[phenixbb] Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked
Gino Cingolani
Gino.Cingolani at jefferson.edu
Tue Aug 17 09:54:51 PDT 2010
Hi All,
I came back from synchrotron with some good SAD/MAD data.
Running some quick autosolve jobs at the beamline already gave interesting Se-mets peaks. At the beamline they use an old version of Phenix (1.3.... I believe).
Strangely, at home my latest version of Phenix finds absolutely nothing and quickly end with the following error message:
********************************************************************************
Failed to carry out AutoSol_scale_and_analyze_mad:
None of the solve versions worked
********************************************************************************
To test is the problem is in our data, I quickly re-run 3 old mad/sad datasets of structures previously solved in the lab
using the old (good) Solve and/or older Phenix versions.
Sadly, all SAD/MAD searches quickly end with the same error message.
I then tested the 'p9_se_w2.sca' that comes with Phenix.. and once again the same premature failure.
Is there something wrong with my Phenix?
I'm using version 1.6.4-486 on an XPS 420 Quad running Ubuntu 10.04.
Thanks,
Gino
PS everything else in Phenix seems to work (e.g. refinement, validation, elbow, utilities, etc.)
******************************************************************************
Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
Philadelphia PA 19107
Office (215) 503 4573
Lab (215) 503 4595
Fax (215) 923 2117
E-mail: gino.cingolani at jefferson.edu
******************************************************************************
"Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"
("You were not born to live like brutes, but to follow virtue and knowledge")
Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)
---- Original message ----
>Date: Fri, 13 Aug 2010 10:44:40 -0700
>From: Nathaniel Echols <nechols at lbl.gov>
>Subject: Re: [phenixbb] geometry weight and rmsd bonds - angles
>To: PHENIX user mailing list <phenixbb at phenix-online.org>
>
> 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
> crystallography.
>
> - 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.)
> -Nat
>________________
>_______________________________________________
>phenixbb mailing list
>phenixbb at phenix-online.org
>http://phenix-online.org/mailman/listinfo/phenixbb
More information about the phenixbb
mailing list