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.
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Re: Problems Loading PDB