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  May 2011

CCPNMR May 2011

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: ARIA to analysis import

From:

Brian Smith <[log in to unmask]>

Reply-To:

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

Date:

Sat, 14 May 2011 16:41:25 +0100

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (102 lines)

I've no real disagreements with Tim.

On Sat, 14 May 2011, Tim Stevens wrote:

>>  It does work in ARIA 2.3 with analysis 2.1.5 and you can control what goes
>>  back into the project to some extent. My personal recommendation is to
>>  export restraints and violations from the final iteration, but not peak
>>  lists (can mangle your assignments if you're not careful)
>
> My preferred way of working is also to not use ARIA assigned peak lists, but 
> rather to add to assignments as the structure improves using the NOE 
> Contributions system, seeding assignments for the solid parts and letting 
> ARIA figure out the rest.
>
> However, I wish to make it crystal clear that the ARIA export to CCPN does 
> not overwrite or change any existing peak lists or resonance assignments.
>
> Brian, can you please explain a bit more about what you mean by the "mangle" 
> comment. Is there something that needs changing?
>
> I do know that the peak lists that come back might have strangely paired 
> protons and hetero atoms, but the extent of the issue is in the new peak list 
> and is easily deleted.

As Tim says, the reimported peak lists are easily deleted restoring 
the project to its unsullied state, but unless I'm out of date on this, 
the reimported peak lists contribute equally to the shift lists with the 
originals and so shift values can be pulled away from their correct 
values. If I'm still right about this then I guess my suggestion would be 
that the reimported peak lists have weight 0 for shiftList calculation. I 
guess that apart from user confusion, the strange pairings you mention can 
also cause havoc with e.g. quality reports - maybe the reimported peak 
lists should be flagged to be ignored by them?

>>  or structures (don't have fine enough control about how many go back and
>>  from which iteration leading to project bloat).
>
> To be clear, you can use ARIA to export the last iteration and water 
> refinement structure ensembles. You can also delete old structures. This 
> keeps the bloat to a minimum.

...but if I remember right you get all the structures calculated in those 
iterations rather than the "best" N whatever N is. If you're running ARIA 
with the defaults (I would not advise this as a rule!) you get 20 
structures per iteration which is manageable, but if you're running a more 
realistic number then bloat is a real issue. If I'm wrong or out of date 
about this I apologise.

>>  The slickest way to get structures in again is to make the ones you want
>>  (lowest energy selection from final iteration or refinement) into a
>>  multimodel pdb file (I find the old aqua joinpdb file script handy for
>>  this) and import through the structures popup in analysis.
>
> You can select and load multiple PDB files in analysis and [Merge Into 
> Ensemble] rather than use external scripts.

OK that's a good feature I'd so far missed. Any chance of the import being 
able to interpret ARIA .float files to get prochirals the right way round, 
or do you see that as ARIA's responsibility?

> Also, I would say that subjectively selecting PDB files

Whoaa! who said anything about subjectively? I would absloutely advise 
objective selection - lowest restraint energy, lowest overall energy, or 
some other appropriate objective criterion. Definitely not "do I like the 
look of it"! And I would advise including a large enough number of 
structures to get good stats on NOE violations etc.

> from an ensemble is not for the uninitiated. Certainly structure 
> calculations can go awry, to the point where they are not so useful, but 
> also this can be minimised by gentler MD annealing.

Certainly - the default ARIA number of steps are only suitable for quite 
small proteins and/or very clean input data.

> I would say that pruning an ensemble can be dangerous in early 
> calculations because of the risk of biasing toward one conformation. And 
> in general I think it is better to focus on getting the interpretation 
> of the NMR data correct, and let the ensemble reflect the precision in 
> the data.
>
> Personally I like to see some outliers because it gives me more information 
> about potential problems in the assignment.

Absolutley with you there. One comment on the link between the 
violations/peak/assignment popups and the integrated structure viewer - it 
would help to keep users away from focusing their violation analysis on a 
single conformation (and risk biasing it towards that structure) if the 
"show on structure" functionallity worked nore slickly as you switch the 
structure displayed from an ensemble. But that would be icing on the 
already good cake.

Brian

-- 
Dr. Brian O. Smith ------------------------ Brian Smith at glasgow ac uk
School of Life Sciences, College of Medical, Vetinerary & Life Sciences,
   Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089                        Fax: 0141 330 4600
----------------------------------------------------------------------
The University of Glasgow, charity number SC004401

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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

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