RE: Problems Loading PDB -- June 04, 2015 - 17:03

I posed these questions some time ago, but I have not heard from anyone or 
whether my message was accepted by the moderator. I guess I am not on the 
list. Below is what I wrote initially.

We have a question concerning our results from our latest calculations using 
relaxGUI. We have fed the program NMR relaxation data at 500 and 600 MHz on 
the free protein and a structure of the protein in complex with DNA from an 
X-ray structure. We know that binding of DNA induces some secondary 
structures because the free protein has sections missing in the pdb. Because 
the free protein structure has residues missing presumably due to disorder in 
the crystal, we chose to use the structure of the bound protein. Could the 
use of a structure of our protein with more order than expected cause 
problems with the selection of the rotational diffusion tensor? The diffusion 
tensor the program has selected doesn’t seem to match the overall shape of 
the protein. If it can cause a problem, how do I add the residues missing 
from the crystal structure for the refinement? Furthermore, can the program 
handle some residues missing in crystal structures?

Thanks,
Dave

> -----Original Message-----
> From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx]
> On Behalf Of Edward d'Auvergne
> Sent: 27 April 2015 22:13
> To: Ian A Bennet
> Cc: relax-users@xxxxxxx; David Finger
> Subject: Re: Problems Loading PDB
>
> Hi Ian,
>
> Welcome to the relax mailing lists!  For this problem, it is just relax not
> knowing which of the alternate coordinates in the PDB file to use.  See 
> altLoc
> at http://www.nmr-relax.com/api/3.3/lib.structure.pdb_read-
> module.html#atom
> (this is a copy of the PDB standard).  This is usually only for side chains
> anyway, and it is generally safe to set it to 'A'.  It is a character which 
> starts at
> 'A', so you will find in column or position
> 17 of the PDB file 'A' and 'B' for some atoms (sometimes 'C' and even 'D',
> though more is rather rare).  I have deliberately not set the default to 
> 'A', just
> in case someone encounters a file with alternate coordinates.  Then you can
> look at the PDB file and determine which, if any, of the coordinates should 
> be
> used.  For a model-free analysis, if altLoc is set for the backbone N or H,
> deselecting the residue might be the best strategy.  But it is up to you to
> determine what the best approach for this PDB file is.  If you have any 
> other
> issues, please don't hesitate to ask!
>
> Regards,
>
> Edawrd
>
>
> On 27 April 2015 at 19:16, Ian A Bennet <iabennet1@xxxxxxxxxxxxxxx> wrote:
> > Hello,
> >
> > We are new relax users and are struggling to load structural
> > information for each residue.  We have tried loading a pdb file
> > (attached) generated by Pymol after proton addition, however we get this
> error:
> > RelaxError: Multiple alternate location indicators are present in the
> > PDB file, but the desired coordinate set has not been specified.
> >
> > When we set the "alternate location indicator" to any number (I have
> > no clue which number it should be set to) it says the structure is
> > loaded, but when trying to extract the atomic positions it spits out
> > an error about no positional information could be found.
> >
> > Is there some sort of easy format that PDB files should be in so that
> > relax can extract the information from them?
> >
> > Many thanks,
> >
> > Ian.
> > _______________________________________________
> > relax (http://www.nmr-relax.com)
> >
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> >
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