- phenixbb - phenix-online.org

geometry weight and rmsd bonds - angles
by Lionel Costenaro 17 Aug '10

17 Aug '10

Hello, 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). I set the bonds rmsd_max and angles rmsd_max to these values and try different values for: 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. Whatever the parameters, phenix never reached final rmsd better than 0.022 and 2.2. I refine the structure with refmac so far, but need to refine the occupancies (so phenix). Am I doing something wrong? Should I just use phenix to refine only the occupancy (I am actually doing it)? Any help or comment are welcome. Some information: space group: P21, 2 molecules (180 aa) / au, 510 waters, about 20% alternate conformations, ligand covalently link to the protein (correct dictionary and link parameters for refmac or phenix -add link to cif), 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) phenix version 1.6 289 (gui) Best regards, Lionel

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HKL_base
by Ed Pozharski 17 Aug '10

17 Aug '10

MTZ-files generated by phenix (at least some of them) are missing the base dataset (HKL_base) which is a requirement since CCP4 5.0. Is this deliberate? Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

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AutoSol scaling error
by Yogesh Gupta 17 Aug '10

17 Aug '10

I got following error while running MIR in phenix: "Failed to carry out AutoSol_scale_and_analyze_MIR: list index out of range". Could some one tell me how to fix this? Thanks, Yogesh

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Re: [phenixbb] Restraints file for a new amino acid residue
by Joseph Noel 16 Aug '10

16 Aug '10

Pavel, I sent you the associated pdb file as an attachment. The site in question is 169 in both monomer A and monomer B. I think one way around the problem for me is to create alternative conformations for the residues on either end of the modified cysteine. In that way I can refine each as a section of alternative conformations and then I think things should link up both in Phenix and COOT. COOT is particularly problematic. It only recognizes conformer A and not any additional conformers for a particular position if the name of the amino acid changes. I guess my case is not that common - ie a mixture of oxidation states of a regular amino acid. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Re: [phenixbb] Restraints file for a new amino acid residue
by Joseph Noel 13 Aug '10

13 Aug '10

Thanks all for the advice. Basically that is what I have been doing. It is actually an oxidized cysteine to sulfenic acid. I am refining the site as alternative conformers with the normal Cys, the single oxidation state to sulfenic acid (CSO) and the double to sulfinic acid (CSD). I know that CSO is in the phenix library but it adds hydrogens to the amino group every time I run elbow or ready set. I then I have to edit the PDB file to delete the hydrogen or Phenix will not refine. I also have problems in COOT. It will not let me move the residues torsional angles. I have checked other structures in the PDB and the density fits perfectly with the structures of many such oxidized systems but for some reason Phenix is giving me some problems. I was going to create a "new" residue and explicitly define the oxygen as charged rather then protonated since the pKa of sulfenic acid is quite low. Maybe the problems all stem from refining this particular position with three alternative "conformers", each conformer of which is chemically distinct. For now, I have CSO labeled as convention BCSO for conformer B. Cys is ACYS. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Autobuild error message
by bschmidt＠berkeley.edu 13 Aug '10

13 Aug '10

Hello all, I am trying to use phenix.autobuild from the command line to generate either composite omit maps or prime and switch maps. In either case, when I try, the program starts to run for a while before failing and giving me the following error message: "Failed to carry out AutoBuild_build_cycle: Sorry...the file AutoBuild_run_2_/TEMP0/refine_pdb_in.mtz is missing..." I'm not sure why that would be the case, or where that mtz is supposed to come from. Can anyone explain what might be the problem? Thanks, Bryan

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Phaser SAD module - resolution question
by Peter Grey 13 Aug '10

13 Aug '10

Dear Phenix community, I am using Phaser SAD module with a poor MR model to locate the initial heavy-atom sub-structure. I have a 3A dataset but the anomalous signal is weak at the higher resolution shells. I would like to ask for your advice regarding the resolution I should use in Phaser. I thought that for the sake of just locating the sites I should use relatively low resolution (let's say 3.5 or even 4A) and then run Phaser a second time. In this second run I would use the highest-resolution and let Phaser only refine the sites (located in the first run) during one cycle and calculate the combined phases. Thank you in advance for your suggestions and advice, Peter

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Where to find optimized wxc_scale/wxu_scale weighting factors after optimization
by amadrona＠uci.edu 13 Aug '10

13 Aug '10

Hello, I ran a refinement optimizing geometry and B factor weighting factors using optimize_wxc=true optimize_wxu=true. I was given these statistics in the pdb header: Rwork Rfree Bonds Angles start .1588 .1838 .007 1.235 end .1454 .1780 .016 1.601 (1.37 A resolution) 1. I would like to find the optimized weighting factors in the log file but cannot. Instead I find the following (pasted below). However, the scale here doesn't make sense to me because many our greater than 0.5. How do I find the optimized values so that I can use them in further rounds of refinement? I'm sorry if this has been covered in previous posts but I could not find an answer. 2. Can anyone explain the concept of optimizing the B-factor? I don't understand how changing it brings you closer or further from an ideal model as oppose to xray. (which is how I make sense of refining the geometry) Thank you -Yarow ================================ xyz refinement =============================== Start r_work= 0.1462 r_free= 0.1784 bonds= 0.015 angles= 1.53 r_work= 0.1492 r_free= 0.1792 bonds= 0.005 angles= 1.08 scale= 1.00 r_work= 0.1484 r_free= 0.1788 bonds= 0.006 angles= 1.14 scale= 1.40 r_work= 0.1480 r_free= 0.1787 bonds= 0.007 angles= 1.19 scale= 1.80 r_work= 0.1476 r_free= 0.1785 bonds= 0.008 angles= 1.23 scale= 2.20 r_work= 0.1473 r_free= 0.1785 bonds= 0.008 angles= 1.26 scale= 2.60 r_work= 0.1471 r_free= 0.1784 bonds= 0.009 angles= 1.29 scale= 3.00 r_work= 0.1469 r_free= 0.1784 bonds= 0.010 angles= 1.32 scale= 3.40 r_work= 0.1467 r_free= 0.1783 bonds= 0.010 angles= 1.34 scale= 3.80 r_work= 0.1465 r_free= 0.1782 bonds= 0.011 angles= 1.36 scale= 4.20 r_work= 0.1464 r_free= 0.1782 bonds= 0.011 angles= 1.39 scale= 4.60 r_work= 0.1463 r_free= 0.1782 bonds= 0.011 angles= 1.40 scale= 5.00 r_work= 0.1461 r_free= 0.1781 bonds= 0.012 angles= 1.45 scale= 6.00 r_work= 0.1458 r_free= 0.1781 bonds= 0.013 angles= 1.49 scale= 7.00 r_work= 0.1456 r_free= 0.1781 bonds= 0.014 angles= 1.53 scale= 8.00 r_work= 0.1454 r_free= 0.1781 bonds= 0.015 angles= 1.57 scale= 9.00 r_work= 0.1453 r_free= 0.1780 bonds= 0.016 angles= 1.60 scale= 10.00 r_work= 0.1495 r_free= 0.1794 bonds= 0.005 angles= 1.05 scale= 0.85 r_work= 0.1501 r_free= 0.1797 bonds= 0.005 angles= 1.02 scale= 0.70 r_work= 0.1507 r_free= 0.1800 bonds= 0.004 angles= 0.98 scale= 0.55 Final r_work= 0.1453 r_free= 0.1780 bonds= 0.016 angles= 1.60

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Restraints file for a new amino acid residue
by Joseph Noel 13 Aug '10

13 Aug '10

Hi All, How does one create a new CIF file using Elbow for a non-natural amino acid not found yet in the PDB? I know how to carry it out for the isolated residue readily (but of course thinks it is isolated and doesn't include the necessary peptide bonding) but how does one ensure the correct backbone restraints for it are included since it is not isolated but part of the chain? Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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too many outliers
by intekhab alam 13 Aug '10

13 Aug '10

Hi there I have recently solved a structure at 2.71A resolution using CCP4 (Refmac5) with R and R free of 22 and 29 respectively. The model is nicely fitted in the map and everything looks except in some loop region where the map is not fitted well. I just finished modelling and checked ramachandran plot which is showing unreasonably high number of outliers (12%) with only 65% in the favoured region. I am thinking to use phenix_refine with simulated annaeling and using the option fix bad chain rotamers. What else i can do aprt from this. i will be highly thankful for the suggestions. Apart from this can anyone let me know how -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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