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

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: [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)

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Date: Fri, 13 Aug 2010 10:44:40 -0700 From: Nathaniel Echols Subject: Re: [phenixbb] geometry weight and rmsd bonds - angles To: PHENIX user mailing list

On Fri, Aug 13, 2010 at 10:20 AM, Lionel Costenaro 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 ________________ _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] 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