Alternate conformations in CNSsolve 0.9a

Mitchell Guss M.Guss at
Wed Jan 19 16:53:52 EST 2000

The answer is that you specify the disordered residues in the minimize.inp
step by their "segid" not by their residue names.

By default "alternate.inp" assigns segids AC1, AC2 etc to the different
conformers.  It doesn't matter how many residues are disordered there will
only be two segids assigned if any one residue has a maximum of two
conformers.  Check the pdb file output by alternate.inp and you will see
segids assigned to the disordered residues in the right hand column.

In minimize.inp you specify the disordered residues by segid.  That is,
{===>} conf_1=(segid "AC1 ");
{===>} conf_2=(segid "AC2 ");

Note the spaces in the quoted fields for segid.  You should also ensure that
you are using the msf file output by alternate.inp as well as the pdb file.

In general I find the whole procedure a bit tedious.  If would be improved
if someone could modify alternate.inp so that it could read two input
coordinate files and automatically assign the alternate conformer rather
than cutting and pasting by hand.

Hope this helps,

Mitchell Guss

Michael Theisen wrote:

> Hello,
> I am trying to introduce alternate side chain conformations into my
> refinement.  I followed the recommendations (correctly, I think) on the
> CNSsolve website's FAQ to produce the ".pdb" and ".mtf" files with the
> alternate conformations in place.  Here is part of my "alternate.inp" :
> {* select atoms to have multiple conformations *}
> {===>} atom_select=
>                 (
>                   (  resid  27  or
>                      resid 288 or
>                      resid 309 or
>                      resid 338 or
>                      resid 359 or
>                      resid 366 or
>                      resid 375 or
>                      resid 391
>                   )
>                      and not (name n or name ca or name cb or name c or
> name o)
>                 );
> "Alternate.pdb" looks fine, with all the appropriate atoms duplicated
> (new segid's) and occupancies set to 0.5 for both the original and new
> conformations of the atoms.
> Then I change the positions for the new alternate conformations by
> cutting and pasting the coordinates.
> Here is a relevant piece of the next input file, "minimize.inp" :
> {* select atoms in alternate conformations *}
> {===>} conf_1=( resid  27);
> {===>} conf_2=(resid 288);
> {===>} conf_3=(resid 309);
> {===>} conf_4=(resid 338);
> {===>} conf_5=(resid 359);
> {===>} conf_6=(resid 366);
> {===>} conf_7=(resid 375);
> {===>} conf_8=(resid 391);
> I then run "minimize.inp".  CNS complains that some of the side chain
> atoms are too close together.  This seems to be a problem only  for
> alternate conformations where some atoms are overlapping (e.g. two
> partially overlapping phenyl rings, but not two widely separated serine
> hydroxyl oxygens).  CNS then moves the offending side chains far apart,
> well out of density, while the R-factor goes up by some small amount.
> Has anyone else experienced similar problems?
> Am I making some sort of simple mistake (although no one around here has
> found one yet)?
> Could anyone provide me with a section from an input file with alternate
> conformations, hopefully something more illustrative than what's on the
> CNS website?
> If I can't get this to work, I will just fix the alternate conformations
> in place and refine that way, or maybe go back to X-PLOR.
> Many thanks in advance for any help!
> Michael Theisen
> theisen2 at

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