- phenixbb - phenix-online.org

Rosetta-MR - How long does it take?
by Tri Ngo 27 Jan '12

27 Jan '12

Hi Phenix users, I tried to utilize the Rosetta-MR to solve an Esterase structure (389 residues, 2 molecules/asu) which has 22% sequence identity to the know structure. I used HHPred to prepare the alignment input and Robetta fragment server to generate the fragment files. I also performed a quick test of mr-rosetta by running the command phenix_regression.wizards.test_command_line_rosetta_quick_tests. I think there is no error on my input files or the system. However, the program never finished. It still shows me the "Placing Model..." status. It's running around 48 hours and still show the same log file (at "Running group of place_model" step). I am not sure if it's normal to wait days or weeks to get the work done when running Rosetta-MR? Thank you for your helpful input. Best wishes, Tri -- * TriNgo * Structural Biology Lab School of Medicine - Sungkyunkwan University Phone: 031-299-6150 Cell: 010-7774-8210

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Problems with opening Coot and Firefox from gui under RHEL 6.2
by Brick, Peter 26 Jan '12

26 Jan '12

Hi, I've installed Phenix 1.7.3-928 on a linux workstation by downloading the binary phenix-installer-1.7.3-928-intel-linux-2.6-x86_64-fc3.tar I'm running Red Hat Enterprise Linux Workstation release 6.2. (Mainly 64 bit libraries but some additional 32 bit libraries that are necessary to run Alwyn Jones' 32 bit version of O.) *Help and Firefox* When I click on the Help icon in the Phenix GUI I get the message: [pbrick@pb1 ~/test]$ phenix phenix_gui.htm Using browser /usr/bin/firefox phenix_gui.htm Using browser /usr/bin/firefox /usr/lib64/firefox-3.6/firefox: symbol lookup error: /usr/lib64/libgnome-2.so.0: undefined symbol: g_dgettext But if firefox is already running it opens a new tab and I receive no error message. Firefox is the version shipped with RHEL 6.2: firefox 3.6.24 (I notice that the mozilla website is offering version 9.0.1 for i686 processors.) *Starting Coot* When I click on the Coot icon in the Phenix gui no window opens but I can see the processes: coot, coot_build_phenix_coot.csh and coot-real running. In fact coot-real consumes 100% of the cpu of one of the cores. What I find really weird is if I look at the processes with the system monitor gui and right click and 'kill' coot-real then instead of killing the process the coot window opens. At the same time coot_build_phenix_coot.csh disappears and the cpu usage drops to zero. (Note: I've also tried the fc12 version. I found that the version of pymol distributed with phenix uses 32 bit libraries and I needed to install libXmu.so.6) Any suggestions as to what I might be doing wrong? Peter

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a story of acetoacetate decarboxylase
by Kevin Jin 26 Jan '12

26 Jan '12

Dear all, I wrote a story for acetoacetate decarboxylase catalysis. I hope you will like it. http://www.jinkai.org/AAD_history.html http://www.jinkai.org/AAD_catalysis.html Regards, Kevin

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Bond to symmetry mate
by Eike Schulz 26 Jan '12

26 Jan '12

Dear phenixbb, I am sure this is a trivial problem encountered before and that there is a solution to it however, I was unfortunately not able to solve it myself or with the help of the online documentation. The problem: In one of my structures a nucleic acid chain extends over several symmetry mates. How can I create and refine a bond (in my case 5'-phosphate to 3'-end ) to that symmetry mate? Many thanks in advance Eike

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Twin_law in GUI Phenix Refinement
by Tri Ngo 25 Jan '12

25 Jan '12

Hi phenix users, I have two questions when using Phenix Refinement. 1. I'd like to run phenix refinement with twin data but I don't know how to define twin_law using GUI Phenix refinement module in Linux. 2. I used phenix refinement in Windows to refine a 2.3A structure. My problem is the Rfree is quite high. - I applied twin refinement + TLS + NCS and SA refinement (wxu_scale = 1) Start: r_work = 0.2149 r_free = 0.2833 bonds = 0.016 angles = 1.988 Final: r_work = 0.2029 r_free = 0.2735 bonds = 0.008 angles = 1.448 - Then I use auto-weight to optimize the Rfree. optimize_xyz_weight = True optimize_adp_weight = True wxc_scale = 0.5 wxu_scale = 1 Start: r_work = 0.2152 r_free = 0.2735 bonds = 0.008 angles = 1.322 Final: r_work = 0.2309 r_free = 0.2781 bonds = 0.003 angles = 0.848 I think the bond rmsd and angle rmsd were too small in this final refinement. Do you think it's normal or I need to try more? Thank you very much for your helpful input. Best wishes, -- * TriNgo * Structural Biology Lab School of Medicine - Sungkyunkwan University Phone: 031-299-6150 Cell: 010-7774-8210

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model_vs_data
by Karolina Michalska 25 Jan '12

25 Jan '12

Hi everybody, I 've run model_vs_data for one of my structures and here is what I got: Information extracted from PDB file header: program_name : REFMAC year : None r_work : 0.15793 r_free : 0.19845 high_resolution : 1.45 low_resolution : 36.92 sigma_cutoff : None matthews_coeff : None solvent_cont : None TLS : False (number of groups: 0) After applying resolution and sigma cutoffs: n_refl_cutoff : 26357 r_work_cutoff : 0.1450 r_free_cutoff : 0.1687 Can someone, please, explain why there is such a big difference in R values? When I do refinement in phenix I get practically the same results that Refmac produces. Thanks, Karolina

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links in phenix
by Christian Roth 25 Jan '12

25 Jan '12

Hi, I have a pdb with a sugar chain as ligand. I used phenix ready set to get the links according to the link remarks in the pdb. However when I look into the edits file. All links are defined as geometry restraints and despite it is alpha 1-4 all bond restraints differ slightly in their length. Within the pdb file the definitions for the links were set to alpha1-4. A Similar thing happend with a peptide link between 2 Aminoacids which have not a continously numbering because of a deletion, but it is a simple peptide bond. I modified the .link.edits file accordingly for the sugars like this ---------- refinement.geometry_restraints.edits { apply_cif_link { data_link = ALPHA1-4 atom_selection_1 = name O4 and chain B and resname GLC and resseq 1 atom_selection_2 = name C1 and chain B and resname GLC and resseq 2 } } ------------ And applied a trans link for the peptide bond I added the modified file as additional parameter file in the gui. However in the final .eff file I found just the old restraints from the previous run. In the final .eff file it is stated that the file with my updated links is loaded ------ gui { base_output_dir = "/homes/roth/structure/250/082_c2_5/refinement/phenix" tmp_dir = "/homes/roth/structure/250/082_c2_5/refinement/phenix/phenix/tmp" send_notification = False notify_email = "christian.roth(a)bbz.uni-leipzig.de" add_hydrogens = True skip_rsr = False phil_file = "/homes/roth/structure/250/082_c2_5/refinement/phenix/refmac20link.link.edits" ----- Somehow the old restraits are already in the .eff file and the new ones are ignored how I could I avoid this. Simply closing the GUI an reopening? A second question is a very non standard peptide link due to a SNN residue in the chain. Based on the link a geometry restrain is created througn phenix.link_edits There is a slight difference in the length between the N- terminal and the C-terminal peptide bond. Which is probably fine and the resoution is good enough (roughly 2 Ang.) that is looks fine, but no angle definitions for phi psi and so on are stated. What is the best way to define this two bonds correctly for the subsequent refinement? A third question is a alpha1-4 link which extend to a symmetry related sugar. How I incorporate the symmetry information into the link? A last question regarding the hydrogens in refinement. For rebuilding it is nice to remove the hydrogens. Normally I use the commandline for this purpose. But It would be nice to do it automatically after refinement as a third pdb output in addition to the two standard outputs phenix_output.pdb and the phenix_output_reduce.pdb. Is there an option in the GUI to do this automatically. I thought I have seen this previously but cannot find it anymore I am sorry for this long Mail and so many question. I hope you could help me to clarify some the things. Best Regards Christian

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DEN Refinement in phenix 1.7.3
by Eike Schulz 24 Jan '12

24 Jan '12

Dear phenixbb, I have noticed that in (since?) the latest release it is possible to activate DEN refinement in phenix.refine. I assume this refers to deformable elastic networks right? What is your experience with DEN refinements ? As I could not find any reference to it in the documentation I would be happy to have feedback on when to use and when to avoid it e.g. resolution limits etc. and what to watch out for. Many thanks in advance Eike

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cif files
by Shya Biswas 23 Jan '12

23 Jan '12

Hi all, It appears that the cif file generated from prodrg (REFMAC format) is not recognised by phenix during refinement. Did anyone have similar issues or i am doing something wrong? somehow the geometries obtained from elbow are not right for my ligand so had to use prodrg to generate cif files. thanks, Shya

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Refinement of two co-factors/ligands at the same position
by Kornelius Zeth 23 Jan '12

23 Jan '12

Dear all, how can I refine two different co-factors/ligands ('XXX and YYY', with differing occupancy and cif-Files) located at the same position within an enzyme? What about the chain IDs, segment IDs etc? Thanks and best wishes Kornelius -- Kornelius Zeth ZMBP, Uni-Tuebingen Auf der Morgenstelle 1 72076 Tübingen Germany

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