[phenixbb] Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked

[Gino Cingolani]

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
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