- phenixbb - phenix-online.org

Re: [phenixbb] PHENIX user mailing list <[email protected]>
by Ralf W. Grosse-Kunstleve 16 Apr '07

16 Apr '07

Hi James, > Number of atoms with unknown nonbonded energy type symbols: 14 > "CD CD D 1 " > "CD CD D 2 " This problem should be fixed in the latest phenix development release (1.26 beta @ http://www.phenix-online.org/download/index.html) and the slightly more recent CCI Apps (link at same web page). Are you using phenix.refine from an older release? Could you please try the latest phenix or CCI Apps? Ralf

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Interpreting Cd atoms
by James Fraser 16 Apr '07

16 Apr '07

Hello, I'm trying to refine a structure with Cadmium bound. Is there a standard way to define "energy type symbols"? Thanks, James Number of atoms with unknown nonbonded energy type symbols: 14 "CD CD D 1 " "CD CD D 2 " "CD CD D 3 " "CD CD D 4 " "CD CD D 5 " "CD CD D 6 " "CD CD D 7 " "CD CD D 8 " "CD CD D 9 " "CD CD D 10 " ... (remaining 4 not shown) Time building chain proxies: 2.36, per 1000 atoms: 1.27 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 14 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions. Note that elbow.builder is available to create restraint definitions.

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Re: [phenixbb] Special positions
by Ralf W. Grosse-Kunstleve 11 Apr '07

11 Apr '07

Hi Morton, > I have a symmetrical ligand, malonate -OOCCCOO-, that binds right on the > crystallographic axis of a C2 structure. Is the correct approach to set > the occupancy to 0.5 and then refine or is there a better way to handle is > in Phenix? The 0.5 trick currently doesn't work in phenix.refine since we don't provide a way to turn off nonbonded interactions between symmetry copies. However, we fully support handling of atoms on special positions and bonds involving symmetry operations. For this to work, you have to give only an asymmetric unit worth of atoms, i.e. in your case half of your molecule. Is the C in the middle exactly on the two-fold axis? If so, delete these atoms from the PDB file: -OOCCCOO- ^^^ Then use the custom bond and angle feature (for the angles you'll need the 2007_04_06 CCI Apps) to define the required bonds and angles, including the bonds to the protein. I hope it is straightforward. If not, could you send me the fragments from you pdb file with the malonate and the piece of protein it is linked to? Then I could work out the bond and angle definitions for you. Ralf

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Special positions
by morteng＠bioxray.dk 11 Apr '07

11 Apr '07

Hello everybody I have a symmetrical ligand, malonate -OOCCCOO-, that binds right on the crystallographic axis of a C2 structure. Is the correct approach to set the occupancy to 0.5 and then refine or is there a better way to handle is in Phenix? Best regards -- Morten K Grøftehauge PhD student Department of Molecular Biology Gustav Wieds Vej 10 C 8000 Aarhus C - Denmark Phone: +45 89 42 50 10 Fax: +45 86 12 31 78 www.bioxray.dk

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phenix.refine: How to define links and bond distances
by Matthew Bowler 03 Apr '07

03 Apr '07

Dear All, I have been trying to find the utility in elbow_builder to define bond distances and link distances with no luck, the .py file has bond order information for my ligand but nothing regarding distances etc, can anyone help? Thanks in advance, yours, Matt. Matthew Bowler MRC Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 2XY Tel: 0044 (0) 1223 252826 Fax: 0044 (0) 1223 252825

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Re: [phenixbb] coordination of metal ions
by Ralf W. Grosse-Kunstleve 29 Mar '07

29 Mar '07

Hi Jesper, could you send me the fragments from your PDB file with the metal ion and the bound residues? I'll work this into an example for making the required cif definitions manually. Ralf

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coordination of metal ions
by Jesper Lykkegaard Karlsen 29 Mar '07

29 Mar '07

Dear Phenix-devels Is it possible set up geometric restrains for metal ions bound to protein in phenix.refine? elbow.builder seems only to work on separate molecules and not on metal ions with its coordinating sidechains. I found the feature to introduce custom bond distance between two atoms, but what about custom angles? And by the way will this these custom setting ignore Van Der Waals radii? or is there a way to set these for special atoms? Thanks! Jesper

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riding hydrogen and mlhl
by Jianghai Zhu 29 Mar '07

29 Mar '07

Hi All, I just found a refinement.hydrogens entry in the phenix.refine. Can we use phenix.refine to generate riding hydrogens to help the geometry in low- or mid-resolution refinement now? Using hydrogens in refmac5 really gives a better result than not using hydrogens. Another question. Is there a way to blur the experimental or density modified phases when using mlhl target? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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NCS weighting
by Jianghai Zhu 28 Mar '07

28 Mar '07

Hi, I am wondering how the NCS weighting in phenix.refine works. I guess the default values (coordinate_sigma = 0.05, b_factor_weight = 10) are pretty tight. What kind values would be appropriate for medium and loose NCS? Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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Re: [phenixbb] ls_wunit_k1
by Ralf W. Grosse-Kunstleve 26 Mar '07

26 Mar '07

> All right. The target for my TLS is also LS. Is that intentional too? Pavel, who wrote the TLS code, is current offline. I don't know if Pavel ran systematic tests to determine the default target for TLS. A couple of months ago I ran systematic tests exercising rigid body refinement using both the LS and ML targets. Overall it turned out that ML is slightly better than LS. For an individual structure and a particular starting point it can be the other way around, but averaged over about 70 structures with 100 random starting points each ML generally outperforms LS. We should have updated the default accordingly, but it fell through the cracks. If you have the time to try out both ML and LS in the refinement of your structure, we'd be interested to know the results. Ralf P.S.: What's the version of phenix.refine you are using? -- I'm still puzzled why you didn't get the "automatic adjustment" messages.

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