May 2009 - phenixbb - phenix-online.org

Re: [phenixbb] phenix.automr ensemble/component question
by Thomas C. Terwilliger 23 Jul '10

23 Jul '10

Hi Scott, Your first command looks good to me. It is saying that the composition of the crystal is 2 copies of each chain: component_1.component_copies=2 component_2.component_copies=2 and you want to search for 2 copies of each of your search models: ensemble_1.copies_to_find=2 ensemble_2.copies_to_find=2 All the best, Tom T > Hi Phenixers, > > I'm a bit confused about the proper syntax for my phenix.automr job. > This is probably a simple concept, but I'm running on 3 hours of sleep > as my kid was up all night, and my synapses aren't working so good. > > I expect 2 copies of my protein per AU > > My protein is composed of two domains > > I have a single PDB search model for each domain > > is either of these commands correct? > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=2 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=2 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > or > > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=1 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=1 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > essentially I'm not really using an ensemble of search models, I only > have a single PDB for each domain. So should ensemble_1.copies_to_find > and ensemble_2.copies_to_find be set to 1 or 2? > > > Thanks, > Scott > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Scott Classen, Ph.D. > SIBYLS Beamline 12.3.1 > http://bl1231.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 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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"phenix.fobs_minus_fobs_map" new tool in PHENIX
by Pavel Afonine 27 Jun '09

27 Jun '09

Hi Everyone, for all of you who asked about computing Fo-Fo map in PHENIX: I added a new command line tool called "phenix.fobs_minus_fobs_map". For usage details just type phenix.fobs_minus_fobs_map and hit Enter, and it will print a couple of examples. Any feedback will be very appreciated. This is available in development version of PHENIX starting from 1.4-51: goto: http://www.phenix-online.org/download/ then click "Latest installers" under "Nightly builds (version 1.4-4 and above)" section. Pavel.

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Refining partially occupied DNA on top of itself
by bschmidt＠berkeley.edu 26 Jun '09

26 Jun '09

Hello, I am having difficulty using Phenix to build and refine a DNA duplex. The issue is that my asymmetric unit consists of one protein monomer bound to DNA, but the protein is a dimer and the DNA is not palindromic, so each monomer is bound to a different sequence of DNA. As such, the density for the two different DNA half-sites is averaged out in the asymmetric unit. I have tried to place two duplexes directly on top of one another, each with 0.5 occupancy, and then refine. But I have noticed two problems. The first is that when xyz refinement is off, and I look at the output files, the density for DNA is awfully green, as if there were only *one* helix with 0.5 occupancy there. The other problem I noticed is that when I turn xyz refinement on, and look at the output files, one of the two half-sites gets moved several angtroms, so that it is in a region that generally has no density. I expect that, if done properly, the backbone of both half-site DNAs ought not to move. Any advice would be greatly appreciated. Thanks, Bryan Schmidt

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Water/residue alternative conformations
by Roeland Boer 08 Jun '09

08 Jun '09

Dear all, I'm refining a 1.45 Ang structure in which I have several residues that have alternate conformations. These alternate conformations in some cases coincide with additional density that suggests the presence of a water molecule, appropriately positioned to make hydrogen bonds with near atoms. I have modeled partially occupied waters in these additional densities and linked their occupancies with the alternate conformation that is not clashing with the water in question. My problem is that these partially occupied waters are pushed away by the 'overlapping' alternate conformation of the amino acids. I guess there's an antibump restraint somewhere? How can I tell phenix that these alternate waters are not sterically clashing with the amino acid (since the sum occupancies of the water plus alternate conformation is 1)? The attached image shows one of those disordered residues after refinement. Water 1519 is pushed away from one alt conf (A) of Gln13, whereas the density suggests it should be making a hydrogen bond to OE1 of the altconf B of Gln13. I describe the occupancies of the situation in the attached image as below. refinement { refine { occupancies { constrained_group { selection = chain A and resseq 13 and altloc A selection = (chain A and resseq 13 and altloc B) or (resname HOH and resseq 1519 and altloc A) } } } } Thanks, Roeland Boer.

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mutate to polyAla in phenix.automr?
by Francis E Reyes 28 May '09

28 May '09

Is there an option or a phenix.* utility to mutate a MR model to poly ALA before the MR is done? Thanks! FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Failed to carry out AutoBuild_build_cycle: Word too long.
by Gino Cingolani 28 May '09

28 May '09

Hi Folks, does anybody know what this means? My AutoBuild dies off in the middle with this error message ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /home/gino/XTAL/SYN/V1/DASETs/Se3/SAD/REF/AutoBuild_run_2_/TEMP0/RUN_FILE_1' Word too long. ******************************************************************************** Thanks, Gino *********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: cingolag(a)upstate.edu *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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covalently linked ligand
by Joerg Standfuss 27 May '09

27 May '09

Dear phenix users, I am currently building a model where the ligand is linked via schiff base to a lysine residue. To let phenix know about the link I provide the ligand.cif file and created the link parameter file as described in the manual. The type of link I defined with Jligand as it does not appear in the standard ccp4 library. Unfortunately phenix.refine stops with the error message below when I provide the so created files. It seems phenix has problems to apply the needed ligand modifications ie removing hydrogens and oxygens and stops with the refinement. I have no idea why this doesn't work and am getting a little desperate so any suggestions how to do this properly would be greatly appreciated. Could I use for example elBOW to create the link description? many thanks, Joerg File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/pdb_interpretation.py", line 499, in __init__ mod_mod_id=self.mon_lib_srv.mod_mod_id_dict[apply_data_mod]) File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/pdb_interpretation.py", line 771, in apply_mod mod_mon = self.monomer.apply_mod(mod_mod_id) File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/cif_types.py", line 339, in apply_mod result.delete_atom_in_place(mod_atom.atom_id) File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/cif_types.py", line 244, 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: H151

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AutoBuild can't align sequence file
by Moritz.Metlitzky＠sbg.ac.at 27 May '09

27 May '09

Hi all, i'm currently trying to solve my structure with phenix and i tried to do it via AutoMR. At first everything works fine, it finds a MR solution, but then i get this error: Chain too short or poor match to sequence: MYIQVLGSAAGGGFPQWNCNCVNCKGYRDGTLKATARTQSSIALSDDGVHWILCNASPDIRAQLQAFAPMQPARALRDTGINAIVLLDSQIDHTTGLLSLREGCPHQVWCTDMVHQDLTTGFPLFNMLSHWNGGLQWNRIELEGSFVIDACPNLKFTPFPLRSAAPPYSPHRFDPHPGDNLGLMVEDTRTGGKLFYAPGLGQVDEKLLAMMHGADCLLVDGTLWEDDEMQRRGVGTRTGREMGHLAQNGPGGTLEVLDGFPRQRKVLIHINNTNPILDENSPERAEVLRRGVEVAFDGMSIELL NOTE: chain A (residues 1-304) MYIQVLGSAAGGGFPQWNCNCVNCKGYRDGTLKATARTQSSIALSDDGVHWILCNASPDIRAQLQAFAPMQPARALRDTGINAIVLLDSQIDHTTGLLSLREGCPHQVWCTDMVHQDLTTGFPLFNMLSHWNGGLQWNRIELEGSFVIDACPNLKFTPFPLRSAAPPYSPHRFDPHPGDNLGLMVEDTRTGGKLFYAPGLGQVDEKLLAMMHGADCLLVDGTLWEDDEMQRRGVGTRTGREMGHLAQNGPGGTLEVLDGFPRQRKVLIHINNTNPILDENSPERAEVLRRGVEVAFDGMSIELL did not match the input sequence... ignoring alignment and rebuilding segment without sequence information. *************************************** AutoBuild Input failed Sorry, the PDB file and sequence file could not be aligned (with no gaps and >50.0% identity) Please restart the wizard... You have several possibilities to try .... You can set rebuild_in_place=No You can set input_sequence_file=None You can set min_seq_identity_percent to a lower value You can set highest_resno to a higher value You can specify start_chains_list if your PDB file sequence starts with a residue number greater than the number of residues in the sequence. what can i do now? the pdb file has nearly the same sequence (2 mutations) but he says that he can't align them, i use a .dat file for this is this correct? i also have a fasta line in it >... but it doesn't work without this line either. i tried with different phenix versions and have always the same problem Any suggestions would be appreciated.

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refinement of a ligand with alternate conformations in one region but not the other.
by Pascal Egea 26 May '09

26 May '09

Dear All, I am refinining a protein-NAD complex structure at ~1.9A resolution. I have included a main conformation for my NAD ligand but while I see clearly the position for the nicotinamide- first ribose part, my density bifurcates when it comes to the second ribose-adenine. It seems that I have two (at least) conformations for this part of the ligand molecule. Can I refine these two alternate conformations in Phenix knowing that a part of the ligand will be common (have an occupancy of one) while the two other ones will be separate? Do I need to enter two ligand molecules or do I have to do more elaborate things? Last question is it possible that for the variable regions I may end up with a sum of occupancies that is not 1 while for the fixed region it might end up being one? That's three questions for the wizards. Thanks in advance. Pascal Egea UCSF

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Attaching H onto phosphate group and ATP
by Young-Jin Cho 25 May '09

25 May '09

Hello phenix users, I am wondering if phenix.elbow can attach H onto phosphate group for refinement. The reason for that, based on different pH environment, phosphate group should have different charges with respect to how many protons attached. In addition, how can I know normal distance restraints such as ATP? What I only know from the coot is that it shows P-O bond length is 1.61A and P-O bond (delocalized double bond) is 1.5A. The reason for this is, I heard about phosphate ion, if it is protonated, then the bond length of HO-P is longer than that of non-protonated O-P. I want to try if is true for ATP as well. Is there anyone who knows practically testing this fact by using phenix? Thanks in advance, YoungJin

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