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  October 2014

CCPNMR October 2014

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: stereospecific assignments

From:

Wayne Boucher <[log in to unmask]>

Reply-To:

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

Date:

Mon, 27 Oct 2014 15:23:40 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (150 lines)

Hello,

There is a non-obvious step you must take first, and that is to create an Entry and that is most easily done via the ECI interface, which can be reached inside Analysis via the Structure --> ECI dialog.  After you create an Entry you can then proceed (I hope!).  (The ECI allows NMR-STAR 3.1 export, but beware there are a fair few bugs in the interface.  The Format Converter does NMR-Star 2.1.1, if I remember correctly.)

Wayne
 
On 27 Oct 2014, at 14:59, Aswani Kumar Kancherla wrote:

> Hello Dr. Wayne,
> 
> thanks for the reply. However, I have another question to ask.
> 
> I am trying to use format converter to export chemical shift information to
> NMR-STAR format. However, I get the following error message in a pop-up.
> 
> "Could not set up export menu for project: no
> 'project.currentNmrEntryStore.sortedEntries()' information available". What does
> this mean?
> 
> Many thanks for your time.
> 
> with warm regards,
> Aswani
> 
> 
>> Hello,
>> 
>> You can definitely rename the top-level ccpnmr directory, I do that all the time
>> (I have N versions on my computer, so I do this all the time).  (It might not be
>> on your PATH any more, but likely that would be what you wanted.)
>> 
>> On the doc front, I think that help page never existed (nor for most of the
>> Format Converter dialogs).  So likely that button should just be grayed out.
>> 
>> Wayne
>> 
>> On 27 Oct 2014, at 13:45, Aswani Kumar Kancherla wrote:
>> 
>>> Hello Dr. Wayne,
>>> 
>>> many thanks for the prompt reply.
>>> 
>>> I figured out that I could also go to "MainMenu:: Resonances" and then
>>> re-assign
>>> the Hba and Hbb to appropriate stereospecific assignments.
>>> 
>>> As I have mentioned in my previous mail, I am not able to access some of the
>>> help pages. Where could be the problem? Also, kindly clarify if what I did was
>>> right for updating the analysis version i.e. I renamed the "ccpnmr" directory
>>> containing the old version to "ccpnmr_x.y" and uncompressed the downloaded
>>> file
>>> to "ccpnmr".
>>> 
>>> with regards,
>>> Aswani
>>> 
>>> 
>>>> Hello,
>>>> 
>>>> You can stereospecifically assign a peak (dimension) by clicking on the peak
>>>> in
>>>> the peak table and clicking on the Assign button (or clicking on a peak in a
>>>> spectrum display window and hit the 'a' key).  Then (in the Assignment:
>>>> Assignment Panel dialog) click on the relevant Hba (or whatever) in the
>>>> relevant
>>>> dimension table at the left, then click the Re-assign **** button (****
>>>> specific
>>>> to what you are doing).  In that (the Molecule: Atom Browser dialog) you can
>>>> click on Hb2 (or whatever), although you need to make sure that
>>>> "stereospecific"
>>>> is checked in the Options tab in order for this option to be shown.  That
>>>> should
>>>> do it.
>>>> 
>>>> Wayne
>>>> 
>>>> On 27 Oct 2014, at 07:28, Aswani Kumar wrote:
>>>> 
>>>>> Hello Analysis Developers,
>>>>> 
>>>>> I  am using Analysis Version 2.4 release 0 on Linux  SuSe11.4.
>>>>> 
>>>>> I have assigned the H-beta methylene protons non-stereopspecifically as Hba
>>>>> and Hbb. Now I have the information to assign them stereospecifically (
>>>>> using
>>>>> 3D-HNHB and HN(CO)HB). What is the best way to change the non-stereospecific
>>>>> assignments to stereopsecific assignmets?
>>>>> 
>>>>> I tried to set the status of prochiral protons using "Format Converter ->
>>>>> Process ->  Check Stereo Status Prochiral". The following error came up
>>>>> (traceback is attached at the end of the e-mail).
>>>>> 
>>>>> I am also not able to access the help page for this pop-up window by
>>>>> clicking
>>>>> the question mark on the right bottom of the pop-up window. The designated
>>>>> html file is not there at the appropriate location. The missing html  help
>>>>> file is supposed to be at the location
>>>>> "/home/nmrware/ccpnmr/ccpnmr2.4/python/ccpnmr/format/doc/ProchiralStatus.html"
>>>>> 
>>>>> Many thanks in advance.
>>>>> 
>>>>> with regards,
>>>>> Aswani Kumar
>>>>> 
>>>>> 
>>>>> PS: I have recently upgraded Analysis from Version 2.1 to 2.4. The way I did
>>>>> this was: (1) I downloaded tar file for the precompiled binaries of latest
>>>>> version. (2). Renamed  the old ccpnmr folder to ccpnmr_2.1 (3). untarred the
>>>>> new file
>>>>> 
>>>>> 
>>>>> traceback
>>>>> =============================================================================================================================
>>>>> Exception in Tkinter callback
>>>>> Traceback (most recent call last):
>>>>> File "/home/nmrware/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line
>>>>> 1410, in __call__
>>>>>  return self.func(*args)
>>>>> File
>>>>> "/home/nmrware/ccpnmr/ccpnmr2.4/python/ccpnmr/format/gui/ProchiralStatusPopup.py",
>>>>> line 424, in setStereo
>>>>>  (stereoStatus,stereoStatusChanged,resChanged,resonances) =
>>>>> self.chainResonancesDict[self.resParent][chain][i]
>>>>> =============================================================================================================================
>>>> --
>>>> This message has been scanned for viruses and
>>>> dangerous content by MailScanner, and is
>>>> believed to be clean.
>>>> 
>>>> 
>>> 
>>> 
>>> --
>>> This message has been scanned for viruses and
>>> dangerous content by MailScanner, and is
>>> believed to be clean.
>> 
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>> 
>> 
> 
> 
> 
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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

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