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

Help for CCPNMR Archives


CCPNMR Archives

CCPNMR Archives


CCPNMR@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

CCPNMR Home

CCPNMR Home

CCPNMR  February 2010

CCPNMR February 2010

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Bugs and possible features

From:

Rasmus Fogh <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Tue, 2 Feb 2010 13:04:44 +0000

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (94 lines)

Dear David,

Thanks for the nice words, and for taking the trouble of reporting your 
bugs. I think it would be easier for us to get hold of problems 1) and 2) 
if we had your project to look at. Would it be possible for you to tar it 
up and send it to us?

The question about Glycine Ha bound to Ca and Cb sounds puzzling. That 
error message ought to mean that the resonance was indeed bound to the 
wrong atom some of the time. The only things tha spring to mind would be 
mutliply assigned peaks, confusion between HAa and HAb, or something 
seriously messed up in the data. I guess we can see that one too if you 
send us the project.

YOurs,

Rasmus

---------------------------------------------------------------------------
Dr. Rasmus H. Fogh                  Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK.     FAX (01223)766002

On Tue, 2 Feb 2010, David Langelaan wrote:

> Hello,
>
> I am a new user to analysis and have just used the software to assign a 3D 
> data set for a peptide I am working on.
>
> First of all I want to say that after several months of use I am very 
> impressed with the software, especially with the structure analysis features. 
> Anyways, as I used it I have noted some bugs / potential enhancements so I 
> will just list them now. I am currently using V 2.1.2 on Mac OSX with all 
> current upgrades.
>
> Possible Bugs:
>
> 1. In peak tab of the quality reports, every single peak from my HNCO 
> spectrum is flagged with 'Impossible bond 57 LysC-58GlyN' etc... This 
> experiment has been set to HNCO, so I doubt this is the problem. As far as I 
> can tell, this is a perfectly normal connection and is being improperly 
> flagged, although I may be wrong.
>
> 2. This problem is a bit more of an enigma. During my initial assignment I 
> set some protons to be the HD1 proton of histidine. I then created distance 
> restraint lists from the NOE data. Later I realized, that the HD1 proton was 
> actually the HD2 proton, so I renamed the appropriate resonances, which were 
> then correctly updated in the restraint lists. The problem is that when I 
> export the restraint list, it is exported as the initial HD1 instead of HD2. 
> Also, if I analyze violations a pdb file, the software looks for a HD1 atom 
> instead of the HD2 atom which the restrain list shows.
>
> 3. Every once in a while if I am assigning a peak and then decide to delete 
> it, the assignment panel will mess up. This isn't really a problem, and I 
> have not been able to reproduce it, but I just thought I would let you know.
>
>
>
> Possible enhancements (I realize that you are not working on enhancements 
> right now, but maybe in the future):
>
> 1. In the resonances tab of the quality reports, some resonances are flagged 
> because one of their peaks have a large delta. However, when I click show 
> peaks it can be tedious to find out which peak exactly is the problem. Would 
> it be possible to include a setting to pull up the violating peak or at least 
> highlight it?
>
> 2. In the format converter would it be possible to include support for Xplor 
> when exporting distance restraints. I am currently using the cns export, 
> which works well because it is simple to modify the output files into xplor 
> format. It is not terribly important, but it would be nice. Similar to this 
> theme, it would be nice to be able to export a sequence list in xplor format.
>
>
>
> Finally I have one question:
>
> Some of my resonances are flagged in the quality report because they have 
> multiple bound partners. Say a glycine Ha bound to both a Ca and a Cb. I 
> understand how this is a problem, but I have not found a way to fix it. I am 
> not sure where this error is coming from, since in some cases there are not 
> any peaks which connect a resonance to the improper bound partner.
>
>
> This is a bit of a list to send you, but I figured that I would give all my 
> suggestions at once. Overall though I am impressed with the software and 
> especially the active support/development. If you need a project file or more 
> detail please let me know.
>
> David Langelaan
> Dalhousie University
>

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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
December 2006
November 2006
October 2006
September 2006
August 2006
July 2006
June 2006
May 2006
April 2006
March 2006
February 2006
January 2006
December 2005
November 2005
October 2005
September 2005
August 2005
July 2005
June 2005
May 2005
April 2005
March 2005
February 2005
January 2005
December 2004
November 2004
October 2004
September 2004
August 2004
July 2004
June 2004
May 2004
April 2004
March 2004
February 2004
January 2004
December 2003
November 2003
October 2003
September 2003


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