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

Tom Terwilliger terwilliger at lanl.gov
Tue Aug 17 10:17:21 PDT 2010


Hi Gino,

I'm sorry for the trouble!  Try this:

yum install tcsh

The problem is that ubuntu does not have csh. I will be changing  
autosol to use sh but I haven't done that yet.

All the best,
Tom T

On Aug 17, 2010, at 10:54 AM, Gino Cingolani wrote:

> 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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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss




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