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As Frances says, you MUST give the correct residue name even if some
atoms are missing. For SHELXL refinements this has two side-effects that
I am frequently asked about:
1. There will be some warning messages about missing atoms in DFIX and
CHIV restraints. These can be ignored (but maybe one should look at the
more detailed messages in the .lst file to make sure that they are all
intentional).
2. The use of HFIX to generate hydrogens automatically will fail if the
connectivity is wrong because of the missing atoms. This can be overcome
by putting HFIX 0 instructions for the specific residues before the
other HFIX cards in the .ins file. For example, If CB is the last atom
that can be seen in Glu23, one should insert 'HFIX 0 CB_23' before the
usual HFIX cards so that the program does not try to put hydrogens on
this atom (which would require knowing where CG_23 is). Similarly if the
N-terminus is missing and the last atom that can be seen is (say) N_3,
one should insert 'HFIX 0 N_3' to prevent the program trying to add the
amide hydrogen. The first HFIX card that applies to a particular atom
takes priority over later HFIX instructions for the same atom.
George
Frances C. Bernstein wrote:
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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
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On Tue, 9 Jan 2007, Nicholas Noinaj wrote:
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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
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Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
