.00
 90.00

Reindex operator from initial to lattice cell: [h,k,l]

   h'   = ( h k l ) (   1   0   0 )
(   0   1   0 )
(   0   0   1 )

 SYMINFO file set to /Applications/ccp4-7.0/lib/data/syminfo.lib

List of possible Laue groups

Cell is the cell reindexed into this Laue group
 in a 'standard' setting, unconstrained to group

'Deviation' is maximum angular deviation (degrees)
 from cell with Laue group symmetry imposed

'Same cell' and 'Other cell' list alternative indexings
 'Other cell' lists the cell difference defined as mean square
   difference in basis vectors (columns of orthogonalisation matrix)

Alternative indexing schemes which lead to identical or similar
 cells are grouped on continuation lines if they are symmetry-related

 Laue groupa b c  alpha  beta gamma Deviation ReindexOperator

   C m m m   92.2 148.8 206.6  90.0  90.0  90.00.00  [h,k,l]


Possible spacegroups:
 
 




 C 1 2/m 1   92.2 148.8 206.6  90.0  90.0  90.00.00  [h,k,l]
  Same cell  [-h,-k,l]
  ... [h,-k,-l]

 C 1 2/m 1  148.8  92.2 206.6  90.0  90.0  90.00.00  [-k,h,l]
  Same cell  [k,-h,l]
  ... [-k,-h,-l]


Possible spacegroups:
 
 




 P 1 2/m 1   87.5 206.6  87.5  90.0 116.4  90.00.00
 [-1/2h-1/2k,l,-1/2h+1/2k]
  Same cell
 [1/2h-1/2k,-l,1/2h+1/2k]
  ...
[-1/2h+1/2k,-l,-1/2h-1/2k]


Possible spacegroups:
 
 




  P -1   87.5  87.5 206.6  90.0  90.0  63.60.00
 [1/2h+1/2k,-1/2h+1/2k,l]
  Same cell
 [1/2h-1/2k,-1/2h-1/2k,-l]
  Same cell
 [-1/2h-1/2k,1/2h-1/2k,l]
  Same cell
 [-1/2h+1/2k,1/2h+1/2k,-l]


#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 29 Nov 2018  17:52:27
#CCP4I MESSAGE Task completed successfully




On Thu, 29 Nov 2018 at 17:23, Damodharan Lakshminarasimhan <
laksdh...@gmail.com> wrote:

> Hi Vijyay,
>
> Did you tried with P212121 system?. RCSB has one structure with similar
> unitcell and the corresponding pdb code is 3BMA. If you have not tried then
> I hope it will solve the problem.
>
> Thanks
> damo
>
> On Thu, Nov 29, 2018 at 11:44 AM Vijay Jayaraman <
> bkvijay.jayara...@gmail.com> wrote:
>
>> Hi all,
>> The data that we collected recently is in space group C 2 2 21 and
>> appears to be twinned. I could not find a twin law which I can use to
>> detwin the data. The R and R free doesn't drop below 0.4 even after
>> multiple rounds of manual and automated refinement.  I have also attached
>> the self-rotation function output as a pdf file here. Kindly suggest a
>> solution. Useful details are here:
>>
>> Space group C 2 2 21
>> Unit cell:92.24  148.78  206.60  90.00   90.00   90.00
>> Maximum resolution: 2.6 Angstrom
>>
>> This is the warning message from the AIMLESS log file:
>>
>> "WARNING: the L-test suggests that the data may be twinned,
>>so the indicated Laue symmetry may be too high
>>Rough estimated twin fraction alpha from cumulative N(|L|) plot 0.151
>> +/-(0.020)
>>Rough estimated twin fraction alpha from 0.141
>>Rough estimated twin fraction alpha from 0.128"
>>
>> Thanks.
>>
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
> --
>
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>



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Re: [ccp4bb] Twinning in C 2 2 21

[Ditlev Egeskov Brodersen]

Unit cell dimensions don’t really matter here. If it’s a centred lattice you 
won’t be able to index it correctly in a primitive system even though C222 and 
P222 both have a<>b<>c and alpha=beta=gamma=90.

Ditlev

---

Ditlev E. Brodersen
Lektor, Associate Professor
Department of Molecular Biology and Genetics, Aarhus University
Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark

Phone:  +45 21669001
Lab home page: www.bioxray.au.dk/~deb
Educational IT portal: curriculearn.dk

Sent from my iPhone

Den 29. nov. 2018 kl. 18.25 skrev Damodharan Lakshminarasimhan 
mailto:laksdh...@gmail.com>>:

Hi Vijyay,

Did you tried with P212121 system?. RCSB has one structure with similar 
unitcell and the corresponding pdb code is 3BMA. If you have not tried then I 
hope it will solve the problem.

Thanks
damo

On Thu, Nov 29, 2018 at 11:44 AM Vijay Jayaraman 
mailto:bkvijay.jayara...@gmail.com>> wrote:
Hi all,
The data that we collected recently is in space group C 2 2 21 and appears to 
be twinned. I could not find a twin law which I can use to detwin the data. The 
R and R free doesn't drop below 0.4 even after multiple rounds of manual and 
automated refinement.  I have also attached the self-rotation function output 
as a pdf file here. Kindly suggest a solution. Useful details are here:

Space group C 2 2 21
Unit cell:92.24  148.78  206.60  90.00   90.00   90.00
Maximum resolution: 2.6 Angstrom

This is the warning message from the AIMLESS log file:

"WARNING: the L-test suggests that the data may be twinned,
   so the indicated Laue symmetry may be too high
   Rough estimated twin fraction alpha from cumulative N(|L|) plot 0.151 
+/-(0.020)
   Rough estimated twin fraction alpha from 0.141
   Rough estimated twin fraction alpha from 0.128"

Thanks.




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Re: [ccp4bb] Twinning in C 2 2 21

[Damodharan Lakshminarasimhan]

Hi Vijyay,

Did you tried with P212121 system?. RCSB has one structure with similar
unitcell and the corresponding pdb code is 3BMA. If you have not tried then
I hope it will solve the problem.

Thanks
damo

On Thu, Nov 29, 2018 at 11:44 AM Vijay Jayaraman <
bkvijay.jayara...@gmail.com> wrote:

> Hi all,
> The data that we collected recently is in space group C 2 2 21 and appears
> to be twinned. I could not find a twin law which I can use to detwin the
> data. The R and R free doesn't drop below 0.4 even after multiple rounds of
> manual and automated refinement.  I have also attached the self-rotation
> function output as a pdf file here. Kindly suggest a solution. Useful
> details are here:
>
> Space group C 2 2 21
> Unit cell:92.24  148.78  206.60  90.00   90.00   90.00
> Maximum resolution: 2.6 Angstrom
>
> This is the warning message from the AIMLESS log file:
>
> "WARNING: the L-test suggests that the data may be twinned,
>so the indicated Laue symmetry may be too high
>Rough estimated twin fraction alpha from cumulative N(|L|) plot 0.151
> +/-(0.020)
>Rough estimated twin fraction alpha from 0.141
>Rough estimated twin fraction alpha from 0.128"
>
> Thanks.
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Twinning in C 2 2 21

[Kay Diederichs]

Hi Vijay,

it could be pseudo-merohedral twinning of C2. In that case,  any of the three 
axes could be the unique one, so you must test all three possible settings. 
Hopefully, reginement works well in one of these.

Best wishes, 
Kay


On Thu, 29 Nov 2018 14:58:52 +, Vijay Jayaraman 
 wrote:

>Hi all,
>The data that we collected recently is in space group C 2 2 21 and appears to 
>be twinned. I could not find a twin law which I can use to detwin the data. 
>The R and R free doesn't drop below 0.4 even after multiple rounds of manual 
>and automated refinement.  I have also attached the self-rotation function 
>output as a pdf file here. Kindly suggest a solution. Useful details are here:
>
>Space group C 2 2 21
>Unit cell:92.24  148.78  206.60  90.00   90.00   90.00
>Maximum resolution: 2.6 Angstrom
>
>This is the warning message from the AIMLESS log file:
>
>"WARNING: the L-test suggests that the data may be twinned,
>   so the indicated Laue symmetry may be too high
>   Rough estimated twin fraction alpha from cumulative N(|L|) plot 0.151 
> +/-(0.020)
>   Rough estimated twin fraction alpha from 0.141
>   Rough estimated twin fraction alpha from 0.128"
>
>Thanks.
>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Twinning in C 2 2 21

[Vijay Jayaraman]

Hi all,
The data that we collected recently is in space group C 2 2 21 and appears to 
be twinned. I could not find a twin law which I can use to detwin the data. The 
R and R free doesn't drop below 0.4 even after multiple rounds of manual and 
automated refinement.  I have also attached the self-rotation function output 
as a pdf file here. Kindly suggest a solution. Useful details are here:

Space group C 2 2 21
Unit cell:92.24  148.78  206.60  90.00   90.00   90.00
Maximum resolution: 2.6 Angstrom

This is the warning message from the AIMLESS log file:

"WARNING: the L-test suggests that the data may be twinned,
   so the indicated Laue symmetry may be too high
   Rough estimated twin fraction alpha from cumulative N(|L|) plot 0.151 
+/-(0.020)
   Rough estimated twin fraction alpha from 0.141
   Rough estimated twin fraction alpha from 0.128"

Thanks.




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Srf.pdf
Description: Adobe PDF document

[ccp4bb] Postdoctoral position University of Oxford (UK)

[Denis Ptchelkine]

Title:  Postdoctoral position University of Oxford (UK)


Message:


We are looking for highly motivated and talented Postdoctoral Scientist to join 
the research group of Professor Catherine Porcher (WIMM, University of Oxford, 
UK) to characterise and solve the structure of a multiprotein complex involved 
in the transcriptional regulation of blood stem cell development in normal and 
malignant conditions.

This exciting project, at the forefront of its field, is a collaboration with 
Dr Denis Ptchelkine leading structural biology research at the MRC Weatherall 
Institute of Molecular Medicine. It will employ molecular, biochemical, 
biophysical and cryo-EM studies. Key residues involved in protein/protein and 
protein/DNA interactions will be identified and functionally analysed. This 
high impact study will provide essential details for a mechanistic 
understanding of the transcriptional activities of this blood stem 
cell-specific complex.


Please apply via this link:  www.recruit.ox.ac.uk

Vacancy ID: 138079







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[ccp4bb] Paired refinement in PDB-REDO

[Robbie Joosten]

Dear CCP4BB-ers,

A recent discussion on the CPP4BB made it clear that people want an easy way to 
run paired refinement on their data. This option has always been available in 
the PDB-REDO webserver (https://pdb-redo.eu), but it was (un)cleverly hidden in 
automation (see https://journals.iucr.org/m/issues/2014/04/00/be5263/). A hack 
was discussed to force paired refinement, but that wasn't exactly 
user-friendly. So due to popular demand we now added an 'advanced option' to 
force paired refinement. There are now three ways to run paired refinement:

  1.  The recommended way: Provide higher resolution data that your model has 
not seen yet. I.e. first refine your model with data to a conservative cut-off 
that won't get you into trouble with referees, then use an extended dataset 
with which you want to 'push the resolution'. This triggers paired refinement 
automatically, starting from your conservative resolution cut-off.
  2.  The 'the referee made me do it' way: Use the 'advanced options' and tick 
'Paired refinement' when submitting a job. In this case the starting resolution 
is the point where the 1% rolling average of I/sigI becomes > 2 or F/sigF > 4 
(starting from the highest resolution reflection). If you have high 
signal-to-noise data (in which case you probably need not run paired 
refinement) paired refinement is done with the 10% highest resolution 
reflections.
  3.  The non-recommended hacky way: Change the resolution in REMARK 3 of your 
input PDB file to any value where you want to start paired refinement. The 
resolution gap should be at least 0.1 A.

Caveat: The idea of paired refinement is to see whether the extra data has a 
positive effect on the refinement of you model against the 'old' data. It works 
best if you model is already in good shape. The PDB-REDO implementation of the 
original algorithm from Karplus & Diederichs 
(http://science.sciencemag.org/content/336/6084/1030) was designed for and 
tested on situation 1 which (IMO) is the least biased way of running paired 
refinement.

Cheers,
Robbie and Tassos




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[ccp4bb] Job Offer: Group Leader in Structural Biology or Biochemistry

[Fan Jiang]

Dear colleagues,  

Viva Biotech, located in Shanghai, China, is specialized in structure-based 
drug discovery providing preclinical drug discovery research services to global 
pharmaceutical and biotech companies. We have opening for program leader in 
structural biology and biochemistry. Anyone who is interested in the position, 
please send CV to jin@vivabiotech.com.  

Job title: Group Leader in Structural Biology or Biochemistry

Job description

We are seeking a highly motivated individual with experience in protein 
biochemistry and structural biology. Candidates will lead the structural 
biology team to carry out the biochemistry studies and/or gene-to-structure 
studies which elucidate the interactions between small molecules/peptides and 
their targets. Experiences with protein expression and purification, excellent 
interpersonal and managerial skills, team player with excellent written and 
verbal communication skills and proficiency in structure biology related 
software. Excellent communication skill in English; 3-5 years working 
experiences with in US or Europe.

Qualifications

1)  Ph.D. in crystallography or protein biochemistry training with minimal 
3-5 years’ working experience

2)  Hands-on experience in protein crystallization, and protein expression 
and purification is optional.

3)  Proficient in structure biology related software is plus.

4)  Demonstrated managerial skill to guide groups through corporate change 
and growth.

5)  Excellent verbal and writing skills in both English and Chinese are 
mandatory.

6)  Strong communication skills and client interaction are required.



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