*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
I cannot answer the question about removing atoms in
determining the structure but I would like to remind people
that, if you know that the residue is lysine, then the
residue name must be given as LYS in the PDB entry. The
sequence on SEQRES records is defined as representing the
material that was studied - there may be missing residues and
some residues may have disordered side chains - but in any case
the sequence must represent the material that was studied.
The residue names used on ATOM records must match the sequence
on SEQRES. When I was processing data for the BNL PDB we had
ongoing issues with coordinate sets that used ALA because
of a disordered side chain. There is a significant difference
between a protein where a residue was mutated to ALA and then
studied and a protein where a residue is LYS but the side
chain is disordered.
Note to software developers: Please fix this in your software
if it has not yet been addressed.
Frances C. Bernstein
=====================================================
**** Bernstein + Sons
* * Information Systems Consultants
**** 5 Brewster Lane, Bellport, NY 11713-2803
* * ***
**** * Frances C. Bernstein
* *** [EMAIL PROTECTED]
*** *
* *** 1-631-286-1339 FAX: 1-631-286-1999
=====================================================
On Tue, 9 Jan 2007, Nicholas Noinaj wrote:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
>
> Hi,
>
> i would like to get opinions on whether or not one removes side-chain atoms
> where there is no density. for example, if one can only observe density up
> to the beta-carbon for lysine (say at > 0.5 sigma), does one leave the lysine
> side chain intact, knowing it must be disordered, or does one terminate at
> the beta-carbon, making the coordinates reflect what is actually observed in
> the density.
>
> It seems both approaches are published and people seem to have conflicting
> opinions on the topic. It would be nice to come to some concensus, possibly
> clear up the issue for us newbies.
>
> Thanks in advance for all feedback!
>
>
>
> Cheers,
> NIck
>
>
>
>
> ________________________________________
>
> Nicholas Noinaj
> University of Kentucky College of Medicine
> Department of Molecular and Cellular Biochemistry
> The Center for Structural Biology
> Biomedical Biological Sciences Research Building, Rm 236
> 741 S. Limestone
> Lexington, Ky 40536
> Lab: 859-323-8183
> Cell: 859-893-4789
> Home: 859-228-0978
> [EMAIL PROTECTED]
> noinaj.com
>
>
>
>
>
>
>
