- phenixbb - phenix-online.org

!!!
by Hexi Zhang 07 Apr '13

07 Apr '13

http://www.pispy.com/mmog/bupedamkfovmstocspifxj.bjyhn

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Atoms with iso. B <=0
by Stephen Weeks 05 Apr '13

05 Apr '13

Dear phenixBBers I have a curious case of refinement of a 2.6 Angs structure, where some of the atoms have a calculated b-factor of 0.00. It seems to be somewhat random where this occurs and includes atoms within the backbone e.g. the nitrogen in the following residue: ATOM 2014 N THR A 264 -2.685 42.357 -35.833 1.00 0.00 N ATOM 2015 CA THR A 264 -3.952 41.776 -35.425 1.00 1.50 C ATOM 2016 CB THR A 264 -4.684 41.052 -36.593 1.00 1.70 C ATOM 2017 OG1 THR A 264 -4.077 39.772 -36.846 1.00 2.24 O ATOM 2018 CG2 THR A 264 -4.669 41.867 -37.855 1.00 1.72 C ATOM 2019 C THR A 264 -3.687 40.729 -34.368 1.00 2.42 C ATOM 2020 O THR A 264 -2.571 40.210 -34.263 1.00 2.63 O The structure contains 4 NCS related monomers but with a quick glance I don't see any obvious correlation between each one as to which atoms are 0.00. I did use phenix.pdbtools to randomise the B-factors (no atoms had a value 0.00 afterwards) but upon repeating the refinement the same problem occurs. Does anyone have a suggestion how to fix this ? Cheers Stephen

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43rd Mid-Atlantic Macromolecular Crystallography Meeting
by Charles Pemble 05 Apr '13

05 Apr '13

*43**rd** Mid-Atlantic Macromolecular Crystallography Meeting* *May 30 – June 1, 2013* *Duke University* *Durham, NC* The 43rd Mid-Atlantic Macromolecular Crystallography Meeting (MAMCM) will be held at Duke University in Durham, North Carolina. This meeting fosters discussion and interaction among structural biologists from around the Mid-Atlantic region. Registration is now open at http://www.mid-atlantic.org. The deadline for registration is May 15th. This year will feature keynote speaker Tom Terwilliger from Los Alamos National Lab, workshops on PHENIX and MolProbity, plus many talks & posters on new and exciting research. Presentations will be selected from submitted abstracts and preference will be given to young researchers. The best presentation and poster by a Graduate Student & Postdoctoral Fellow will be awarded. We encourage you to submit your abstracts and sign up for the workshops as these are separate processes from registration. *IMPORTANT: *A block of rooms have been reserved at the Millennium hotel as well as the Duke dormitories. The deadline for reserving a room at the Millennium is May 9th. With best wishes on behalf of the primary Organizing Committee, Charlie Pemble _____________________________ Charles W. Pemble IV, Ph.D. Duke University Medical Center 308 Research Drive LSRC, A06 Durham, NC 27708 charles.pemble(a)duke.edu

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table 1 no CC values, selenomethionine occupancy refinement
by Georg Mlynek 05 Apr '13

05 Apr '13

Dear All, I have 3 minor questions/problem and would be grateful for some help. 1a. Providing the XDS_ASCII.HKL to phenix tableI works perfect, however there are no values written for CC1/2. The same file in phenix.merging_statistics I get the CC1/2. Am I missing something? 1b. The only value phenix tablel one takes from INTEGRATE.LP (i guess CORRECT.LP will work too) is the wavelength - true? 2. I see some negative density around the seleniums in my selenomethionine labeled protein. I guess this is due to radiation damage. Is the accepted standard to do occupancy refinement for just the sidechain, or just parts of the sidechain, the whole residue or just leave it like it is. For the side chain refinement.refine.occupancies { constrained_group { selection = resname MSE ( name CB or name CG or name SE or name CE or name HB2 or name HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3 } } should work or? I am using version dev-1334 on ubuntu. Best regards Georg.

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C-alpha r.m.s.d. calculation before and after structural alignment
by Bret Wallace 04 Apr '13

04 Apr '13

Dear All, I have solved a complex structure of two proteins, and a reviewer has asked to compare the altered interface binding of one particular binding partner (protein2) in this complex to various other similar deposited PDBs through r.m.s.d. calculations and rotation/translation matrices. After aligning ~4 structures from the PDB (specifically aligning 1 chain to the other binding partner, protein1) to my structure, I want to calculated the rmsd before and after re-aligning the deposited structures (containing protein2) to my complexed protein2. I have used the superpose utility in phenix to align the C-alphas, however, I am getting very large rmsd values after alignment (~3.3). This is rather strange as the aligned proteins are essentially the exact same, both in sequence and secondary structure. Using various different programs such as SSM, Coot, and others give me an rmsd value of ~1, which is far more reasonable, but they do not output a "start" rmsd value. Any suggestions on what the cause of this large rmsd value? Or possibly another program that could provide start and final rmsd values along with rotation/translation matrices for alignment? Thanks, Bret

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links in phenix summary
by Christian Roth 04 Apr '13

04 Apr '13

Dear all, thanks to the phenix team which helped me a lot to resolve all issues regarding the correct link definitions. I have summarised a few things which one might consider if nonstandard links are necessary. Try phenix ready set to get your links out of the pdb. Do not forget to change the possible LINKR to LINK! Inspect the links and decide if they are useful! Peptide links are automatically incorporated if residues are close (inspect geo file) Non standard peptide links could be created using using an now available alpha release script: elbow.ligand_linking model.pdb Inspect the generated cif file and correct angles and incorporate dihedrals and so on if necessary. Sugar links which exists in the mon_lib.cif should be incorporated using the apply_cif link option like refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain B and resname GLC and resseq 1 residue_selection_2 = chain B and resname GLC and resseq 2 } According to the link definition the C1 oxygen of the following sugar with the higher number must be removed. The automatic incorporation of sugar links will be probably soon available in phenix. Nigel is already working on this. If one want use hydrogens in the refinement, they have to be added previously with ready_set and afterwards the OH4 sugar hydrogen has to be removed before the refinement. For links with symmetry related atoms the symmetry operator must be included in a custom bond definition efinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } The operator can be obtained using iotbx.show_distances your.pdb > all_distances Search for keyword "sym" or from Coot clicking on the symm option. Coot print out the operator and the translation term separately. Both has to be merged in the final operator used in phenix! Christian

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Fw:Dialing Pretty
by Dialing Pretty 03 Apr '13

03 Apr '13

http://www.riofoliashow.com/bhblnsv/jx.vohys?dwr Dialing Pretty gzdrrasz

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MR-Rosetta server?
by Mark J van Raaij 02 Apr '13

02 Apr '13

Dear All, for a recent dataset, I would like to try MR-Rosetta, as normal MR didn't work (not surprising perhaps, as the closest model is from NMR and with only about 20% sequence identity). Even though I don't think there is much chance of success, I would like to try MR-Rosetta anyway, although without having to install Rosetta if possible. Is there a server that would take care of the whole process? I.e. take the input mtz and the hopefully homologous structure supplied by me, and run Rosetta followed by MR in Phenix? In its defect, is there an online server that does the Rosetta part of MR-Rosetta, that would give a Rosetta-improved output model for putting into MR by Phenix, which I already have installed? Some side-ways related questions: - is it feasible to install Rosetta under MacOSX for a not very computer-literate user? - Phenix seems to slow down my MacPro a lot, even if I use just one of the 8 processors - is 4 Gb of RAM too little? Sorry for the rather rambling mail... Greetings, Mark Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij

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.::Hexi Zhang::.
by Hexi Zhang 02 Apr '13

02 Apr '13

http://www.shoes4me.com/jpnnv/qkawwtmiigdaxdliiayzmr.opdpdklrvlts

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which monlib in refinement?
by Konrad Bergen 02 Apr '13

02 Apr '13

Hello phenixbb, i was recently refining a DCT and was a bit puzzled when i got outliers in torsion angles (readout from the final .geo file). The DCT was built in coot (using the ccp4 monomer library) and seems to fit these restraints. A closer look gave me a discrepancy in the torsion angles between the ccp4 (ver 6.3.0) and the corresponding phenix (dev1325) file /usr/local/ccp4-6.3.0/ccp4-6.3.0/lib/data/monomers/d/DCT.cif _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period DCT var_1 O3G PG O3B PB -60.011 20.000 1 DCT var_2 PG O3B PB O3A -179.960 20.000 1 DCT var_3 O3B PB O3A PA -179.992 20.000 1 DCT var_4 PB O3A PA "O5'" 179.964 20.000 1 DCT var_5 O3A PA "O5'" "C5'" 179.986 20.000 1 DCT var_6 PA "O5'" "C5'" "C4'" -179.998 20.000 1 DCT var_7 "O5'" "C5'" "C4'" "O4'" 65.696 20.000 3 DCT var_8 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3 DCT var_9 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3 DCT var_10 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1 DCT var_11 "C4'" "O4'" "C1'" N1 -150.000 20.000 1 DCT var_12 "O4'" "C1'" "C2'" "C3'" 0.000 20.000 3 DCT var_13 "O4'" "C1'" N1 C6 -121.764 20.000 1 DCT CONST_1 "C1'" N1 C2 N3 180.000 0.000 0 DCT CONST_2 "C1'" N1 C6 C5 180.000 0.000 0 DCT CONST_3 N1 C6 C5 C4 0.000 0.000 0 DCT CONST_4 C6 C5 C4 N3 0.000 0.000 0 DCT CONST_5 C5 C4 N4 HN41 179.773 0.000 0 DCT CONST_6 C5 C4 N3 C2 0.000 0.000 0 DCT CONST_7 C4 N3 C2 O2 180.000 0.000 0 /usr/local/phenix.test/latest/chem_data/mon_lib/d/DCT.cif _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period DCT var_3 O1G PG O3B PB 2.570 20.000 1 DCT var_4 PG O3B PB O3A 83.412 20.000 1 DCT var_6 O3B PB O3A PA -132.456 20.000 1 DCT var_7 PB O3A PA O5* -51.566 20.000 1 DCT var_9 O3A PA O5* C5* -166.199 20.000 1 DCT var_10 PA O5* C5* C4* 135.553 20.000 1 DCT var_11 O5* C5* C4* C3* 12.096 20.000 3 DCT var_12 C5* C4* O4* C1* 143.686 20.000 1 DCT var_13 C5* C4* C3* C2* -117.819 20.000 3 DCT var_14 C4* C3* C2* C1* -21.471 20.000 3 DCT var_15 C3* C2* C1* N1 150.776 20.000 3 DCT var_16 C3* C2* C1* O4* 32.781 20.000 3 DCT var_17 C2* C1* N1 C2 121.270 20.000 1 DCT var_18 C2* C1* N1 C6 -65.572 20.000 1 DCT CONST_1 C1* N1 C2 N3 180.000 0.000 0 DCT CONST_2 N1 C2 N3 C4 0.000 0.000 0 DCT CONST_3 C2 N3 C4 C5 0.000 0.000 0 DCT var_19 N3 C4 N4 HN41 0.000 20.000 1 DCT CONST_4 N3 C4 C5 C6 0.000 0.000 0 DCT CONST_5 C4 C5 C6 N1 0.000 0.000 0 I am just wondering which values/library to use or if i got something completely wrong. Best regards Konrad

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