[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.



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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>phenixbb at phenix-online.org

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