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Bulk solvent correction
by Ina Lindemann 31 Mar '11

31 Mar '11

Hi, I am refining two crystal structures of the same protein wtih four domains and 687 amino acids. These are the last lines form my log-files after several model building steps - protein altogether fits quite well into the density. But I am confused about these logfiles: 1.Why is there such a big difference between R values with and without bulk solvent correction and anisotropic scale? Start R-work = 0.3765, R-free = 0.5498 (no bulk solvent and anisotropic scale) Final R-work = 0.3733, R-free = 0.5509 (no bulk solvent and anisotropic scale) Start R-work = 0.2356, R-free = 0.2962 Final R-work = 0.2250, R-free = 0.2939 2. (the other structure) Why does the R value without bulk solvent and anisotropic scale decrease so much but with it remains stable? Start R-work = 0.2182, R-free = 0.2856 (no bulk solvent and anisotropic scale) Final R-work = 0.4054, R-free = 0.4223 (no bulk solvent and anisotropic scale) Start R-work = 0.2157, R-free = 0.2827 Final R-work = 0.2147, R-free = 0.2816 I would be very pleased about any helpful comments. Ina Ina Lindemann Philipps-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908

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what to do with disordered side chains
by Ed Pozharski 31 Mar '11

31 Mar '11

The results of the online survey on what to do with disordered side chains (from total of 240 responses): Delete the atoms 43% Let refinement take care of it by inflating B-factors 41% Set occupancy to zero 12% Other 4% "Other" suggestions were: - Place atoms in most likely spot based on rotomer and contacts and indicate high positional sigmas on ATMSIG records - To invent refinement that will spread this residues over many rotamers as this is what actually happened - Delet the atoms but retain the original amino acid name - choose the most common rotamer (B-factors don't "inflate", they just rise slightly) - Depends. if the disordered region is unteresting, delete atoms. Otherwise, try to model it in one or more disordered model (and then state it clearly in the pdb file) - In case that no density is in the map, model several conformations of the missing segment and insert it into the PDB file with zero occupancies. It is equivalent what the NMR people do. - Model it in and compare the MD simulations with SAXS - I would assumne Dale Tronrod suggestion the best. Sigatm labels. - Let the refinement inflate B-factors, then set occupancy to zero in the last round. Thanks to all for participation, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

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phenix migration
by Xtal_bb 31 Mar '11

31 Mar '11

Hi guys, I have just got a brand new iMac, to replace my MacBook, in which I used to run phenix. I have installed phenix in the new iMac, and copied the directory with all the files of my previous runs. However, what should I migrate to have the projects and previous work recognized by the fresh install? Thanks for the help, ciao s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990

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how convert mtz in xplor format
by fulvio saccoccia 30 Mar '11

30 Mar '11

Greetings to all, Does anyone know how convert a .mtz file into a xplor format file? Thanks in advance Fulvio Saccoccia

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rotamers
by Ed Pozharski 30 Mar '11

30 Mar '11

Does refine restrains side chain rotamers to, say, the closest one from the rotamer dictionary or, perhaps, the starting coordinates (I find this less likely, of course)? I am particularly interested in what would happen if a side chain is disordered and there is no strong electron density to support a specific conformation. Do I understand correctly that the real-space refinement for the side chains is on by default, which means that disordered side chains would tend to stay within their biased density? I apologize if I missed the description of this in the manual, just point me to the right section then. Cheers, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

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are the rigid_body group shifts cummulative or stepwise?
by Scott Classen 30 Mar '11

30 Mar '11

i.e. do the translation & rotation values reported in each rigid body step in the log file represent the TOTAL shift from the initial pre-RB model or just the shift for that particular step? Thanks, Scott

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Same enzyme, different space groups ?
by Yuri 29 Mar '11

29 Mar '11

Hello everyone, I was comparing 2 data sets I have and when I run Xtriage I noticed the following: a) for one crystal (data processed in P 4 2 2) | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ------------------------------------------------------------------------------------ | P 41 21 2 | 24 | 0.03 | 1.30 | 0 | 2 | 0.000e+00 | | P 43 21 2 | 24 | 0.03 | 1.30 | 0 | 2 | 0.000e+00 | | P 42 21 2 | 22 | 0.03 | 1.27 | 0 | 4 | 7.187e-02 | | P 4 21 2 | 18 | 0.01 | 1.21 | 0 | 8 | 3.035e-01 | | P 41 2 2 | 6 | 0.11 | 1.59 | 0 | 20 | 9.065e-01 | | P 43 2 2 | 6 | 0.11 | 1.59 | 0 | 20 | 9.065e-01 | | P 42 2 2 | 4 | 0.13 | 1.57 | 0 | 22 | 9.784e-01 | | P 4 2 2 | 0 | 0.00 | 0.00 | 0 | 26 | 1.210e+00 | ------------------------------------------------------------------------------------ b) the other crystal, of the same enzyme (data scaled in P 43 21 2) x triage tells me this crystal is in P 43 21 2. | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ----------------------------------------------------------------------------------- | P 4 2 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 4 21 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 41 2 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 41 21 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 42 2 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 42 21 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 43 2 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 43 21 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | ----------------------------------------------------------------------------------- My understanding is that P 43 21 2 should have 0 systematic absences (if I am wrong, please point it out) My questions are: what is really my space group? Or should I say space groups, if indeed I have two different space groups. How do I nterpret the scores? Could it all be a function of the space group they were processed in? -- Yuri Pompeu

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Target weight optimization (wxu_scale and wxu)
by Zhang yu 28 Mar '11

28 Mar '11

Dear Phenixer, What is the real meaning of the 'wxu_scale' and 'wu'? (scale factor for X-ray/ADP_weight: wxu_scale ADP weight scale: wu) During ADP refinement, it is suggested to refine the 'wxu_scale', what if I change the value of 'wu'? Thanks Yu

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Split Occupancy of a ligand and water
by Brandon Goblirsch 28 Mar '11

28 Mar '11

Hello, Currently I am have a structure which has a ligand bound at less than full occupancy. The ligand in this cause is covalently linked to a CYS residue in the enzyme active site. When the ligand is not present, there are two well conserved waters in the active site in its place. Overall, I have a same space, split occupancy issue. The problem I am having now in phenix 1.7.460 is that I want to refine (simultaneously) these water positions superimposed on the bound ligand position (as both have less than 100% occupancy). However, upon refinement, the waters are always "kicked out" of position and are not allowed to overlay with atoms within the bound ligand. Does anyone know how to get phenix.refine to accept the water and ligands occupying the same coordinate space. Obviously setting the ligand and water positions to sub 100% occupancy does not do the trick. Thanks for any help!! Brandon -- Brandon Goblirsch Research Assistant-Wilmot Lab Biochemistry, Molecular Biology and Biophysics 5-230 Nils Hasselmo Hall Minneapolis, MN 55455 (612)624-0141

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anomalous difference map
by Jason 28 Mar '11

28 Mar '11

Hello Everyone, I have an old question about how to create anomalous difference map. Facts: 1) Synchrotron Fluorescence scan indicates the heavy atom definitely presents in my protein (my control is a second protein with the same ligand showed no absorbance spectrum) 2) xds processed mtz file 3) Data resolution ~ 3 angstron 3) molecular replacement solved apo structure protein.pdb using phenix.refine 4) phenix.maps to generate anomalous map (phenix.refine will also generate it, but let's leave it aside for the moment) Questions: When I load the mtz file to phenix.maps GUI, the mtz label pulldown menu indicates 4 possible choices for the column to use:(1) IMEAN, SIGIMEAN (2) I(+), sigI(+), I(-), sigI(-) merged (3) F(+), sigF(+), F(-), sigF(-) merged (4) F, sigF, Dano SigDano. I have tried the choices of (2) (3) and (4). However, there is barely any anomalous signal at 4sigma, which makes me wondering if something is not right. The first thing coming to my mind is the mtz labels: I(+), sigI(+), I(-), sigI(-) merged. What does merged mean? Could this be the reason? Other issues that could causing the trouble? Thank you all. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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