September 2009 - phenixbb - phenix-online.org

Can PHENIX write the peak list to a PDB file?
by Joe Krahn 04 Dec '10

04 Dec '10

PHENIX has an option to find positive and negative peaks, but only lists them in the log file along with the residue they are closest to. Is it possible to write out the actual peak coordinates, such as to a PDB file? Thanks, Joe Krahn

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Bad ligand parameters
by Joe Krahn 21 Oct '10

21 Oct '10

I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies? Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters. Joe Krahn

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Re: [phenixbb] phenix.automr ensemble/component question
by Thomas C. Terwilliger 24 Jul '10

24 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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Using LigandFit to identify unknown density
by Katya Heldwein 28 Jan '10

28 Jan '10

Hi, I'd like to run LigandFit to identify a small molecule accounting for an unknown density. How do I do that, preferably, in a command-line mode? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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Re: [phenixbb] sigma cutoff
by Kay Diederichs 01 Dec '09

01 Dec '09

> > > Hi, > > According to the Phenix manual, phenix.refine uses no sigma cutoff by > default. Since I haven't changed this manually, why do I see in my pdb > file MIN(FOBS/SIGMA_FOBS) 1.340? > > Thanks for help, > Karolina > > This one I can answer because I asked myself the same question recently. The answer is that Phenix does not impose any sigma cutoff, but rather your data are such that the minimum value of Fobs/Sigma_Fobs is 1.34 . You can verify this for yourself by going through your reflection file, line by line, and calculating Fobs/Sigma_Fobs for each reflection. You will find that all your reflections have a Fobs/Sigma_Fobs larger or equal to 1.34 . So it has nothing to with phenix; phenix just reports a property of your data. An easier way than doing it "manually" is using CCP4 sftools for calculating a new column "ratio", writing out the resulting MTZ file, and looking at this with mtzdmp. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz

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Does PHENIX exclude Rfree reflections in maps?
by Joe Krahn 03 Oct '09

03 Oct '09

Does PHENIX exclude R-free reflections when computing maps? IMHO, it is bad to use test reflections in maps, or anywhere else other than computing R-free, but opinions vary. If some people still want test reflections in maps, maybe it could be an option. Thanks, Joe Krahn

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Re: [phenixbb] refining sugars
by Engin Ozkan 01 Oct '09

01 Oct '09

I just answered Jose's question on this yesterday. The reason you are having trouble is that there is no NAG-NAG link. It is a BETA1-4. Read the post to see what data_link names are allowed, and use them for your sugars. Below is a copy-paste of my post from yesterday: >That's because there is no such data link as NAG-NAG-B-D. Instead, you >should use a BETA1-4 link. This is similar to what CNS used, if you are >familiar with that (I think it was B14 in CNS). >If you want to know where all the phenix link definitions are, type > >phenix.where_mon_lib_list_cif > >and read the file that's listed. > >It is good to read this to know which residue selection is selection_1 >and which is selection_2. In it you'll see this or something like this. > >data_link_BETA1-4 ># >loop_ >_chem_link_bond.link_id >_chem_link_bond.atom_1_comp_id >_chem_link_bond.atom_id_1 >_chem_link_bond.atom_2_comp_id >_chem_link_bond.atom_id_2 >_chem_link_bond.type >_chem_link_bond.value_dist >_chem_link_bond.value_dist_esd > BETA1-4 1 O4 2 C1 single 1.439 0.020 >loop_ >_chem_link_angle.link_id >_chem_link_angle.atom_1_comp_id >_chem_link_angle.atom_id_1 >_chem_link_angle.atom_2_comp_id >_chem_link_angle.atom_id_2 >_chem_link_angle.atom_3_comp_id >_chem_link_angle.atom_id_3 >_chem_link_angle.value_angle >_chem_link_angle.value_angle_esd > BETA1-4 1 C4 1 O4 2 C1 108.700 3.000 > BETA1-4 1 O4 2 C1 2 O5 112.300 3.000 > BETA1-4 1 O4 2 C1 2 C2 109.470 3.000 > BETA1-4 1 O4 2 C1 2 H1 109.470 3.000 >loop_ >_chem_link_tor.link_id >_chem_link_tor.id >_chem_link_tor.atom_1_comp_id >_chem_link_tor.atom_id_1 >_chem_link_tor.atom_2_comp_id >_chem_link_tor.atom_id_2 >_chem_link_tor.atom_3_comp_id >_chem_link_tor.atom_id_3 >_chem_link_tor.atom_4_comp_id >_chem_link_tor.atom_id_4 >_chem_link_tor.value_angle >_chem_link_tor.value_angle_esd >_chem_link_tor.period > BETA1-4 BETA_1 1 O4 2 C1 2 C2 2 C3 0.00 20.0 1 > BETA1-4 BETA_2 1 C4 1 O4 2 C1 2 C2 0.00 20.0 1 > BETA1-4 BETA_3 1 C3 1 C4 1 O4 2 C1 0.00 20.0 1 >loop_ >_chem_link_chir.link_id >_chem_link_chir.atom_centre_comp_id >_chem_link_chir.atom_id_centre >_chem_link_chir.atom_1_comp_id >_chem_link_chir.atom_id_1 >_chem_link_chir.atom_2_comp_id >_chem_link_chir.atom_id_2 >_chem_link_chir.atom_3_comp_id >_chem_link_chir.atom_id_3 >_chem_link_chir.volume_sign > BETA1-4 2 C1 1 O4 2 O5 2 C2 positiv > >Engin On 9/30/09 10:56 AM, Tirumala Kumar Chowdary wrote: > Thanks for the reply, > > here is part of the log file, which shows the parameter input for nag > refinement > > > Monomer Library directory: > "/usr/local/phenix/phenix-1.4-125/chem_data/mon_lib" > Total number of atoms: 6260 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain C and resname NAG and resid 1670 > residue_selection_2: chain A and resname ASN and resid 670 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain C and resname NAG and resid 1784 > residue_selection_2: chain A and resname ASN and resid 784 > apply_cif_link: > data_link: NAG-NAG > residue_selection_1: chain C and resname NAG and resid 1784 > residue_selection_2: chain C and resname NAG and resid 1785 > Number of models: 1 > Model: "" > Number of chains: 3 > Chain: "A" > Number of atoms: 5125 > Number of conformers: 1 > Conformer: "" > Number of residues, atoms: 681, 5125 > > I am presuming that it read what ever it needs to make the ASN-NAG > bonds and NAG-NAG bonds. > > what am I missing here ? > > Tirumal > > > Quoting Engin Ozkan<eozkan(a)stanford.edu>: > >> You don't need to create cif files; phenix has them. NAG is definitely >> there, and you can have two NAGs linked by any biologically-relevant >> glycosidic bond you want. You need to define the links, however. I think >> posting the cif_link.params may get you more help. >> >> Engin >> >> On 9/30/09 8:49 AM, Tirumala Kumar Chowdary wrote: >>> Hi, >>> >>> My question is related to the 'refining sugars in phenix' questions >>> that have been appearing on the bb for the last two days. >>> >>> I am trying to refine my NAGs and somehow phenix is ignoring the sugars >>> in my structure. Neither it is making a bond between my ASN and NAG nor >>> NAG-NAG bond. My nag-nag.cif and cif_link.params are read properly, >>> though. >>> >>> I am using in version 1.4.125 still. Is this the problem ? Does >>> upgrading to any of the later build will help ? >>> >>> >>> Tirumal >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >> >> >> -- >> Engin Özkan >> Post-doctoral Scholar >> Howard Hughes Medical Institute >> Dept of Molecular and Cellular Physiology >> 279 Campus Drive, Beckman Center B173 >> Stanford School of Medicine >> Stanford, CA 94305 >> ph: (650)-498-7111 >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > > -- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111

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GUI fonts
by Frank von Delft 01 Oct '09

01 Oct '09

Hi, I've just been poking around the new GUIs - neat!! But the font is absolutely enormous, which is terrifically annoying. Where do I change it? (I didn't see it in the preferences.) Cheers phx

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refining sugars
by Tirumala Kumar Chowdary 01 Oct '09

01 Oct '09

Hi, My question is related to the 'refining sugars in phenix' questions that have been appearing on the bb for the last two days. I am trying to refine my NAGs and somehow phenix is ignoring the sugars in my structure. Neither it is making a bond between my ASN and NAG nor NAG-NAG bond. My nag-nag.cif and cif_link.params are read properly, though. I am using in version 1.4.125 still. Is this the problem ? Does upgrading to any of the later build will help ? Tirumal

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N-linked glycans in phenix.refine
by Jose Casasnovas 30 Sep '09

30 Sep '09

Dear Phenix users. I am trying to refine N-linked glycans in phenix. The Asn-NAG link appears to be recognize by the program, but the NAG-NAG link is not. I guess the cif_link must be missing. Monomer Library directory: "/home/soft/phenix/phenix-1.4-3/ext_ref_files/mon_lib" Total number of atoms: 8947 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain N and resname NAG and resid 5161 residue_selection_2: chain E and resname ASN and resid 516 apply_cif_link: data_link: NAG-NAG-B-D Sorry: Missing CIF link: data_link_NAG-NAG-B-D Please check for spelling errors or specify the file name with the link as an additional argument. How can I get the required cif_link file and where to place it?? Any suggestion. Thanks. Jose

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