- phenixbb - phenix-online.org

Latest Build Error
by Yuri 22 Jul '11

22 Jul '11

I installed the latest dev-826 version and the GUI does not open phenix_refine. I get a fatal error message. thank you -- Yuri Pompeu

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restraints for D3O+ give problems to run in phenix.refine
by Maxime Cuypers 22 Jul '11

22 Jul '11

hello, apologies if this problem has already been reported, i browsed for a while and i am running out of ideas to solve my problem. i have a neutron structure i was refining fine with phenix.refine untill i had to add a D3O water. description: running phenix.elbow or phenix.refine with .cif file for D3O i am getting the following error: ... Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O D3O W 1 " occ=0.53 ... (2 atoms not shown) pdb=" D3 D3O W 1 " occ=0.53 Number of atoms with unknown nonbonded energy type symbols: 3 "HETATM 2 D1 D3O W 1 .*. D " "HETATM 3 D2 D3O W 1 .*. D " "HETATM 4 D3 D3O W 1 .*. D " Time building chain proxies: 0.01, per 1000 atoms: 2.50 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 3 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). ******************* i then modified the .param file implementing the apply_cif_modification and apply_cif_link parameters: refinement { main { number_of_macro_cycles = 10 ordered_solvent= false scattering_table= neutron } hydrogens { refine= individual } pdb_interpretation.apply_cif_modification { data_mod = D3O residue_selection = resname D3O } pdb_interpretation.apply_cif_link { data_link = D3O residue_selection_1 = chain W and resname D3O } } ... ************************** the .cif file i have was created with phenix.ready_set: ( i added first line after it failed without) data_mod_D3O # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level D3O D3O Unknown ligand 4 1 . # data_comp_D3O # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z D3O O O O -0.475 -12.5180 -14.4044 -43.0985 D3O H1 D D -0.294 -11.4013 -13.8002 -42.6392 D3O H2 D D -0.294 -13.3333 -13.3284 -43.0933 D3O H3 D D 0.063 -12.3324 -14.5311 -44.0190 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd D3O O H1 single 1.350 0.040 D3O O H2 single 1.350 0.040 D3O O H3 single 0.947 0.010 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd D3O H2 O H1 98.14 3.000 D3O H3 O H1 103.20 1.194 D3O H3 O H2 103.22 1.252 ********************************** whatever i do i systematically get the same error: Monomer Library directory: "/usr/local/phenix-1.7.1-743/chem_data/mon_lib" Total number of atoms: 1165 Number of models: 1 apply_cif_modification: data_mod: D3O Sorry: Missing CIF modification: data_mod_D3O Please check for spelling errors or specify the file name with the modification as an additional argument. ******************************** the command i enter is: phenix.refine xxxx.pdb xxxx.mtz D3O.ligands.cif high_res_xxxx-neutron-long-D3O.params \ refinement.input.xray_data.labels='IMEAN,SIGIMEAN' i looked in the online phenix.refine manual but it is not mentionning what to do in such error case. where should i put "data_mod_D3O" in the parameter file? is it the real source of the error? Could someone help me figuring out a solution to get the restraints to work for D3O(+), please? Maxime

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Protein expression, purification and crystallization
by Hena Dutta 21 Jul '11

21 Jul '11

Dear Members of CCP4BB and PHENIXBB, Can you suggest a reliable website where I can get basic and advanced information on protein expression, purification and crystallization. I like to read on the monitor. Thanking you in advance... Hena

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phenix.phaser PATH problem
by G P 21 Jul '11

21 Jul '11

Dear all, It's long story: At beginning, I have phenix installed. I do not have CCP4 installed. Then I run "phenix.phaser params.eff" to call phenix run phaser from script params.eff. It works well. Then, I installed CCP4 with its own phaser inside. Then I run again "phenix.phaser params.eff". The computer start to import files (should be some libraries and supporting files, not input data) from CCP4 installation directory. It seems so strange for me. And because some of the .so files in CCP4 directory are for 32bit, phenix.phaser gave me error message: wrong ELF class: ELFCLASS32 and refused to keep running. I guess I could solve this problem by copying the same .so file in phenix directory into CCP4's directory. What I really want to know is why this happen. Is that the installation of CCP4 changed some kinds of PATH variables for phenix? How could I fix by giving a right path again? I would appreciate to any help. Thanks a lot guys! Best regards, GP

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phenix.phaser multiple models
by G Y 21 Jul '11

21 Jul '11

Dear all, I want to give several input pdb (searching model) at same time and let phaser run MR separately on each of them. I found I can do this by first "Add ensembles" at Ensemble tab and then "Add search" at Search procedure tab then link the correct ensemble ID. However, there is just one output result for the best solution. Is there anyway to get all solutions in separate .mtz and .pdb files for different searching models? Many thanks! regards, G

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problem in rosetta rebuilding
by intekhab alam 20 Jul '11

20 Jul '11

Hi i tried to run rosetta on a unix machine (ubuntu 9.04) for my data. Upto MR step everything goes fine , but during the rebuilding step after 20 cycles the computer shuts down. i have attached the log file for the autobuilding run of rosetta. i am using phenix 1.7.1-743 version. i will be grateful if some one helps me out -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Phenix TLS refined model feeding into next round of refinement
by Daqi Tu 20 Jul '11

20 Jul '11

Hi, I used to think after one round of Phenix TLS refinement, if I need to do further refinements after correcting couple residues, I need to take out the ANISOU records from the pdb file. The reason is if not, all protein atoms might be applied anisotropic individual B factor refinement in the next round. Yesterday, I made a "mistake" directly feeding the pdb file from the previous TLS refinement into the next one. Seems it is fine. Is that true Phenix automatically recognize what I wanted, that is, TLS only, not anisotropic individual B factor refinement? Thank you. Daqi Tu

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How the sharpening were performed in PHENIX.
by zhangh1＠umbc.edu 19 Jul '11

19 Jul '11

Hi, I was trying to do a B-factor sharpening using phenix GUI CreatMaps utilities. The output for the sharpened maps contains 2FOFCWT and PHI2FOFCWT columes, so I think they are sigmaA weighted 2Fo-Fc maps. But from Brunger's paper, the sharpening coefficients seems directly applied on Fo, and I wonder what happened before we get the 2mFoDFc maps. Or, the sharpening coefficients have been applied to the 2mFoDFc maps? Thanks for any information! Hailiang

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Experimental Data Question
by Yuri 16 Jul '11

16 Jul '11

Nat, That helps clarifying things. Thank you -- Yuri Pompeu

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Experimental Data Question
by Yuri 16 Jul '11

16 Jul '11

It looks like phase_and_build only takes reflections input as F SIGF. I had to use a reflection converter as I had a .sca file with I SIGI data. -- Yuri Pompeu

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Re: [phenixbb] Experimental Data Question
by Yuri 15 Jul '11

15 Jul '11

I am not positive, because I had to convert my reflections.sca (I SIGI) into reflections.mtz (F SIGF) -- Yuri Pompeu

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Experimental Data Question
by Yuri 15 Jul '11

15 Jul '11

Hello All, Heres my situation: I collected data on a new crystal, indexed, scaled (2.75 A), ran molecular replacement (40% homologue) and found a solution. I did some building got a new model, did an initial refinement (using my .sca file, not data.mtz from mol rep). I then ran phase_and_build with density modification. The new maps look a lot better and I am able to see some residues I was not able to place before. I did some more building and I am ready to refine. What should I use as experimental data? phase and_build gave me a .mtz file with amplitudes (no I) and "experimental phase" coeeficients (HLAM. HLBM,...) Cheers -- Yuri Pompeu

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Re: [phenixbb] ADP refinement selection
by Pavel Afonine 15 Jul '11

15 Jul '11

Hi Christian, the problem is that you did not ask phenix.refine to refine the rest of the atoms isotropically (with your command below you only refine anisotropic ADPs of atoms in chain Q, and the B-factors of all the other atoms are not refined): > adp { > individual { > anisotropic = "chain Q" > } I would do it like this: adp { individual { anisotropic = chain Q and element CL isotropic = not (chain Q and element CL) } } Pavel.

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off-topic-Question
by Haytham Wahba 14 Jul '11

14 Jul '11

Dear all i have protein soaked in Dimethyltindibromide in the active site 2 cysteine and 1 aspartic acid by help of anomalous map i can see 2 Sn atoms in each subunit in AU there is difference in both subunits, Sub-A shows acetate near Sn and Sub-B show phosphate ion, even the position of one of the 2 cystein is different from unit to other 1-is it normal to see such difference between 2 subunit? also the distances between Sn and surrounding atoms does not suggest covalent binding 2-the important question is how to confirm if the 2 methyl groups or even one methyl group of dimethlytin are still there or cleaved i mean one can not differentiate between density of water and methygroup. How to define coordinate number of Heavy atom and identity of the attached atoms as you will see in the link below (with water) and (with Methyl) the map are the same and as well r-factors 3-what can i do to confirm presence or cleavage of methyl: collect more data or using other technique like exafs, Mossbauer spectroscopy could help (with water) http://dl.dropbox.com/u/12001878/Subunit-A.png http://dl.dropbox.com/u/12001878/subunit-A-anomalous.png http://dl.dropbox.com/u/12001878/Subunit-B.png http://dl.dropbox.com/u/12001878/subunit-B-anomalous.png (with methyl) http://dl.dropbox.com/u/12001878/DimethylTin-subunit-A-alt-conf.png http://dl.dropbox.com/u/12001878/DimethylTin-subunit-B.png N.B: resolution 1.7 A r factors and molprop are perfect. thank you for your time haytham biochimi canada

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Parsing error
by Yuri 14 Jul '11

14 Jul '11

Nat, Thank you. I am still using dev-814. You probably have fixed it already. ill update when I am done running these jobs. -- Yuri Pompeu

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Parsing error
by Yuri 14 Jul '11

14 Jul '11

Hello everyone, I cannot figure out why I keep getting this error. I dont see anything wrong with my PDB. I realize I realize I have breaks in my chain, as there are regions of unclear density as of now I am building in what I can see... Heres what the log says: ======== ================= Separating polymer chains into rigid bodies ================= (chain 'A' and segid ' ' and resseq 393:6) (chain 'B' and segid 'B ' and resseq 401:401) ================== Extract refinement strategy and selections ================= The error is initial RESSEQ index > final RESSEQ index. I do not understand why it is picking them this way It then halts at an error... Any Ideas?

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restraints_edite.params
by Haytham Wahba 13 Jul '11

13 Jul '11

Dear All How to get rid of restraints_edite.params in the following run of phenix.refine, i mean after using it in previous run.and what is .def files. and bond.slack Haytham Udem Biochemi Canada

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R-merge and MOLREP
by Yuri 13 Jul '11

13 Jul '11

Ed and Nathaniel, Thank you for the input. I agree with Ed. The I/sigma values for this data set are well within accepted ranges... I believe the R-merge values are due to some inherent crystal property. They grew in very strange manner. -- Yuri Pompeu

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R-merge and MOLREP
by Yuri 13 Jul '11

13 Jul '11

Hello everyone, I just collected some data on a new protein. It indexes in P3 and looks like I can scale it all the way to P 63 2 2 . My questions are: 1-I see a reasonable chi-square value 1.69 but r-merge 0.15 (0.49 at 2.75 A). It was 0.20 before I excluded some bad frames. I thought this R value is a bit high... Is it? Mosaicty was around 1.00. 2- My search model has an identity of around 40%. I tried MOLREP. Seems I got a solution LLG=486 PAK=10 TFZ ~30 RFZ ~20. My R-free before any refinement is 0.54. Two questions here, a) I think I only fully understand the meaning of LLG, what about PAK and both Z-values? b)is this R-free acceptable or is it also a little high? Thank you for any input

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Summer X-rays at the NSLS
by Robert Sweet 11 Jul '11

11 Jul '11

Summer X-rays at the NSLS The PXRR operates five beamlines at the NSLS: http://www.px.nsls.bnl.gov/. Two of these are the undulator beamlines X25 and X29. The dipole beamlines X12-B and X12-C are available, and are very effective for conventional crystallography. There are efficient ALS-Style Automounters available -- 8400 crystals mounted in the last 12 months. Also, at beamline X26-C, we have a unique-in-the-US station for combined x-ray diffraction and single-crystal optical spectroscopies: http://www.px.nsls.bnl.gov/x26c/x26c_info.html Notice also our world-leading Mail-In crystallography program: http://www.px.nsls.bnl.gov/Mailin.html You may request access to any of these here: http://www.px.nsls.bnl.gov/beamtime_requests.html, and can look at the schedules for all five here: http://www.px.nsls.bnl.gov/ Stay tuned for the announcement in December of RapiData, our annual course in rapid data collection and structure solving: http://www.bnl.gov/rapidata/ Bob Sweet ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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significant figures in reporting Rfree
by Jennifer Weinreich 11 Jul '11

11 Jul '11

Hi. I am wondering what is the common practice with respect to how many significant figures should be used for reporting Rfree at different resolution? Should we always use all 4 figures that are reported by the program? Thank you, Jenn

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How to rebuild a molecular only‏
by dingding830106＠sina.com 08 Jul '11

08 Jul '11

Dear All, There are 8 moleculars in an asymmetry unit, but only one molecular should be rebulit, what can I do ? Thanks a lot! Wei Feng

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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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NCS Restraints
by Yuri 01 Jul '11

01 Jul '11

Hi Pavel, >It's rather packing.. Say, if more than one copy packs in the > asymmetric >unit then you have NCS, roughly speaking.. So is it correct to say that in cases where you have 1 molecule per ASU, there will be no NCS only crystallographic symmetry?? > In other words, if for the same enzyme one crystal goes to 3.1 and > another 1.5 A could one have significant NCS but not the other? >I'm not sure I understood this... May some one else did? I was trying to understand if this phenomenon would be noticeable depending on the resolution only... You and Nathaniel pretty much answered this now... -- Yuri Pompeu

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NCS restraints
by Yuri 30 Jun '11

30 Jun '11

Hello, I have some fundamental questions about NCS: 1- I think its somewhat of a consensus that at higher res. it should not be used to avoid missing out "real" detailed discrepancy. Is this true? 2- Should one try to use it in lower res data (3 A and worse)? 3- Is the presence of NCS macromolecule specific, or crystal specific? In other words, if for the same enzyme one crystal goes to 3.1 and another 1.5 A could one have significant NCS but not the other? Thanks or any clarification -- Yuri Pompeu

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phenix.ligand_identification problem
by Andrzej 29 Jun '11

29 Jun '11

Dear All, I'm having problem with running ligand_identification script. All well up to the point where the ligand library is created and then for each ligand following error is displayed: Running job sequence 13, ligand 14, in /share/scratch/an... Sorry, resolve was not able to finish on the first cycle I suspect it has something to do with resolve size but there is no keyword like resolve_size for ligand_identification. I've tested my input files with 1.7.1-743 and dev-738 release - same results. Thanks in advance for the support! Regards, Andrzej -- Dr. Andrzej Lyskowski (andrzej[.]lyskowski[(a)]acib[.]at) ACIB Austrian Centre of Industrial Biotechnology GmbH Petersgasse 14, A-8010 Graz, Austria http://acib.at/ c/o IMB Institute of Molecular Biosciences, University of Graz Humboldtstraße 50,III/194, A-8010 Graz, Austria http://strubi.uni-graz.at/ +43 316 380 1993 tel +43 316 380 9897 fax

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Phenix.refine and Unusual residues
by Haytham Wahba 27 Jun '11

27 Jun '11

Version: 1.7 Release tag: 650 Platform: intel-linux-2.6-x86_64 linux User: haytham why phenix does not recognise ACT, PO4 Sn and Br (unusual residue) as you see in this part in the Log file.. (see below) Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ACT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ACT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' SN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' SN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' SN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BR': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" SN SN E 1 " occ=0.70 residue: pdb=" SN SN E 2 " occ=0.20 --------------------------------------------------------- when i try to refine specially the Tin atom (not other, ACT,...) in coot after phenix.refine. coot display ((no restraints Found,...lablabla)) ----------------------------------------------------------- this is the PDB (what is the wrong with that) HETATM 3552 O HOH S 361 11.670 -4.327 9.559 1.00 34.14 O TER 3553 HOH S 361 HETATM 3554 OXT ACT C 1 10.133 -3.417 7.937 1.00 20.00 O HETATM 3555 C ACT C 1 9.911 -2.331 7.357 1.00 20.00 C HETATM 3556 O ACT C 1 10.897 -1.607 7.183 1.00 20.00 O HETATM 3557 CH3 ACT C 1 8.550 -1.912 6.905 1.00 20.00 C TER 3558 ACT C 1 HETATM 3559 OXT ACT C 2 10.700 -2.628 9.985 1.00 20.00 O HETATM 3560 C ACT C 2 10.962 -1.952 11.000 1.00 20.00 C HETATM 3561 O ACT C 2 11.756 -2.461 11.809 1.00 20.00 O HETATM 3562 CH3 ACT C 2 10.364 -0.601 11.240 1.00 20.00 C TER 3563 ACT C 2 HETATM 3564 SN SN E 1 6.346 -4.396 -16.894 0.70 20.00 SN TER 3565 SN E 1 HETATM 3566 SN SN E 2 6.492 -2.146 -14.779 0.20 20.00 SN TER 3567 SN E 2 HETATM 3568 SN SN F 1 10.186 0.632 6.366 1.00 30.00 SN TER 3569 SN F 1 HETATM 3570 P PO4 G 1 5.763 10.047 -3.974 1.00 30.00 P HETATM 3571 O1 PO4 G 1 6.960 10.924 -4.190 1.00 30.00 O HETATM 3572 O2 PO4 G 1 4.531 10.872 -4.101 1.00 30.00 O HETATM 3573 O3 PO4 G 1 5.758 8.978 -5.017 1.00 30.00 O HETATM 3574 O4 PO4 G 1 5.835 9.456 -2.607 1.00 30.00 O TER 3575 PO4 G 1 HETATM 3576 P PO4 G 2 9.060 -4.976 -17.812 1.00 30.00 P HETATM 3577 O1 PO4 G 2 10.418 -5.179 -18.415 1.00 30.00 O HETATM 3578 O2 PO4 G 2 8.223 -4.116 -18.710 1.00 30.00 O HETATM 3579 O3 PO4 G 2 8.412 -6.316 -17.597 1.00 30.00 O HETATM 3580 O4 PO4 G 2 9.172 -4.280 -16.485 1.00 30.00 O TER 3581 PO4 G 2 HETATM 3582 BR BR H 1 9.484 11.317 -29.959 1.00 20.00 BR TER 3583 BR H 1 END

3 2

Difference Map positive peaks in release dev-798
by Yuri 27 Jun '11

27 Jun '11

I was wondering if anything changed (weights or something) in the way the difference maps are calculated? I just ran refinement on a 1.3 structure and a hexacoordinated Mg2+ ion has significant positive density peak even at occupancy 1.0. I had not noticed that before. My ligand also does have positive peaks, but refine gives it a .91 occupancy. I wonder if I am missing some parameter cif file or some definition that would make the positive peaks decrease? Thank you -- Yuri Pompeu

3 4

NCS error in Phenix 1.7.1-743
by Ngan Nguyen Bich 26 Jun '11

26 Jun '11

Dear, Thank Nat for your quick reply, I will try the new nightly build and see what happen. I hope it will fix my problem. Ngan

1 0

Difference Map positive peaks in release dev-798
by Yuri 25 Jun '11

25 Jun '11

Pavel, I just ran the same job using the last official release (743). Some differences: >When the change occurred (between which version numbers)? Some where in between 743 and dev-798. >Does the peak disappear if you do the same calculation using an older > version? Yes, I see no positive or negative peaks for the Mg ion (nor my ligand). >There is no general remedy - it's all case-dependent. >Does its B-factor differ significantly from surrounding atoms? Yes, the B-factor for the ligand is 20 on average. The surrounding residues and cofactor are 10 or below. But, as I mentioned above, I see no positive peak density this time around. -- Yuri Pompeu

2 1

NCS error in Phenix 1.7.1-743
by Ngan Nguyen Bich 24 Jun '11

24 Jun '11

Dear all, I've got a problem when rerunning the same job of my project in the new laptop. I've found that it's because of the NCS restraint groups set-up In the old computer I set two NCS restraints groups as: First group: Reference group: chain A and sidechain and resid 3:216 and not (resid 63 or resid 66 or resid 81 or resid 93 or resid 133 or resid 135 or resid 181 or resid 184 or resid 193 or resid 194 or resid 212) Second group: Reference group: chain A and backbone and resid 3:217 and not (resid 63 or resid 133 or resid 135 or resid 184) And the refine_phenix run well in the old computer, but the new laptop with the error in the end of this letter. I've found that if I delete the backbone in the second group, it runs again. So I wonder that how I could refine NCS restraint of backbone now? Thank you in advance. Ngan RuntimeError : mean() argument is an empty array Traceback: File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/libtbx/thread_utils.py", line 223, in run return_value = self._target(self._args, self._kwargs, self._c) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/libtbx/runtime_utils.py", line 58, in __call__ result = self.target() File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/runtime.py", line 68, in __call__ call_back_handler=callback) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 1278, in run reference_model_manager = self.reference_model_manager) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/strategies.py", line 322, in refinement_machine monitors.collect(step = "0 :", model = model, fmodels = fmodels) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/refinement/__init__.py", line 51, in collect rigid_body_shift_accumulator = rigid_body_shift_accumulator) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/refinement/print_statistics.py", line 263, in collect ignore_side_chain = True, File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/model.py", line 971, in geometry_statistics restraints_manager = self.restraints_manager) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/model_statistics.py", line 38, in __init__ compute_gradients = True) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/restraints.py", line 66, in energies_sites normalization=False) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 686, in energies_sites self.compute_operators(sites_cart=sites_cart) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 679, in compute_operators self.operators.append(group.operators(sites_cart=sites_cart)) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 336, in operators return _operators(group=self, sites_cart=sites_cart) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 442, in __init__ other_sites=sites_cart.select(pair[1])) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/scitbx/math/superpose.py", line 58, in __init__ self.reference_shift = reference_sites.mean() Platform info: __FILE__ = /net/patchnose/scratch1/phenix/phenix-1.7.1-743/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Apr 28 2011 __TIME__ = 02:15:10 __i386__ __APPLE_CC__ = 5367 __GNUC__ = 4 __GNUC_MINOR__ = 0 __GNUC_PATCHLEVEL__ = 1 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __VERSION__ = 4.0.1 (Apple Computer, Inc. build 5367) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 __SSE2__ = 1 BOOST_LIB_VERSION = 1_47 PY_VERSION = 2.7.1 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 4 sizeof(std::size_t) = 4 sizeof(void*) = 4 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG os.name<http://os.name>: posix sys.platform: darwin sys.byteorder: little platform.platform(): Darwin-10.7.4-x86_64-i386-32bit platform.architecture(): ('32bit', '') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 4 Memory total: 4,294,967,296 Memory free: unknown import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = √Ö

2 1

B-factor and phenix.refine+Occ+charge
by Haytham Wahba 23 Jun '11

23 Jun '11

June 23, 2011, 9:30 AM Dear all dimer in AU average B factor 21 resolution: 1.78 each subunit shows 2 Tin atoms in the active site B factor for 2 tin in chain A 15 and 19 but B factor for other 2 tin in chain B 30 and 41 41 for tin which is between the 2 cysteine (photo attached) (occ: 0.25) this one which i am worry about ((because the average B factor for the surrounding amino acid is 20)) and 30 of the other one near phoshate (occ: 0.70) 1- i tried to change the occupancy or refine the occupancy for tin trying to reduce B factor (41) it works (reduced to 30) but it gives me a +ve peak what could i do to solve this problem?? 2- other trial to define charge for that tin HETATM 3241 SN SN C 3 6.543 -2.139 -14.821 0.25 41.55 SN4+ but it was the same result. --- is this definetion for that charge is OK or it is not enough in PDB file --- is this way is understandable by phenix.refine? i mean does phenix differentiate in refinment between SN, SN2+ and SN4+?? N.B: protein soaked in DimethylTindiBromide Haytham Wahba Biochemistry UdeM Canada

3 2

Re: [phenixbb] rosetta fragment files (Thomas C. Terwilliger)
by Leonid Sazanov 21 Jun '11

21 Jun '11

Hi Tom, Thanks for that! Native support for several large chains would be very useful. Leonid > Message: 3 > Date: Thu, 16 Jun 2011 13:24:55 -0600 (MDT) > From: "Thomas C. Terwilliger"<terwilliger(a)lanl.gov> > To: "PHENIX user mailing list"<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] rosetta fragment files -- adjusting residue > numbers to combine them > Message-ID:<50912.128.165.72.7.1308252295.squirrel(a)webmail.lanl.gov> > Content-Type: text/plain;charset=iso-8859-1 > > Hi Leonid and others wanting to use phenix.mr_rosetta with large chains, > > After looking at the Rosetta code and conferring with Frank DiMaio from > the Baker laboratory... > > You can paste several fragment files together to represent your entire > chain, but you need to edit all but the first one to set the position in > the sequence file that each set of fragments goes with. > > Here is a little script that will take a fragments file that you have > created that started with residue 651 and edit it in a way that you can > just add to the end of your fragments file for residues 1-650. Run it > with: > > phenix.python adjust_robetta_resid.py \ > fragments_in fragments_adjusted 651 > > -------------------------------- > # adjust_robetta_resid.py > # use: phenix.python adjust_robetta_resid.py fragments_in > fragments_adjusted 651 > # to adjust the first residue of fragments_in to be 651 > > import sys > args=sys.argv[1:] > if len(args) != 3: > print "USE: phenix.python adjust_robetta_resid.py fragments_in > fragments_adjusted<start_resno>" > sys.exit() > file_in=args[0] > file_out=args[1] > start_resno=int(args[2]) > > print "Copying %s to %s offsetting start residue number to %d" %( > file_in,file_out,start_resno) > > f=open(file_out,'w') > new_resno=0 > for line in open(file_in).readlines(): > if line.find('position:')> -1 and line.find('neighbors:')>-1: > spl=line.split() > current_resno=int(spl[1]) > new_resno=current_resno+start_resno > print "Residue %d changed to %d" %(current_resno,new_resno) > spl[1]=" %d " %(new_resno) > new_line=" ".join(spl) > else: > new_line=line > print>>f, new_line.rstrip() > > f.close() > -------------------------------- > > I will add this to phenix as "phenix.adjust_robetta_resid" as well. > > > However...there still is a problem if you have multiple chains...as > mr_rosetta has only one set of fragments files the same fragments files > are being applied to all your chains. I will add a way to specify which > fragments files go with which chains. > > All the best, > Tom T >

2 1

scattering factors
by Goragot Wisedchaisri 20 Jun '11

20 Jun '11

Hi, I am new to Phenix but I have used Solve/Resolve in the past. I am currently using Phenix 1.6.2 and I have electron diffraction data to ~2A from a 300kV electron microscope that I would like to use Autobuild and phenix.refine to iteratively rebuild and refine my partial structure. I have a file containing electron scattering factors for 300kV EM that has been used successfully for refinement with CNS before for electron diffraction data. How can I tell Phenix to use electron scattering factors during refinement? I think currently Phenix has 4 choices for X-ray and neutron scattering factors but not for electron scattering. Is there a good way to implement electron scattering factors into phenix library? Any suggestions are welcome. George Wisedchaisri

5 12

phenix.validate ? Or RSCC from command line?
by Francis E Reyes 20 Jun '11

20 Jun '11

Phenixers Is there a great phenix cmd line utility that computes a real space correlation for each residue given model and data? I'll take a .py if necessary. Thanks! --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

2 1

Errors in latest build dev-790
by Yuri 19 Jun '11

19 Jun '11

Dear phenixers, I ran into some errors after my last upgrade. First, I noticed that all of the data plots are gone in the GUI, instead I get a message that says :plotting disabled due to missing library. Second I was running phenix.refine and got the following message, they may be related I am not positive: AttributeError : 'RefinementStatsPlot' object has no attribute 'null_fmt' Traceback (most recent call last): File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Runtime.py", line 172, in OnUpdate self.propagate_event(event, "OnUpdate") File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Runtime.py", line 228, in propagate_event fn(event) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Programs/Refine/Output.py", line 536, in OnUpdate self.stats_plot.update_stats(callback.data) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Programs/Refine/Output.py", line 796, in update_stats stats.bs_ave) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Programs/Refine/Output.py", line 809, in set_plots ax1().xaxis.set_major_formatter(self.null_fmt) AttributeError: 'RefinementStatsPlot' object has no attribute 'null_fmt' Platform info: __FILE__ = /net/anaconda/scratch1/phenix/phenix-dev-790/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Jun 17 2011 __TIME__ = 04:12:36 __x86_64__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __LP64__ = 1 __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 __SSE2__ = 1 BOOST_LIB_VERSION = 1_47 PY_VERSION = 2.7.2 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 8 sizeof(std::size_t) = 8 sizeof(void*) = 8 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 gnu libc version: 2.5 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-2.6.18-238.12.1.el5-x86_64-with-redhat-5.6-Tikanga platform.architecture(): ('64bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 2 Memory total: 3,692,077,056 Memory free: 16,236,544 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Å -- Yuri Pompeu

2 1

phenix.model_vs_data
by Yuri 17 Jun '11

17 Jun '11

I just realized it is under Comprehensive Validation! -- Yuri Pompeu

1 0

phenix.model_vs_data
by Yuri 17 Jun '11

17 Jun '11

> I would refine in parallel with and without the twin law and check > the > resulting maps and R-factors. > I had a case where the twin fraction was 0.06, which I expected to be > negotiable. When I included the twin law in refinement, my R-factors > dropped dramatically. >This is what phenix.model_vs_data does: it runs Xtriage internally and >tries all suggested twin laws, scores the results by R-factor and > prints >out the verdict: >phenix.model_vs_data model.pdb data.mtz >phenix.model_vs_data: >http://phenix-online.org/documentation/model_vs_data.htm >Pavel. Is this accomplished in polygon in the GUI? -- Yuri Pompeu

1 0

General Questions about Joint x-ray/neutron refinement
by Louis Lazar 17 Jun '11

17 Jun '11

Developers/all: I have been running some Joint X/N jobs, and I have some questions that perhaps you can help me with. First, doing joint refinement gave a total of 53 waters (thanks to ordered_solvent=true), yet the electron density seems to show that there are several more waters that are actually present (however it should be noted that there is no nuclear density associated with those waters, and in some cases no nuclear density associated with the 53 that were chosen by ordered_solvent=true). Should I add in manually to the electron density what I believe are these extra waters, or simply ignore them? Second, when I try to real space refine any of the residues, I get an error message telling me about exploding atoms. What is the cause of this message, and is it possible to real space refine any of these residues and specifically the hydrogen atoms associated with them. Third, during the joint refinement run, I chose to refine occupancies of all atoms. This breaks down into several questions: A) Should I be refining occupancies at 2.0 A resolution (of the neutron structure; 1.05A for the X-ray)? B) How does Phenix go about refining occupancies of hydrogen/deuterium sites? C) If the resulting occupancies result in values of, for example, 60% deuterium and 40% hydrogen, am I to presume that deuterium presence is significant if the nuclear density looks "good". At what point of deuterium occupation (while examining the nuclear density), would I say that there is likely no deuterium present (or that it is insignificant)? Hopefully all of these questions make sense, and if I need to clarify anything, please let me know. Thanks so much in advance for the help, I appreciate it as always. Regards, Louis

4 5

tls group and anisotropic
by ChenTiantian 16 Jun '11

16 Jun '11

Dear Phenixers, I refined my structure with TLS, I did not mean to refine it with anisotropic strategy, but I got ANISOU record. As the manual metioned, when doing TLS refinement, It always happens like this. What does this ANISOU record mean ? Does that mean TLS is a grouped anisotropic refinement? Tiantian -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

2 1

no density on the anchored proteins
by zhangh1＠umbc.edu 16 Jun '11

16 Jun '11

Hi, I am using phenix.refine to calculate the map of the 50S RNA (1FFK). It is weird that there is no density on the anchored proteins even for the Fc map. Following is the code I am using: phenix.refine ${f}.pdb ${f}.mtz main.number_of_macro_cycles=0 xray_data.high_resolution=${res} xray_data.r_free_flags.generate=True export_final_f_model=mtz Thanks for any advice! Hailiang

3 3