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:   [email protected]
******************************************************************************
"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 <[email protected]>  

Subject: Re: [phenixbb] geometry weight and rmsd bonds - angles  

To: PHENIX user mailing list <[email protected]>

 On Fri, Aug 13, 2010 at 10:20 AM, Lionel Costenaro

 <[email protected]> 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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