[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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> _______________________________________________
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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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