Hello, <br><br>Thanks for your answers. <br>To follow on my problem(s), I am replying to some questions/advices and ask more:<br><br>1-"At 1.32A I would expect phenix.refine resulting in something like 0.022 and 2.2" (Pavel): 0.022 and 2.2 might indeed be correct for my structure at 1.32A. <br>
However, if I set bonds_rmsd_max = 0.012 and angles_rmsd_max = 1.5, providing I set the wc weight correctly, I would expect refine to -at least try to- reach this rmsd values. Or are they just indicative values that can be modified during the refinement?<br>
<br>2- I did use optimize_wxc=true and optimize_wxu=true without much better results.<br>- I used mostly the default parameters of the gui and just modified strategy (individual_sites all, individual_adp all, occupancy), 10 macro_cycles, and target_weights already mentioned.<br>
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.<br>
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.<br>Do you recommend to automatically update waters, even during late stages of refinement?<br>
<br>3- Ligand and link definition were done with ProDRG and JLigand (with some cif errors) and refinement raise several problems, for example: <br>with distances or angle from refined model, ideal ProDRG, ideal readyset (with my pdb), eLBOW optimisation of ProDRG cif. eLBOW from smiles<br>
- bond outlier CAD - OAC model 1.26 - ideal: ProDRG single 1.36, readyset deloc 1.30, eLBOW deloc 1.429, smiles deloc 1.269<br>- bond outlier CBC - OBD model 1.30 - ideal: ProDRG deloc 1.23, readyset double 1.23, eLBOW aromatic 1.768, smiles double 1.234<br>
- angle outlier CAG CAF CAD model 99 - ideal: ProDRG 111, readyset 117, eLBOW 109, smiles 117<br>- dihedral outlier CBC NBB CAY CAZ model 2.2 - ideal: ProDRG 180, readyset 131.66, eLBOW 62.5, smiles 68<br>
<br>It seems to me that chemistry clearly depends on the software used, amazing. So, aside refinement problems, my question would be:<br>Which method to obtain a "correct" ligand and link definition from scratch should I use?<br>
<br>Best regards, <br>Lionel<br><br>PS: I might not be able to reply during the next week.<br><br><br><div class="gmail_quote">2010/8/12 Lionel Costenaro <span dir="ltr"><<a href="mailto:lcocri@ibmb.csic.es" target="_blank">lcocri@ibmb.csic.es</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hello, <br><br>I'm using phenix.refine for the first time and have some problem to get it reach reasonable rmsd bonds (0.012-0.015) and angles (1.5-1.8).<br>
I set the bonds rmsd_max and angles rmsd_max to these values and try different values for: <br>
wxc_scale (from default 0.5 downto 0.015), wxu_scale (from default 1 down to 0.03), wc (from default 1 up to 8), with and without optimising wxc wxu.<br>Whatever the parameters, phenix never reached final rmsd better than 0.022 and 2.2.<br>
I refine the structure with refmac so far, but need to refine the occupancies (so phenix).<br>Am I doing something wrong? Should I just use phenix to refine only the occupancy (I am actually doing it)?<br>Any help or comment are welcome. <br>
<br>Some information: <br>space group: P21, 2 molecules (180 aa) / au, 510 waters, about 20% alternate conformations,<br>ligand covalently link to the protein (correct dictionary and link parameters for refmac or phenix -add link to cif),<br>
resolution: 1.32, refine xyz for all, Baniso for all (refmac), ncs not used, R 13.6 Rfree 17.7 fom 0.913 rmsd 0.012 1.56 (last refmac)<br><br>phenix version 1.6 289 (gui)<br><br>Best regards, <br><font color="#888888">Lionel<br>
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