- phenixbb - phenix-online.org

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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installing phenix 1.5-2
by Tirumala Kumar Chowdary 02 Oct '09

02 Oct '09

Hi, My 1.5-2 build installation is failing with this error 'installing binary components making directory build-binary/intel-linux-2.6-x86_64/beryl/tmp/binary gzip: /nfs/home/chowdary/Download/phenix-installer-1.5-2/bundles/bundle-1.5-2-intel-linux-2.6-x86_64.tar.gz: invalid compressed data--format violated finding installed versions finding binary versions cat: build/intel-linux-2.6-x86_64/version: No such file or directory no pre-existing binary components detected installing new binary package configuring PHENIX components Error configuring: see /nfs/home/chowdary/Download/phenix-installer-1.5-2/build-binary/intel-linux-2.6-x86_64/beryl/log/binary.log for details' and the log file shows this error. /bin/tar: Unexpected EOF in archive /bin/tar: Unexpected EOF in archive /bin/tar: Error is not recoverable: exiting now /nfs/home/chowdary/Download/phenix-installer-1.5-2/bin/install-from-binary: line 349: /nfs/home/chowdary/phenix/phenix-1.5-2/build/intel-linux-2.6-x86_64/base/bin/python: No such file or directory. Earlier builds (1.4.175) are installing and running fine on the same machine. Help please.. Tirumal

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RESOLVE question
by Peter Grey 01 Oct '09

01 Oct '09

Hello, We use iterative cycles of manual building (coot) - refinement (phenix) - density modification to improve maps for the next building step (RESOLVE). Should we use FMODEL,PHIFMODEL from phenix or FCALC,PHIFCALC in the input to RESOLVE. MODEL structure factors are closer to experimental ones but are they better for density modification purposes ? I think that if the program uses , as in DM, only Fobs and phases to calculate the maps then PHIFCALC is better (no contribution of solvent) but if the programs calculates 2Fo-Fc maps then FMODEL,PHIFMODEL is better since it was shown that these maps are beter when bulk solvent correction is used. Could you please comment whether this reasoning is correct and give information as to which is the case in resolve. Thanks, -- Peter

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Re: [phenixbb] refining sugars
by Jose M Casasnovas 01 Oct '09

01 Oct '09

Dear Ralf. I just solved the problem with the sugar refinement. Somehow the way the BETA1-4 cif defines the link is in the reverse order to the NAG-ASN cif link (at least to way I was used to do it). In the NAG-ASN cif, residue_selection_1 in the phenix.refine input must be the NAG and residue_selection_2 the ASN, such as I was used to do in CNS. However, the BETA1-4 cifs follows the opposite way: residue_selection_1 must be the first sugar residue (linked through O4) and residue_selection_2 the second sugar (linked through the C1), which is the most distant residue to the Asn. Thanks so much for your help and to all who sent comments and suggestions. Jose M Casasnovas -- Centro Nacional de Biotecnología (lab. B16) CSIC, Campus UAM Darwin 3 28049 Madrid Spain Ph. 34 915854917(8) Fax. 34 915854506 email: jcasasnovas(a)cnb.csic.es

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Re: [phenixbb] refining sugars
by Engin Ozkan 30 Sep '09

30 Sep '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 30 Sep '09

30 Sep '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 30 Sep '09

30 Sep '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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Phenix version 1.5 Released
by Paul Adams 30 Sep '09

30 Sep '09

The Phenix developers are pleased to announce that version 1.5 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.5-2) are: - A new Graphical User Interface (accessed by typing phenix at the command line) - Two-way communication with Coot - The latest version of Phaser (2.2) - A development version of torsion angle dynamics available in phenix.refine - Real space refinement in phenix.refine - New GUIs for Autosol, AutoBuild and LigandFit wizards - A number of MolProbity and other validation tools now available - Fast loop building with phenix.fit_loops - Improved ligand geometry generation with phenix.elbow - Inclusion of Nicholas Sauter's LABELIT system for autoindexing and more For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology 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: Patty Jimenez [ PAJimenez(a)lbl.gov ] [ 1-510-486-7963 ] --

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anomalous difference map demonstration in pymol
by crystallogrphy 30 Sep '09

30 Sep '09

Hi, I have used anomalous data to do refinement. The crystal diffracts to 3.5A. The resulting mtz file shows good anomalous density around the heavy atoms. Now I want to demonstrate the density in Pymol. Does anyone know how to generate the map use the map file in MTZ format in Pymol? Thanks!

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