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GUI for Auto-MR
by Laurie Betts 27 Jan '10

27 Jan '10

I installed version PHENIX 1-5-2 under Linux, and the main GUI has an option for AutoMR Phaser that says (old PHENIX GUI) - if that crashes is it because we don't have the old GUI installed? THe other main items seem to work fine. The last error message in the terminal window seems to suggest that is the case.... Thx, Laurie BEtts

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twin data set
by r n 26 Jan '10

26 Jan '10

Hi I did processed a data set, which seems P3. I did molecular replacement and end up with solution with higher R factor. Then, I did used xtriage to check the data, it gave me possible space group P321 and few twin laws, this space group did not given me any solution , data seems have translation symmetry along z axis? Also I did processed in P1 and did molecular replacement end up in high R-factor. I really appreciate if any one has any suggestion what is going on with data? I given log file from xtriage, --------------------------------------------------------------------------------------------- | Point group | mean R_used | max R_used | mean R_unused | min R_unused | BIC | choice | ---------------------------------------------------------------------------------------------- | P 3 | None | None | 0.314 | 0.027 | 8.149e+03 | | | P 6 2 2 | 0.314 | 0.460 | None | None | 1.856e+05 | | | P 3 2 1 | 0.027 | 0.027 | 0.446 | 0.432 | 5.667e+03 | <--- | | P 6 | 0.432 | 0.432 | 0.249 | 0.027 | 1.856e+05 | | | P 3 1 2 | 0.460 | 0.460 | 0.242 | 0.027 | 1.859e+05 | | ---------------------------------------------------------------------------------------------- Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | -h,-k,l | M | 0.432 | -0.009 | 0.046 | 0.022 | | h,-h-k,-l | M | 0.027 | 0.450 | 0.478 | 0.478 | | -k,-h,-l | M | 0.460 | -0.012 | 0.049 | 0.022 | ------------------------------------------------------------------ Patterson analyses - Largest peak height : 34.261 (corresponding p value : 7.017e-04)

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map averaging
by Gabriela Guédez 24 Jan '10

24 Jan '10

Hi dear Phenixbb, Is there a command tool to make ncs density averaging in a high oligomerization model that has some maps clearer than others? not multi-crystal but the same crystal. Thank you, Gabriela -- ---------------------------------------------------------------------- Gabriela Guédez R. gabriela.guedez(a)bzh.uni-heidelberg.de

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how to convert .cif with multiple datasets
by Zheng Zhou 24 Jan '10

24 Jan '10

Dear phenix experts: I am using phenix.cif_as_mtz to convert a .cif file downloaded from pdb, but when I run ################################################ phenix.cif_as_mtz XXXX-sf.cif Sorry: Crystal symmetry is not defined. Please use the --symmetry option. ################################################ Then I run ############################################### phenix.cif_as_mtz XXXX-sf.cif --symmetry=XXXX.pdb Multiple data sets found => ignored: XXXX-sf.cif What should I do? Thanks for your help. Joe

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explicit pdb output file name (refine)
by Ed Pozharski 21 Jan '10

21 Jan '10

Do I understand correctly that there is no way to force refine to skip the serial in the output pdb file name, i.e. foo.pdb, not foo_001.pdb? -- Ed Pozharski <epozh001(a)umaryland.edu> University of Maryland - Baltimore

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polygon resolution control
by Young-Jin Cho 21 Jan '10

21 Jan '10

Hi I was using polygon from GUI. One question I have now is how I can control the resolution limit. As I cut the resolution during refinements but polygon gave me from the uncut-high resolution. Is there any way, I can ask polygon to get statistics upto certain resolution as shown on pdb file? As always, thanks in advance. YoungJin

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Re: [phenixbb] polygon resolution control
by Alexandre Urzhumtsev 21 Jan '10

21 Jan '10

Dear YoungJin >I was using polygon from GUI. One question I have now is how I can control >the resolution limit. As I cut the resolution during refinements but >polygon gave me from the uncut-high resolution. Is there any way, I can >ask polygon to get statistics upto certain resolution as shown on pdb file? Honestly, I do not know for the phenix version; let's wait what Pavel & Nat answer you. Very probably they already implemented it and your problem will be solved easy. Another simple solution will be to cut explicitly your MTZ file by the resolution you wish before run the polygon. If not, such an option (to define explicitely the resolution; that will select for comparison the PDB structures refined previously at such a resoluton) exists in the original Tcl/tk based version of the polygon. Please, let me know if your are interested in it. Best regards, Sacha

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occupancy refinement default selections - bug or feature?
by Ed Pozharski 21 Jan '10

21 Jan '10

There is a ligand residue in the structure that have its occupancy set to 0.75. refine with default parameters apparently refines every atom individually, so in the end I have a strange situation where ligand atoms have different occupancies. Of course, regular alternate conformers in the protein part of the structure have single occupancy refined per residue. Interestingly, when I place altLoc identifier "A" in front of the residue name of the ligand, single occupancy value is refined (although there is no second conformation). It settles down near 0.7 (close to what I selected previously based on a traditional approach of eliminating difference density and roughly matching B-factors of hydrogen-bonded protein atoms with ligand), so apparently constraints (e.g. total occupancy for all the conformers) are not applied. Is this intentional behavior (I understand that groups can be defined in the input file but adding altLoc letter seems like a simple trick)? I think most people would initially expect that occupancy will not vary within a residue, so the default behavior may seem like a bug to some (the only situation I can think of where such variation is justified is to model radiation damage). -- Ed Pozharski <epozh001(a)umaryland.edu> University of Maryland - Baltimore

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Dear everybody
by YuYong Tao 21 Jan '10

21 Jan '10

Dear everybody: I installed phenix-1.6, when i run 'phenix.solve', it showed as follows: ustc-lifescience:~> phenix.solve binary=/usr/local/phenix-1.6-288/build/intel-linux-2.6/solve_resolve/exe/solve SOLVEDIR=/usr/local/phenix-1.6-288/solve_resolve/ext_ref_files SYMOP=/usr/local/phenix-1.6-288/solve_resolve/ext_ref_files/symop.lib SYMINFO=/usr/local/phenix-1.6-288/solve_resolve/ext_ref_files/syminfo.lib CCP4_OPEN=UNKNOWN SOLVE_RESOLVE_MALLOC_MAX=399459600 /usr/local/phenix-1.6-288/build/intel-linux-2.6/solve_resolve/exe/solve: error while loading shared libraries: libsvml.so: cannot open shared object file: No such file or directory and when i run 'phenix.resolve' ,it seems to be ok. So i donn't know what to do. Can you tell me? Best Wishes!

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How do different sections of TLS groups affect refinment
by Bart, Aaron G 20 Jan '10

20 Jan '10

Greetings everyone, I am still fairly new to crystallography, so forgive me for my naivety. My question involves how the TLSMD server segments my protein and the effects it has on refinement. For instance when i use "Multi-Chain Alignment Analysis", which lines the sequence for all of my chains (a total of 12) and shows how TLS groups are divided among them, it shows varying selections of TLS groups among the different chains. It should be noted that the sequence is the same for all the chains in my protein. Also if a TLS group splits a alpha helix into multiple parts, would this be valid? I have come to understand that helices move more like rigid bodies than segmented groups... Thanks! -Aaron

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