April 2012 - phenixbb - phenix-online.org

Sugar woes
by Simon Kolstoe 17 Apr '12

17 Apr '12

Hi phenixbb, Every couple of years I come to build a sugar chain into a protein structure and hope the process is less painful than last time, however it seems things still are not smooth yet! I'm trying to build a fairly standard sugar chain onto a protein and am encountering many problems. What I am doing is using coot to get the coordinates for each sugar using the "File-> Get monomer" option and then putting the appropriate link in my phenix.refine .def file after renumbering the sugars. For example: apply_cif_link { data_link = "BETA1-2" residue_selection_1 = chain Z and resname NAG and resid 5 residue_selection_2 = chain Z and resname MAN and resid 4 } apply_cif_link { data_link = "BETA1-4" residue_selection_1 = chain Z and resname GAL and resid 6 residue_selection_2 = chain Z and resname NAG and resid 5 } For some reason I keep getting the following error: --------------- Chain: "Z" Number of atoms: 220 Number of conformers: 1 Conformer: "" Sorry: Traceback (most recent call last): File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1042, in apply_mod mod_mon = self.monomer.apply_mod(mod_mod_id) File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/cif_types.py", line 399, in apply_mod result.delete_atom_in_place(mod_atom.atom_id) File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/cif_types.py", line 316, in delete_atom_in_place raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) RuntimeError: delete_atom_in_place: unknown atom_id: HO2 apply_mod failure: pdbres="NAG Z 5 " segid="Z " comp id: NAG-b-D mod id: DEL-HO2 ------------------ I haven't deleted the hydrogens that came with the sugars so what I thought it was doing was trying to delete an atom that isn't there, however adding a dummy atom with the name HO2 didn't work - any ideas? Also it seems happy with BETA1-4 links but not ALPHA2-6 links? How do I specify this link? Thanks, Simon

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Phaser-MR issues?
by Noinaj, Nicholas (NIH/NIDDK) [F] 15 Apr '12

15 Apr '12

Hi, I just installed the latest installer (1036) and having issues with Phaser-MR. i have a multi-domain structure (6-domains) and trying to search for the domains individually but starting with the most conserved first using the Direct search method. However, my issues are... 1- Phaser-MR appears to still be using the 'automatically determined search order' instead of the order I have selected despite me having this turned OFF 2- Phaser-MR appears to still be using the 'FAST method' despite me having DIRECT method chosen Anyone else seeing this or could i be doing something wrong here? Thanks in advance for any feedback! Cheers, Nick

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alternate conformation clashes with its symmetry mate
by Page, Rebecca 15 Apr '12

15 Apr '12

Dear phenix BB, I am having an alternate conformation clashing problem that I am having difficulty resolving: I have a protein in which the N-terminal residue is in two conformations.When the residue is in the 'A' conformation, the sidechain overlaps with the 'A' conformation sidechain density of its symmetry mate. I have modeled the occupancy at 50%. However, every time I refine, phenix pushes the 'A' conformer out of the density, likely due to clashing with its symmetry mate. Is there anyway to get around this? Thanks in advance, Rebecca

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help with validating a very low res structure
by Yunji Wu 14 Apr '12

14 Apr '12

Hi there-- Any old school experimental phasing experts want to help me out? I have an 8 angstrom structure solved using molecular replacement, refined to Rwork 0.38 and Rfree of 0.47. I also have a heavy atom (not SeMet) derivative data set to 10 angstroms. The idea is to get as much information from these data as possible so as to validate my current MR model. My approach is to calculate a difference map using the isomorphous difference Fouriers OR anomalous difference Fouriers as the amplitudes, with phases derived from the MR model-- then using the difference map to locate putative heavy atom sites. I would use various controls and experiments to (computationally) validate the credibility of these sites (e.g. cross-phasing with only iso/ano differences). Anyone have any suggestions for how to do this using Phenix? I use the GUI (generally the nightly builds), and am a newcomer to Phenix. Thanks!!

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Re: [phenixbb] on the protonation state of HIS
by Ho Leung Ng 14 Apr '12

14 Apr '12

Hi Dialing, What resolution is your structure? We are developing a method to predict hydrogen atom positions from structures of more modest resolution (out to about 1.7 A). We'd be happy to take a look at the histidines in your structure. Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry hng(a)hawaii.edu

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Windows installer now available
by Paul Adams 13 Apr '12

13 Apr '12

Dear Colleagues, as a result of some very hard work by several members of the Phenix Team, especially Nat Echols, I'm happy to report that we now have an experimental Windows installer for Phenix available for testing in the latest nightly builds. This includes most of the Phenix components, including the GUI, and should run on Windows XP or newer. Coot and PyMOL integration is supported if these are installed. Details are available here: http://www.phenix-online.org/platforms/windows.html We encourage anyone using this to submit the automatic bug reports, or email us concerning any other problems at bugs(a)phenix-online.org. An official, fully supported Windows installer, including 64-bit version, will be available later this year. The Phenix Team -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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amazing good statistics
by Christian Roth 11 Apr '12

11 Apr '12

Dear Phenix people, is there a major improvement in the algorithm? I have refined a 2.2 Ang. room temperature dataset with very good data statistics (I think) Rmerge 3.7%(8.9%) completeness 96%(92%) I/sigI 16,6(8,8) in parentheses are the values for the highest resolution shell. After refinement I have a R/Rfree of 0.1294/0.1670. In some shells there are values close to 0.100 and in the lowest shell Rfree is lower than Rwork. The quality of the data are really quite good, what is probably one of the reasons, but I am close or below to the border of the Range of R values in the pdb. Great for me, but I wanna be sure that it is really true. It was a MolRep with a close homolog, but I run a torsion angle sim annealing to decouple R/Rfree and the MolRep was done with an poly-Ala model to prevent too much model bias. Best Regards Christian

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Unrestrained refinement and reported RMSD values
by Yuri 10 Apr '12

10 Apr '12

Hi all, I wonder if there is a way of turning off (loosening) restraints for certain residues and a ligand specifically, and will the bond/angle rmsd be printed out somewhere? Thanks -- Yuri Pompeu

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Limit Ramachandran restrain to certain region
by Nian Huang 04 Apr '12

04 Apr '12

Dear all, Is it possible to limit Ramachandran restrain to specified residues in phenix.refine? I have a couple of loops with very poor density. The refinement process always made some residues fall out of ramachandran plot no matter how I tightened the weight and adjusted the residues back. Because the diffraction is about 2.3 A, I don't want the ramachandran restrain to impact the rest of structure. Thanks. Nian Huang

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modelling a flexible peptide
by intekhab alam 04 Apr '12

04 Apr '12

Hi All I have a 3.0A dataset (SG P1211) of a protein-protein complex having mol.wt 60 and 8 Kda respectively. Molecular repalcement (60Kda protein as template) with Phaser gave a solution with 6 molecules in ASU. A continuous density is also obersved near two different chains which i consider as the second protein. I refined the density using a poly Alanine model but still i can't recognise the side chains confidently for modelling. Considering the fact that the smaller protein partner is rich in lysine, arginine, Asp and Glutamate with only 3 tyr and 4 phe, i tried to modell fragments one by one but the B-factor of the segments are quite high (in the range of 110) what will be the best strategy to improve the map for modelling. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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