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Re: [phenixbb] Elbow and smiles to make CO coordinates
by Yarrow Madrona 08 Jul '11

08 Jul '11

Thanks! Didn't realize it was so easy. > For getting carbon monoxide coordinates: In coot, go to File > Get > Monomer... > Type in "CMO" and click OK. > > A carbon monoxide molecule will po up in the middle of the window > (provided everything is set up correctly). > > If you are trying to fit an electron density, place that density in the > middle of the window before you retrieve the ligand. > > Hope that helps. > > Cheers! > MM > > On Jul 8, 2011, at 1:41 PM, Yarrow Madrona wrote: > >> >> Hi, >> >> I am trying to use Elbow and smiles to generate carbon monoxide >> coordinates. I thought it would be easy enough. I made two waters in >> coot >> and changed the the oxygens to C and O and set the distance around 1.13 >> angstrom. Saved these coordinates as a PDB. I then used this in Elbow >> but >> it gives me a methyl group. Not sure what is going on. Any help would >> be >> appreciated. Thank you! >> >> -Yarrow >> >> -- >> Yarrow Madrona >> >> Graduate Student >> Molecular Biology and Biochemistry Dept. >> University of California, Irvine >> Natural Sciences I, Rm 2403 >> Irvine, CA 92697 >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > > -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Elbow and smiles to make CO coordinates
by Yarrow Madrona 08 Jul '11

08 Jul '11

Hi, I am trying to use Elbow and smiles to generate carbon monoxide coordinates. I thought it would be easy enough. I made two waters in coot and changed the the oxygens to C and O and set the distance around 1.13 angstrom. Saved these coordinates as a PDB. I then used this in Elbow but it gives me a methyl group. Not sure what is going on. Any help would be appreciated. Thank you! -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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AutoSol question
by Laurie Betts 08 Jul '11

08 Jul '11

If I want to run Autosol with a set of previously determined heavy atom positions (seleno-Met protein) that I might have edited, and NOT search for any more sites, just use those sites for phasing and density modification and model building, I can't seem to find in any of the parameter buttons a way to do this - every time I try it seems to just re-run hyss and find the same sites again. It seems to find multiple Se sites on top of each other that are closer than the minimum distance I specified in the input. Thanks LAurie Betts

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NCS Question
by Yuri 07 Jul '11

07 Jul '11

Dear PHENIX community, Could someone please point me toward a good paper on NCS? Cheers, -- Yuri Pompeu

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SA omit map
by Tjaard Pijning 06 Jul '11

06 Jul '11

Hi, I would like to generate an SA-omit Fo-Fc map for a ligand bound to protein. Using the GUI I selected the AutoBuild-Create Omit Map module and set the following : - data.mtz - protein.pdb (no ligand, no solvent) = start model - ligand.pdb (just ligand) = omit map atoms - omit map type = simulated annealing - omit region = omit around pdb The resulting map (/OMIT/resolve_composite_map.mtz) shows density for both the protein and the ligand. When I feed this into the CCP4 module FFT to generate an nF1-mF2 map (with n=1 and m=1) I still get density for both the protein and ligand. However I need only the ligand Fo-Fc density. What is the right way to do this ? Thanks, Tjaard Ing. Tjaard Pijning Research Assistant Protein Crystallography Group Nijenborgh 7 9747 AG Groningen The Netherlands (31)(0)50 363 43 85

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Re: [phenixbb] phenix.mr_rosetta: Inconsistent query numbering
by Thomas C. Terwilliger 06 Jul '11

06 Jul '11

Hi Pietro, There is something that phenix.mr_model_preparation cannot read in Japanin.hhr (attached): phenix.mr_model_preparation Japanin.hhr gives the same error. I'll copy Gabor Bunkoczi and see if he can help with this. All the best, Tom T >> Dear all, >> >> my run of phenix.mr_rosetta stops with: >> >> ******************* ERROR ENDING *************** >> Inconsistent query numbering >> >> ******************* ERROR ENDING *************** >> >> I attach script and logfiles. >> >> Any suggestions? >> >> Thanks >> >> Pietro >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Validation question: R-factor (all) and # of unique reflections (all)
by Young-Jin Cho 05 Jul '11

05 Jul '11

Hi everyone, While I am trying to deposit, I am faced with several things that I am not sure: FYI. I am in the <Refinement Statistics> section (Auto Dep Input Tool) in the PDB bank. Most values are came from pdb file that was made from phenix.refine but it asks me "R-factor (all)" that satisfy the limits established by high & low resolution cut off and "number of unique reflections (all)". My simple question is if phenix has those kind of information, if so where I can find them. Another question is if I changed water (deletion or changed occupancy) based on 'precheck', should I run phenix.refine again to get R/Rfree values in correct? I am not sure if these are captured by PDB automatically or not. (seemingly they do like that at this point but not 100% sure yet.) With many thanks~ Young-Jin

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Re: [phenixbb] Validation question: R-factor (all) and # of unique reflections (all)
by Pavel Afonine 05 Jul '11

05 Jul '11

Hi Young-Jin, > I feel like I should calculate R(all). As mtz file is usually big, > how can I extract Fobs and Fmodel from phenix generated mtz file? If you feel you want it, then go ahead, and this command might be of help here: phenix.mtz.dump data.mtz --column-data-format=spreadsheet -c Yet another (easier) alternative is to run a dummy phenix.refine run like this: phenix.refine data.mtz model.pdb xray_data.r_free_flags.ignore_r_free_flags=true main.number_of_mac=1 strategy=none output.prefix=junk then take the reported R-factor (Rwork will be equal to Rfree, so take any of them), and discard the files. All the best! Pavel.

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phenix.mr_rosetta: Inconsistent query numbering
by Pietro Roversi 05 Jul '11

05 Jul '11

Dear all, my run of phenix.mr_rosetta stops with: ******************* ERROR ENDING *************** Inconsistent query numbering ******************* ERROR ENDING *************** I attach script and logfiles. Any suggestions? Thanks Pietro

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Ligand woes
by José Trincão 05 Jul '11

05 Jul '11

Hello all, I have been having very weird problems refining a structure with several ligands. The weirdest problem is that if I try to run ligand fit giving just the name of the ligands, no problem - it finds the ligands (FAD and MTE). I save the pdb with all the ligands in and phenix.refine complains that MTE is not recognised, I have to run ready-set. I do it. Run phenix.refine again, and now it complains with the following: Number of atoms with unknown nonbonded energy type symbols: 116 "HETATM18439 C1' MTE A3003 .*. C " "HETATM18441 C2' MTE A3003 .*. C " "HETATM18443 C3' MTE A3003 .*. C " "HETATM18444 O3' MTE A3003 .*. O " "HETATM18474 N9A FAD A3005 .*. N " "HETATM18475 C8A FAD A3005 .*. C " "HETATM18476 N7A FAD A3005 .*. N " "HETATM18477 C5A FAD A3005 .*. C " "HETATM18478 C6A FAD A3005 .*. C " "HETATM18480 N1A FAD A3005 .*. N " ... (remaining 106 not shown) Any help will be greatly appreciated. Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

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