April 2011 - phenixbb - phenix-online.org

Re: [phenixbb] How to define link in phenix (rna3p) ?
by Ralf W. Grosse-Kunstleve 07 Apr '11

07 Apr '11

> Hi. I came across with the following post when I was dealing with a > similar issue (adding a modified nucleotide to RNA). I could create > .cif using elbow/reel as well, but I was wondering where to define > the link type between residues in phenix. You can use the apply_cif_link parameters. > For RNA, I typically see "rna3p', but with my newly created residue > linked to normal oligo, the link is formed, but recognized as Link ID > 'p'. Also, the newly created molecule is recognized as 'peptide', > although I defined _chem_comp.group in .cif file as RNA. The _chem_comp.group value is ignored by phenix.refine. The classifications are obtained via analysis of the atom names and the bonding in the monomer definitions. >------------------------------------------ >Chain: "Q1" > Number of atoms: 74 > Number of conformers: 1 > Conformer: "" > Number of residues, atoms: 3, 74 > Classifications: {'RNA': 2, 'peptide': 1} > Modifications used: {'5*END': 1, 'rna3p': 2} > Link IDs: {'p': 1, 'rna3p': 1} >------------------------------------------ It is strange that it thinks there is a peptide but still applies two rna/dna links. Could you send me (not the list) the part from the pdb file with the Q1 chain? Ralf

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CUA Ligand issue
by Bradley Hintze 07 Apr '11

07 Apr '11

Hello, I am trying to refine PDB 1YEW using the default phenix settings. $phenix.refine 1yew.pdb 1yew.mtz yields: ''' Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 6 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. ''' $ phenix.ready_set 1YEW_H.pdb yields: ''' Sorry: Atoms in the input are supposed to be bound CU1(CUA) - CU2(CUA) = 2.58 Fix the input file and retry ''' I assume this means that the Cu atoms in CUA are at an inappropriate distance. Is there an easy way to find out what the appropriate distance is? Can I fix this in coot? Thanks, Bradley

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How to define link in phenix (rna3p) ?
by Maehigashi, Tatsuya 07 Apr '11

07 Apr '11

Hi. I came across with the following post when I was dealing with a similar issue (adding a modified nucleotide to RNA). I could create .cif using elbow/reel as well, but I was wondering where to define the link type between residues in phenix. For RNA, I typically see "rna3p', but with my newly created residue linked to normal oligo, the link is formed, but recognized as Link ID 'p'. Also, the newly created molecule is recognized as 'peptide', although I defined _chem_comp.group in .cif file as RNA. ------------------------------------------ Chain: "Q1" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Classifications: {'RNA': 2, 'peptide': 1} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'p': 1, 'rna3p': 1} ------------------------------------------ Any input will be appreciated. Sincerely, "T" On Wed, Nov 17, 2010 at 7:43 AM, Gerwald Jogl <Gerwald_Jogl at brown.edu<http://phenix-online.org/mailman/listinfo/phenixbb>> wrote: > Hi All, > > I am refining several modified nucleotides in ribosomal RNA > (N2-methyl-guanosine and similar). While the restraints generation with > phenix.reel work quite well, I am unable to get the phosphate oxygen > restraints applied properly. Phenix.refine recognizes the links but for some > reason the phosphate groups come out quite distorted... > > For example, angles after refinement: > O3 (1) - P (2, modified) - OP2 (2) = 80 deg and > O3 (1) - P (2, modified) - OP1 (2) = 127 deg > > > Here is part of the phenix.refine log on reading the coordinates: > > Chain: "A" > Number of atoms: 32526 > Number of conformers: 1 > Conformer: "" > Number of residues, atoms: 1513, 32526 > Unusual residues: {'MA6%rna3p': 2, '5MC%rna3p': 3, '5MC%rna2p': 1, > '7M > G%rna3p': 1, '2MG%rna3p': 1, 'UR3%rna2p': 1, 'M2G%rna3p': 1, '4OC%rna3p': 1} > Classifications: {'undetermined': 11, 'RNA': 1502} > Modifications used: {'5*END': 1, 'rna3p': 1318, 'rna2p': 195} > Link IDs: {'rna3p': 1318, 'rna2p': 194} > Chain breaks: 1 > > I am at a loss about how to fix this as all links and restraints seem to be > in place. > > Many thanks for advice, > Gerwald ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Re: [phenixbb] B-factors vs resolution
by miket＠chem.ucla.edu 07 Apr '11

07 Apr '11

Usually one will describe ordered parts of a protein vs disordered parts based on B factors. Is the higher resolution protein more ordered and that may have contributed to its stronger diffraction? -- Are the two crystals with different max resolution isomorphous? B-factors contain contributions from both dynamic and static disorder. Your difference in b-factors and resolution are both likely due to the fact that your higher-resolution data comes from a more ordered crystal, not a less dynamic protein. More ordered crystals diffract better, but if the two crystals were grown in the same conditions and the crystals are isomorphous I doubt that there is any difference in the dynamics of the molecules. If you are interested in which parts of your protein are more dynamically disordered you may want to consider (within a single dataset) which atoms have high b-factors relative to the average b-factor for all the atoms in that dataset. Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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tools to obtain ADP?
by Jason 07 Apr '11

07 Apr '11

Hi, Is there a convenient tool to obtain ADP for each chain or ligand or a selective group? phenix.model_vs_data only gives an averaged ADP for everything and it takes really long. Thanks. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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Question about anisotropic refinement
by Louis Lazar 06 Apr '11

06 Apr '11

I have several structures that I am refining (~1.05A), and I have a question about anisotropic refinement. I have read a couple things about whether or not to refine waters anisotropically, as opposed to hydrogen, which I never refine anisotropoically. I am wondering what the general consensus is on it, and if anyone has anything from the archives (I'm having trouble searching through) or papers that I should read, please don't hesitate to let me see them. Thanks very much in advance Regards, Louis

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Ligand conformations.
by Yuri 06 Apr '11

06 Apr '11

Has anyone ever reported seeing 2 different binding confromations for a ligand that was soaked vs. the same ligand co-crystallized? -- Yuri Pompeu

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How to fix c-beta deviation?
by Jason 06 Apr '11

06 Apr '11

Hi, I have tried to regularize my protein structure in coot and use ramachandran restrain to improve statistics (and then release them). However, I can not make the c-beta deviation be zero. Is there some special way to improve c-beta deviation? Thanks. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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B-factors vs resolution
by Yuri 06 Apr '11

06 Apr '11

I am refining a 1.3 A structure the maps look great and I notice the main chain B factors are all around 7~12. I have refined the same enzyme at resolution 2.2 A and the B factors here were around 25~30. The question that comes to mind is: Usually one will describe ordered parts of a protein vs disordered parts based on B factors. Is the higher resolution protein more ordered and that may have contributed to its stronger diffraction? Or are the B factors values artifacts of refinement? -- Yuri Pompeu

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why are my B factors being "refined"
by Scott Classen 06 Apr '11

06 Apr '11

Hello Phenix community, I'm currently using nightly build 718, but this behavior is exhibited since sometime in the 1.6.xx releases too. I've turned off ADP refinement (only doing rigid_body refinement) and set the b_iso specifically as such: modify_start_model { selection = None adp { atom_selection = None randomize = None set_b_iso = 55 convert_to_isotropic = None convert_to_anisotropic = None shift_b_iso = None scale_adp = None } Yet the output PDB file has all b-factors in the 100s. Whazzup with that? Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 sibyls.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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