user queries for the Xplor-NIH biomolecular structure determination program

S.P. Skinner | 2 Mar 2012 14:08

file generation for PRE docking with more than 6 spin labels

Dear All,

At present I have generated pdb, psf and par for PRE docking using spin 
labels in 6 positions with four orientations for each.  I have recently 
attempted to utilise the same script for generation of the above files 
for 9 spin labels.  However, when I do so I am presented with a 
parameter error, such that it cannot find a specific atom of 7th spin 
label and therefore xplor terminates.  I have not encountered this error 
before using 6 positions and all I have done is to increase the total 
number of spin labels and included the relevant mutation sites for xplor 
to read.  Is it possible that xplor cannot handle too many i.e. > 24 
spin labelled positions due to the number of coordinates being read in 
and created at one time?  I have further tried using 7 spin labels and I 
am presented with the same error. 

Many Thanks and Kind Regards

Simon Skinner

--

-- 
Simon P Skinner
Protein Chemistry Group
Leiden Institute of Chemistry, Universiteit Leiden
Phone: +31 71 527 6089 / Fax: +31 71 527 4349
E-mail : skinnersp <at> chem.leidenuniv.nl

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Charles Schwieters | 2 Mar 2012 15:53

Re: file generation for PRE docking with more than 6 spin labels


Hello Simon--
>
> At present I have generated pdb, psf and par for PRE docking using spin
> labels in 6 positions with four orientations for each.  I have recently
> attempted to utilise the same script for generation of the above files
> for 9 spin labels.  However, when I do so I am presented with a
> parameter error, such that it cannot find a specific atom of 7th spin
> label and therefore xplor terminates.  I have not encountered this error
> before using 6 positions and all I have done is to increase the total
> number of spin labels and included the relevant mutation sites for xplor
> to read.  Is it possible that xplor cannot handle too many i.e. > 24
> spin labelled positions due to the number of coordinates being read in
> and created at one time?  I have further tried using 7 spin labels and I
> am presented with the same error.
>

Please send the error output, and we should get to the bottom of this
issue quickly. I modified eginput/pre/refine/generate.py in the
Xplor-NIH distribution to generate 9 tags, and that worked just fine.

best regards--
Charles

--
Charles Schwieters     email:   Charles <at> Schwieters.org
                       www:     http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt

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