[phenixbb] geometry weight and rmsd bonds - angles

Lionel Costenaro lcocri at ibmb.csic.es
Fri Aug 13 10:20:31 PDT 2010


Thanks for your answers.
To follow on my problem(s), I am replying to some questions/advices and ask

1-"At 1.32A I would expect phenix.refine resulting in something like 0.022
and 2.2" (Pavel): 0.022 and 2.2 might indeed be correct for my structure at
However, if I set  bonds_rmsd_max = 0.012 and angles_rmsd_max = 1.5,
providing I set the wc weight correctly, I would expect refine to -at least
try to- reach this rmsd values. Or are they just indicative values that can
be modified during the refinement?

2- I did use optimize_wxc=true and optimize_wxu=true without much better
- I used mostly the default parameters of the gui and just modified strategy
(individual_sites all, individual_adp all, occupancy), 10 macro_cycles, and
target_weights already mentioned.
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.
Do you recommend to automatically update waters, even during late stages of

3- Ligand and link definition were done with ProDRG and JLigand (with some
cif errors) and refinement raise several problems, for example:
with distances or angle from refined model, ideal ProDRG, ideal readyset
(with my pdb), eLBOW optimisation of ProDRG cif. eLBOW from smiles
- 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.
So, aside refinement problems, my question would be:
Which method to obtain a "correct" ligand and link definition from scratch
should I use?

Best regards,

PS: I might not be able to reply during the next week.

2010/8/12 Lionel Costenaro <lcocri at ibmb.csic.es>

> Hello,
> I'm using phenix.refine for the first time and have some problem to get it
> reach reasonable rmsd bonds (0.012-0.015) and angles (1.5-1.8).
> I set the bonds rmsd_max and angles rmsd_max to these values and try
> different values for:
> wxc_scale (from default 0.5 downto 0.015),  wxu_scale (from default 1 down
> to 0.03), wc (from default 1 up to 8), with and without optimising wxc wxu.
> Whatever the parameters, phenix never reached final rmsd better than 0.022
> and 2.2.
> I refine the structure with refmac so far, but need to refine the
> occupancies (so phenix).
> Am I doing something wrong? Should I just use phenix to refine only the
> occupancy (I am actually doing it)?
> Any help or comment are welcome.
> Some information:
> space group: P21, 2 molecules (180 aa) / au, 510 waters, about 20%
> alternate conformations,
> ligand covalently link to the protein (correct dictionary and link
> parameters for refmac or phenix -add link to cif),
> resolution: 1.32, refine xyz for all, Baniso for all (refmac), ncs not
> used, R 13.6 Rfree 17.7 fom 0.913 rmsd 0.012 1.56 (last refmac)
> phenix version 1.6 289 (gui)
> Best regards,
> Lionel
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100813/a89e98fd/attachment-0003.htm>

More information about the phenixbb mailing list