JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for CCP4BB Archives


CCP4BB Archives

CCP4BB Archives


CCP4BB@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

CCP4BB Home

CCP4BB Home

CCP4BB  June 2008

CCP4BB June 2008

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: JCSG dataset archive

From:

"Miller, Mitchell D." <[log in to unmask]>

Reply-To:

Miller, Mitchell D.

Date:

Thu, 12 Jun 2008 12:07:56 -0700

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (86 lines)

I would like to also add that depending on what you want to
use the test data for, you may find that the data JCSG has deposited
with the PDB is sufficient. 

The JCSG crystal structures include the following data sections in 
the structure factor file deposited with the PDB (since spring 2004).

1. First section -- loop over merged Fobs, (or Iobs), sigF (or sigI), 
   Fcalc, Phicalc, FreeR-flag (status)

2. For each wavelength of data used in phasing there is a separate loop 
   over the scaled, unmerged, original index intensities and sigI.

3. Then there is a data loop for the experimental phasing results listing
   the HL-coefficients from the phasing program (usually autoSHARP or solve).

4. The last loop is over fom, pdbx_fom_weighted_fmap and phase from
   density modification. The Fmap coefficient and the DM phase is the 
   starting map used for automated model building.

(For MR structures, the just the first 2 data sections are present).

If you are interested in testing MAD or SAD phasing, DM or autobuilding, 
algorithms etc, then the data deposited with the PDB is probably sufficient 
for your needs. 
http://www.pdb.org/pdb/search/navbarsearch.do?newSearch=yes&isAuthorSearch=no&radioset=All&inputQuickSearch=JCSG%20crystal 

If you wanted to reintegrate the data from the diffraction 
images or if you wanted to compare your autotraced model with the
autotraced model we obtained, then these additional data (as well as
log files) are only available through the JCSG dataset archive. So
as Ashley mentioned, please request access to the archive if you are 
still interested in this additional data.

Regards,
Mitch 

-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Deacon, Ashley
Sent: Thursday, June 12, 2008 9:41 AM
To: [log in to unmask]
Subject: [ccp4bb] JCSG dataset archive

All, 

Thanks to everyone who has recently requested access to the 
JCSG dataset archive. We have a large and growing number of users.
Your requests will be handled shortly and you will receive 
notification via e-mail.

Our registered users fall into 3 main classes:

1) Methods developers who want access to a wide array of test data.

2) Students and postdocs who want datasets for training purposes.

3) Researchers interested in one of our structures, who want access
To all the data we have available, including datasets from different
constructs or crystal forms that didn't necessarily make it into our 
final PDB deposition.

For those who may still be interested, the dataset archive can 
be accessed through our structure gallery page:

http://www.jcsg.org/prod/scripts/structure_gallery/gallery.shtml

The datasets are available without restriction, most of them are Se MAD/SAD
or distant homology MR. 

We do ask you to register and explain why you want access. This is largely
for tracking/statistics purposes (we won't be sending you a lot of junk mail). 
Hopefully in the future we can improve the system to better serve our users.

Soon we will be adding diffraction image datasets for *all* our structures as 
Soon as they are deposited.

In the meantime, if there is a dataset you would like that is not currently 
available through the archive just drop me an e-mail.

Suggestions are always welcome.

Sincerely,

Ashley Deacon
Joint Center for Structural Genomics.

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

May 2024
April 2024
March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager