[phenixbb] geometry weight and rmsd bonds - angles

Nathaniel Echols nechols at lbl.gov
Fri Aug 13 10:44:40 PDT 2010

On Fri, Aug 13, 2010 at 10:20 AM, Lionel Costenaro <lcocri at ibmb.csic.es>wrote:

> So hydrogens were not added (find_and_add_hydrogens = False) and none was
> in the input pdb, but refined as riding (hydrogens.refine=riding), solvent
> was not updated (ordered_solvent = False) -there is already 510 waters
> almost all well defined.
> To my knowledge, parameters were fine (including refining riding hydrogens)
> except maybe for the anisotropy of waters for which Pavel recommend isotropy
> at this resolution.

This is a common point of confusion, especially for people used to REFMAC.
 The "riding" model only specifies how existing hydrogen atoms
should be treated; it does not actually model hydrogens in those positions
if they are not present in the input file.  So if there weren't any
hydrogens in the input file, it was being refined hydrogen-free. To actually
place the hydrogens, you need to click the box labeled "Automatically add
hydrogens to model", which will run phenix.ready_set to place the new atoms.
 The find_and_add_hydrogens option is more specialized anyway and should be
left alone unless you are working at ultra-high resolution or doing neutron

- bond outlier  CAD - OAC   model 1.26 - ideal: ProDRG single 1.36,
> readyset deloc 1.30,   eLBOW deloc 1.429,   smiles deloc 1.269
> - bond outlier  CBC - OBD   model 1.30 - ideal: ProDRG deloc  1.23,
> readyset double 1.23,   eLBOW aromatic 1.768,   smiles double 1.234
> - angle outlier CAG CAF CAD   model 99 - ideal: ProDRG 111,   readyset
> 117,   eLBOW 109,   smiles 117
> - dihedral outlier CBC NBB CAY CAZ   model 2.2 - ideal: ProDRG 180,
> readyset 131.66,   eLBOW 62.5,   smiles 68
> It seems to me that chemistry clearly depends on the software used,
> amazing.

This shouldn't be a huge surprise - the programs use different methods to
specify (or guess) molecule parameters, some of which are more effective
than others, and different approximations when optimizing the geometry, most
of which are optimized for speed rather than theoretical rigor (unless you
are running quantum chemical calculations like the AM1 optimization in
eLBOW).  As a general rule, it is very difficult to accurately guess the
chemistry of a molecule based on a PDB file alone; I suspect that CIFs may
have similar problems, but Nigel can clarify.

Which method to obtain a "correct" ligand and link definition from scratch
> should I use?

I think the correct answer is: use eLBOW with a SMILES string for the
ligand, then run ready_set to generate the link, but be sure to supply the
CIF file for your ligand to ready_set (instead of letting ready_set create
one from scratch based on coordinates).  I need to double-check what the GUI
returns in a situation like this, because I have not tested this particular
case.  However, if ready_set tries to make a new CIF with just ligand
restraints (*not* the link information), you probably want to ignore that,
and keep the rest of the output files.  Feel free to email me if you have
difficulty running it.  (And as mentioned before, you should definitely
update to the newest version, because the behavior of some programs has
changed, and the eLBOW GUI is relatively new anyway.)

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