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Twin Law question
by Young-Jin Cho 28 Oct '10

28 Oct '10

Dear Phenix users, Thanks in advance to answer my question. As my recent data did not give me perfect statistics, I was wondering what the problem was (one of things is ice ring though). When I ran Xtriage with my struggling current data set and looked like I got twinned data. I reran PHASER as was suggested and confirmed that current space group is right. My question is now how I can handle this problem. First, as was recommended I input twin_law, however not all the cases (I have a couple of data sets) were working. One favorite(!) error message was as following: "Map type 'Fc' not supported for twinned structures. Allowed types: Fo-Fc, Fobs-Fobs-Fmodel, 2mFo-DFc, 2mFobs-DFmodel, mFo-DFc, mFobs-DFmodel, gradient, m_gradient." I got this from both GUI and shell environment. . 1. Now from now on, whenever I want to phenix.refine, should I include twin_law command such as 'twin_law=-h,l,k'? 2. In this case, what do I expect to see such as lowering Rfree or else? If it doesn't help lowering Rfree, what to do next? 3. Do I have to report I did with twinlaw option in case of preparing a paper or presentation? I mean I also heard that if one got twinned data, they re-collected data. How much can I convince my refinement is OK with twined data? Additionally, I checked other data, and applied twin_law but the result R/Rfree were exactly same as the one I refined without twin_law option, it this normal case? With many thanks in advance, Young-Jin Cho

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maximum allowable B-factor value
by Christian Roth 27 Oct '10

27 Oct '10

Dear all, I did a refinement run with a built in ligand. Within the ligand the B-factor jumps between two connected atoms from 60 up ~110, which is i think a bit too much. Is there a way to restrain the B-factors that they could not jump so much. I would accept negative difference density for the atom. Maybe the ligand is a bit degraded. Best regards Christian @Pavel Tanks for your suggestions with occupancy refinement and B-factors. -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319

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Re: [phenixbb] Sigma-A vs Resolution plot
by Bryan Lepore 25 Oct '10

25 Oct '10

On Thu, Oct 21, 2010 at 12:04 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > the plot "Sigma-A vs Resolution" will be available in the next PHENIX > nightly build: Looks nice - I greatly appreciate this - thanks Pavel, Nat, anyone else I forgot. -Bryan

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nightly builds
by Bryan Lepore 22 Oct '10

22 Oct '10

is it me, or was there just a dev-562? ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: dev Release tag: 562 Platform: intel-linux-2.6 linux User: ------------------------------------------------------------------------------- but latest is : dev-555 2010-10-10 successful cctbx, cci_apps, phaser, phenix, misc docs; changelog

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R-free problem with phenix.refine
by Vinson LIANG 22 Oct '10

22 Oct '10

Dear all, Recently I deposited a structure to PDB. However, I was told >> The R value of SF check are different from your reported value. >> >> R work in SF check = 0.2859 >> your reported R work = 0.1474 >> Also there are no R free flags in your sending files, but you reported R >> free value in your all deposition. So, I rerun my deposited file with phenix.refine, and it gave a R-work=0.1475, R-free=0.1742. However, when I tried to run the same file with refmac5, error came with "Free R label has not been set". I guess phenix.refine gives Rree-R label that other program could not recognize. Could anyone please help me to solve this problem? Thank you very much in advance. I don't know why structure refined with phenix.refine has such problem. I wish this problem will disappear in the future, since I so like phenix.refine. Best, Vinson,Liang

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refine : peculiar TLS tensors
by Bryan Lepore 22 Oct '10

22 Oct '10

[ phenix 1.6.4-486 ] [ ALSO : tlsanl, refmac, etc. from ccp4 6.1.3 ] [ molscript/povscript ] the one-liner : i have some TLS tensors that sometimes do not compare at all well with refmac/anisoanl tensors. sometimes, the principal axes of a TLS tensor refines *very* far away from the center of mass(=center of reaction), or the axes from tlsanl are exceptionally small as if not scaled properly. the eigenvalues are really small too. see [*] for troubleshooting and strategy used. i suspect i am missing something. i also understand this might not be a phenix question. -bryan [*] i compared another .def that gave sensible TLS results with a different dataset/model, and my {} are all good AFAIK. anisoanl/refmac/parvati results are reasonable. the phenix refinement appears well behaved. these are all using tlsextract to get the eigenvalues/origins, and molscript to check the axes/centers of mass. input B factors are Beq unless i made an error. the tls group selections can vary - however, simple groups also can give these results. in general, using strategy (excerpt) : refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies *group_anomalous sites { individual = None torsion_angles = None rigid_body = None } adp { individual { isotropic = None anisotropic = None } group_adp_refinement_mode = *one_adp_group_per_residue \ two_adp_groups_per_residue group_selection group = None tls = "chain A and (resid 1:41 or resid 42:159 or resid 195:237 or resid 263:420)" tls = "chain A and resid 160:194" tls = "chain A and resid 245:252" } [...cut off ... ] example output of an ill-behaved S tensor from tlsanl : SCREW ROTATION AXIS ABSOLUTE POSITION (A) PITCH (A) X Y Z 1 70.667 154.197 308.627 -144.435 2 977.334 819.588******** 6222.947 3 640.7191431.084 471.341 269.382

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maps : sigma-a
by Lepore, Bryan 21 Oct '10

21 Oct '10

how might one start to go about getting phenix to automatically write out the value of sigma_A vs. resolution? e.g. when making maps, to get that nice table in Randy Read's SIGMAA program output of ln(sigma_A) vs. resolution. -bryan

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Bad ligand parameters
by Joe Krahn 21 Oct '10

21 Oct '10

I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies? Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters. Joe Krahn

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refine : a priori TLS tensor eigenvalues
by Bryan Lepore 21 Oct '10

21 Oct '10

[ phenix 1.6.4-486 ] i gather that phenix.refine will not take a priori refined TLS tensor eigenvalues - either from input or from the pdb header. is this right? -bryan

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Joint X-ray/Neutron Refinement
by Louis Lazar 21 Oct '10

21 Oct '10

Hello, Sorry for reposting, I am trying to get a better response with a more detailed subject line. I am seeing an internal error while trying to conduct joint x-ray/neutron refinement, and any help with the issue below would be greatly appreciated. Thank you very much in advance: ================================ ADP refinement=============================== Traceback (most recent call last): File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1182, in run call_back_handler = call_back_handler) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py", line 735, in refinement_machine h_params = h_params) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py", line 192, in __init__ all_params = all_params) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py", line 216, in refine_adp model.set_refine_individual_adp() File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/model.py", line 1035, in set_refine_individual_adp iselection = selection_iso.iselection()) RuntimeError: cctbx InternalError: /net/anaconda/scratch1/phenix/phenix-1.6.4-486/cctbx_project/cctbx/xray/scatterer_flags.h(417): CCTBX_ASSERT(f.use_u_iso()) failure. This error occurs during the 2nd macro cycle of refinement using this general command: phenix.refine model.pdb data_xray.hkl neutron_data.file_name=data_neutron.hkl input.xray_data.labels=FOBSx input.neutron_data.labels=FOBSn Thanks again. Regards, Louis

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Stretched Maps
by Joel Weadge 21 Oct '10

21 Oct '10

Hi all,I have just finished doing molecular replacement and an initial round of refinement (with simulated annealing) on a number of different datasets. They have all be straightforward since most of them are either point mutants and/or co-crystal structures. However, two of the structures are giving me some trouble. The data appears to be of good quality and resolution (2.25 and 2.55Å). The MR proceeds as normal with good scores and then in the subsequent round of refinement the maps (2Fo-Fc and Fo-Fc) look strange. The density is stretched or flattened in one direction. Can anyone help me with what I may be overlooking?Thanks in advanceJW

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occupancy refinement of a metal ion
by Christian Roth 20 Oct '10

20 Oct '10

Dear all, if I understood the manual correctly I could refine the occupancy and set the B-Factor to a constant value, or vice versa. Is there a possibility that phenix refine the B-Factor automatically to the value of the coordinating residues and adjust than the occupancy to a good value? I seems to be that the metal site is not fully occupied. I guess I have to set the B-value manually to the value of the surrounding residues and do than a refinement, right? Best regards Christian

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fix rotamers question
by Peter Grey 20 Oct '10

20 Oct '10

Dear Phenix community, I would like to have some additional information regarding fix_rotamers. In particular : - How Phenix chooses which rotamers need to be fixed ? - Does Phenix really re-calculate the three maps after correcting each rotamer ? For very large structures this is very time-consuming and one can settle for calculating a new map every 10-20 residues. Perhaps this could be a user-controlled parameter ? -Can you please explain how fix_rotamers works together with ncs restraints ? Thank you in advance for shedding light on this, Peter

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about low resolution refinement
by crystallogrphy 18 Oct '10

18 Oct '10

Hi, I am refining a low resolution data. According to sigma vs. resolution, my resolution is 4.7A. Because there are four identical molecular per asymetric unit, I can use positional refinement. There are about 65% alpha-helices in the structure, so I want to use secondary structure restrain. Does phenix has this restrain in the refinement? I am using Phenix-1.4 version.

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Question
by Louis Lazar 18 Oct '10

18 Oct '10

Hello, I am seeing an internal error while trying to conduct joint x-ray/neutron refinement, and any help with the issue below would be greatly appreciated. Thank you very much in advance: ================================ ADP refinement =============================== Traceback (most recent call last): File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1182, in run call_back_handler = call_back_handler) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py", line 735, in refinement_machine h_params = h_params) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py", line 192, in __init__ all_params = all_params) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py", line 216, in refine_adp model.set_refine_individual_adp() File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/model.py", line 1035, in set_refine_individual_adp iselection = selection_iso.iselection()) RuntimeError: cctbx InternalError: /net/anaconda/scratch1/phenix/phenix-1.6.4-486/cctbx_project/cctbx/xray/scatterer_flags.h(417): CCTBX_ASSERT(f.use_u_iso()) failure. This error occurs during the 2nd macro cycle of refinement using this general command: phenix.refine model.pdb data_xray.hkl neutron_data.file_name=data_neutron.hkl input.xray_data.labels=FOBSx input.neutron_data.labels=FOBSn Thanks again. Regards, Louis

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real space refinement or fix rotamers
by helene.krueger＠staff.uni-marburg.de 14 Oct '10

14 Oct '10

Hi, I want to fit bad fitting residues into electron density of my 2.0 A dataset. To do so should I use the "real space" option or the "fix bad sidechain rotamers" option? or both? Thanks Helene -- Helene Köster Philipps-Universität Marburg Institute of Pharmaceutical Chemistry AG Klebe Marbacher Weg 6 35032 Marburg, Germany Phone: +49-6421-28-25908 Mail: helene.krueger(a)staff.uni-marburg.de www.agklebe.de

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How to eliminate or decrease negative electron density at ligand position
by J J 14 Oct '10

14 Oct '10

Hello everyone, I have fine electron density 2Fo-Fc around a small ligand (~20 atoms) binding to my protein (at 1sigma level, all of the ligand atoms are surround by electron density, resolution=3 angstrom). However, I also see some negative electron density Fo-Fc surrounding some of the ligand atoms. My question is should I care about these negative electron density? If I should, what should I do in order to decrease or eliminate these negative electron density? I have tried occupancy refinement. It does help to decrease the negative density. However, it also makes 2Fo-Fc weaker. Another method I tried is to use tls refinement only for the ligand. It also helped to decrease the negative electron density. But since the data resolution is only 3 angstrom, I do not know if I am even allowed to do tls refinement? Thank you all in advance. Jason University of Pittsburgh

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Average B-factors when using TLS
by Phil Jeffrey 13 Oct '10

13 Oct '10

I'm having a discussion with a colleague here about what we expect to see on a model with and without TLS being used. I had the expectation that if you'd compared both models the Biso values reported in the ATOM line for the same atom w/ and w/o TLS would be somewhat comparable. Not the same, because the ADP model is different, but similar. However in the case of the TLS-refined model the average B-factors are systematically higher over the whole structure (86 A^2 vs 69A^2 for one polypeptide chain). Is this reasonable ? Expected ? Phil Jeffrey Princeton

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Re: [phenixbb] When to freeze crystal?
by miket＠chem.ucla.edu 13 Oct '10

13 Oct '10

Just last week I had crystals on Friday, then by Monday they dissolved back into the drop. I don't really understand how or why this happens, but it does. After experiencing this and complaining about it, I heard several other similar stories from around the department. Lesson learned: if you think you have a decent crystal, freeze it. Having said this, I've also heard of good data being collected from a crystal that was over a year old. Like Bert said, I think that occasionally a crystal survives or even improves over time, but those cases are much more rare than cases where the crystal deteriorates. Do how many crystals do you have? You might try freezing some and saving the others in the drop, then you can see for yourself. Good luck, Mike ----- Original Message ----- From: "Nathaniel Echols" <nechols(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Wednesday, October 13, 2010 8:44:42 AM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] When to freeze crystal? On Wed, Oct 13, 2010 at 4:16 PM, J J <phenix.upitt(a)gmail.com> wrote: > Hi everyone, > Sorry to ask a question that is not really related to phenix. I hope someone > here will be able to help me out. > I have a few crystals at hand right now, but I will not be able to look at > them for at least another month or so due to beamline schedule. Do you think > I should freeze them now or wait till I have my beamtime, or it is crystal > dependent? Thanks in advance. (Bert meant to send this to the list, but since he's using the wrong email address, it went to the list admin instead:) From: "Van Den Berg, Bert" <Lambertus.VandenBerg(a)umassmed.edu> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Date: Wed, 13 Oct 2010 11:27:32 -0400 Subject: Re: [phenixbb] When to freeze crystal? It is crystal dependent, but if they are big enough I would freeze them now. I have seen many crystal forms deteriorate over time and wouldn’t take the risk of that happening. It can happen though that old crystals get better (presumably due to slow dehydration of the drop), but I think these cases are fairly rare. Bert _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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When to freeze crystal?
by J J 13 Oct '10

13 Oct '10

Hi everyone, Sorry to ask a question that is not really related to phenix. I hope someone here will be able to help me out. I have a few crystals at hand right now, but I will not be able to look at them for at least another month or so due to beamline schedule. Do you think I should freeze them now or wait till I have my beamtime, or it is crystal dependent? Thanks in advance. Jason University of Pittsburgh

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Merging low resolution mtz file with high resolution sca file with phenix_reflection_file_editor
by Pei-Chun Lin 13 Oct '10

13 Oct '10

Hi, If I merge my low resolution mtz file with the high resolution sca file with phenix.reflection_file_editor GUI, is it the same as : Merge in hires data phenix.autobuild data=solve_2.mtz hires_file=w1.sca seq_file=seq.dat in Phenix Autobuild? PC

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secondary structure restraints question
by Peter Grey 12 Oct '10

12 Oct '10

Dear Phenix community, I have a very large model with many chains (due to NCS and complexity of model) where chain-id is not unique (e.g. there are several chain A) but segid is. All atom selections (for rigid body refinement, ncs restraints, tls etc...) are defined by segid. When I look at the output of phenix.secondary_structure_restraints I see that these restraints are defined by chain-id and residue number. Does this mean I must have unique chain-id names to correctly apply these secondary structure restraints or am I missing something ? Thank you for your time, Peter

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refine : annealing and bulk solvent
by Lepore, Bryan 12 Oct '10

12 Oct '10

[ phenix 1.6.4-486 ] from the program output, it appears that prior to annealing ( e.g. torsion ), a bulk solvent grid search is run using the initial model. after that ends, all the annealing steps are carried out on the model using the initially optimized bulk solvent. When annealing is done, another search is conducted on the final model. i.e. there are no bulk solvent changes during annealing. is this right? -bryan

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DNA base pairing restraints work for GC only
by Phoebe Rice 07 Oct '10

07 Oct '10

We're trying to refine a large, low-resolution protein-DNA complex structure (4A in the good direction), and we need every restraint we can get, so I'm trying to use secondary structure restraints (in addition to ncs and 3 known substructure models). I found this from the newsletter: phenix.secondary_structure_restraints model.pdb > ss.eff ran it, editted it, and plugged into the gui, where it seems to be taken into account if I also say "yes" to "find automattically". Then I ran torsion angle dynamics to see if things were restrained as requested. It only seems to be restraining G:C pairs - the ATs fly apart! The log file makes a very suspicious set of remarks under "secondary structure": No entry for base pair AT with type WWT (H=False). (repeated about the same # of times as we have AT pairs). I thought maybe it was a nomenclature problem, but if "Gd" is OK I don't see what's wrong with "Ad", and the usual suspect, the thymine methyl, stays coplanar with the rest of its base, so the program must be recognizing our base/atom names. Question 2 is that I wanted to view the restraints in pymol, but this command, also cribbed from the newsletter: phenix.secondary_structure_restraints partry1noss.pdb ss_manual.eff format=pymol > h_bonds.pml seems to overwrite the manual editing in my .eff file. Help? I'm new to phenix, so please be explicit about where I've gone wrong. thanks, Phoebe ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alph… http://www.rsc.org/shop/books/2008/9780854042722.asp

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maps : scattering corrections
by Lepore, Bryan 07 Oct '10

07 Oct '10

i'd like to define anomalous scattering corrections for phenix.maps, it looks like i'm not doing it right. it appears that simply pasting in various adjustments of : anomalous_scatterers { group { selection = element = Ni f_prime = 2.4 f_double_prime = -0.1 refine = *f_prime *f_double_prime # not sure about this one } in various places in maps.params mostly causes phenix.maps to report "unused parameter", e.g: maps.anomalous_scatterers.group.selection this should work, right? what am i missing here - is there a scope missing, what scope does this go in, did i miss this in the docs... -bryan

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Phenix.refine stops running in the background
by José Trincão 07 Oct '10

07 Oct '10

Hello all, I've been running phenix.refine over ssh on a remote computer, on command line. I always run it in the background (adding & to the command line). If I disconnect the ssh (or it gets disconnected) the job hangs. Any way of leaving it running even after the ssh disconnects? Thank you. 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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phenix.refine : mask
by Lepore, Bryan 07 Oct '10

07 Oct '10

i gather that the only way to define an "a priori" mask of the molecular envelope in phenix.refine is to generate Fmask and combine those in refinement - is that right? i.e. there isn't a more intuitive way using a mama mask or somesuch to keep the bulk solvent from flattening out parts you think are model, besides the model that is being refined in the first place? -bryan

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Re: [phenixbb] refine .log : loggraph flags
by Lepore, Bryan 06 Oct '10

06 Oct '10

On Wed, 6 Oct 2010, Nathaniel Echols wrote: > > loggraph [...] OR am i just missing something (CL flag, GUI...) > The GUI already does this nifty - does the entire gui have to be run? i.e. is that a "smaller" plotter you used?

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refine .log : loggraph flags
by Lepore, Bryan 06 Oct '10

06 Oct '10

[ thanks for the comments on sigma-A ] a related thread : its nice how xtriage puts loggraph specifications ($TABLE etc.) in the output. what is the source file that writes this? or is it more complicated than that? the .log can be hacked, but its a miserable thing to do. e.g. to incorporate such lines into phenix refine output - esp. a ln(sigma-A) plot - would be handy in such a format. then the course of refinement or all the dmin-dependent stats can be graphed. OR am i just missing something (CL flag, GUI...) -bryan

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refinement / alpha_beta
by Kay Diederichs 06 Oct '10

06 Oct '10

Dear Phenix developers, I'd like to refine (using phenix.refine) a _very_ incomplete model (obtained by molecular replacement with one subunit of the complete structure) against the native amplitudes, with the goal to obtain meaningful phases and figures_of_merit which should serve to find heavy atom sites in derivative datasets. If I "just refine" in phenix.refine, then the R-factors are in the 50s and the program estimates the coordinate error to be very large. Thus I would like to tell phenix.refine that the coordinates are actually quite accurate, but that a lot of the model is simply missing. I found alpha_beta free_reflections_per_bin= 140 number_of_macromolecule_atoms_absent= 225 n_atoms_included= 0 bf_atoms_absent= 15.0 final_error= 0.0 absent_atom_type= "O" method= *est calc estimation_algorithm= *analytical iterative verbose= -1 interpolation= True fix_scale_for_calc_option= None number_of_waters_absent= 613 sigmaa_estimator kernel_width_free_reflections= 100 kernel_on_chebyshev_nodes= True number_of_sampling_points= 20 number_of_chebyshev_terms= 10 use_sampling_sum_weights= True in the documentation but I have trouble understanding its meanings and defaults - but I do think this should be used. Maybe I should switch to method=calc and specify number_of_macromolecule_atoms_absent= as well as bf_atoms_absent= ? Can anyone advise me, please? thank you, Kay

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best strategy using two datasets?
by Manoj saxena 05 Oct '10

05 Oct '10

Hi , I have data 2.4 A for a protein ( Se-Met derivative) unit cell dimensions. 53.098,60.207,142.382. I have used this data to solve the partial structure with phenix.autosol and phenix.autobuild. The model from this data was then used as MR model in phaser with another data set from a crystal at 2.2 A (group P212121 ) .unit cell dimensions are 53.86,61.47,142.49. Currently my R free is 23%. My question is 1) Is there a a better way to use the two datasets. can I merge the reflection files from two datasets and does using a merged reflection file have an advantage over the strategy I used. 2) Although not directly related to phenix I was wondering can we use the merged reflection file for PDB depositions? Thanks . I will greatly appreciate any suggestions and guidance in this regard Manoj

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Re: [phenixbb] Help on multi-start-simulated-annealing sigmaA-weighted 2fofc map - WORKING EXAMPLE
by Pavel Afonine 03 Oct '10

03 Oct '10

Hi Fengyun, no problems, here is the updated script and inputs files to illustrate how it works: http://cci.lbl.gov/~afonine/mssa2/ All it needs is a bunch of PDB files and corresponding map coefficients. Let me know if you have any questions. Pavel. On 9/9/10 7:48 PM, fn1(a)rice.edu wrote: > Hi Pavel, > > The script works fine. I hope you could slightly revise the script for > me. > > Since right now, I could run the multi-sa on different nodes at the > same time. So I could get the refined models in the name of sa-#.pdb > within a short time. > > So I could begin with the different models and combine them to > "all.pdb" and calculate the average map after that. But I don't know > how to revise the run.py to do that. > > Wait for your help. > Thanks! > Fengyun > > 引用 Pavel Afonine <pafonine(a)lbl.gov>： > >> Hi Fengyun, >> >> my previous email actually doens't answer your question - I realized >> this after I pushed Sent button -:) >> >> To really answer your question I just wrote a Python script that does >> the following: >> - run multi-start Simulated Annealing, >> - combine all refined models into one multi-model PDB file (models >> separated by MODEL-ENDMDL records), and >> - compute averaged 2mFo-DFc map. >> >> The complete working example is here: >> >> http://cci.lbl.gov/~afonine/mssa/ >> >> You have two options at this point: >> >> - take this example, slightly change inputs by editing the run.py >> file (change input data and model file names, number of SA runs, etc) >> and run it as following: >> >> phenix.python run.py >> >> (since I spent 15 minutes on writing this script it's obviously not >> thoroughly tested or parameter-optimized, although I believe it >> should do the job right) >> >> or >> >> - wait a few days for one of the next PHENIX nightly builds where the >> above script will be available as a user-friendly either >> phenix.multi_start_sa command or an option of phenix.maps (I haven't >> decided yet what is better). >> >> Let me know if you have any questions. >> >> Pavel. >> >>> I read on the paper that they use CNS (model_map.inp) to calculate >>> the avarage sigmaA-weighted 2fofc map. Right now I have set up the >>> simulated annealing with different random seeds. I wonder whether >>> phenix could calculate the average map with the multiple coordinates >>> from different starts? >> >> >> > > >

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Job Opening Announcement
by Lance Westerhoff 01 Oct '10

01 Oct '10

Hello All- We have a number of computational chemist and computational crystallographer post doc positions available. One has a significant focus on x-ray refinement method development, and the other one will explore computational chemistry method research and development. We are excited to fill these openings with talented individuals, so if you think you would be a good fit, we invite you to take a look at our careers website below and submit your CV (along with cover letter) to careers(a)quantumbioinc.com http://www.quantumbioinc.com/careers/ Thank you for your time! -Lance ____________________ Lance M. Westerhoff, Ph.D. General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909

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using custom_param file from the gui
by Sebastiano Pasqualato 01 Oct '10

01 Oct '10

Hi all, I have a custom parameter file that I used to use running phenix.refine from the command line. Is there a way to use it from the gui? ciao, s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990

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question on the weight for adp
by fn1＠rice.edu 01 Oct '10

01 Oct '10

Hi everyone, I have some questions the weight for adp. My case is that some part of the model will be refined to large B values (about 100) if the default value of wxu_scale (1.0) is used. The other part of the model will have average B value of about 40, which the wilson B is about 35. The corresponding 2FOFC map has very poor density for the region with large B values. If the value of wxu_scale set to be 0.1, that part with large B will be refined to about 80 for B. The corresponding 2FOFC map has some better (but not good enough) density for this region. My question is that can I keep the wxu_scale at the small value for the refinement? Or finally do I need to loose this value? Thanks! Fengyun

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Seeking Postdoctoral Researcher
by Francois Berenger 30 Sep '10

30 Sep '10

Laboratory: Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, Japan. (Unit Leader: Dr. Kam Zhang) Job title and Job description: Postdoctoral Researchers Job description: We are seeking a highly motivated and experienced computational structural biologist to join the Zhang Initiative Research Unit at RIKEN. The successful candidate will use computational tools to tackle problems in the area of protein folding, structure prediction, and structure-based drug design. Our ability to predict the structure of proteins from their primary sequences will greatly facilitate our understanding of the important biological functions that proteins play in their host systems. The 3D structure information will also facilitate the rationale design of drugs for the treatment of various diseases with unmet medical needs. Qualifications: This position requires a PhD in areas related to biophysics, biochemistry, computational chemistry, bioinformatics, or structural biology with experience in employing computational tools to solve biological or chemical problems. Experiences in protein folding, protein structure prediction, protein structure analysis, protein crystallography, or structure-based drugs are highly desired. Proficiency in object-oriented programming such as C++, Java, scripting languages such as Python, Perl are also desired. Experiences in high performance computing, network computing, or grid computing would be a plus. The ideal candidate should possess a track record of accomplishments demonstrating technical proficiency, independent thinking, and scientific creativity. The research environment will be international and hence communication in English is encouraged. The complete job ad, as well as how to apply can be viewed here: http://www.riken.jp/engn/r-world/info/recruit/k100817_s_asi.html Best regards, Francois.

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Ligand restraints editing with REEL -summary
by Joseph Brock 29 Sep '10

29 Sep '10

Hi all, I just wanted to post a quick summary of how my problem was resolved. I later realised that the 'native glutahione' molecule I was transferring ligand restraints from was actually produced by eLBOW released under the Phenix package v1.4, and was therefore defined differently to those restraints created by v1.6.4-486. I was advised by Nigel (author of eLBOW and REEL) to download the latest nightly build (dev-541) and create a clean subdirectory. Copying my model.pdb and data.mtz file into this, running phenix.ready_set on these files and running phenix.refine with the resulting .pdb and .cif files, resulted in a ligand that was correctly restrained to refine into the density extremely well. Hope this is of help to anyone with a similar problem. Cheers, Joe. > From: phenixbb-request(a)phenix-online.org > Subject: phenixbb Digest, Vol 58, Issue 18 > To: phenixbb(a)phenix-online.org > Date: Sat, 18 Sep 2010 12:00:01 -0700 > > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Ligand restraints editing with REEL (Joseph Brock) > 2. Re: Ligand restraints editing with REEL (Ralf W. Grosse-Kunstleve) > 3. Resolve NCS masks (Florian Schmitzberger) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 18 Sep 2010 08:09:23 +0000 > From: Joseph Brock <joeylives2ride(a)hotmail.com> > To: <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Ligand restraints editing with REEL > Message-ID: <SNT120-W580E16EA4DC524ED59A3209B7C0(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi all, > > I'm working on a 1.5A structure that contains a novel ligand within the active site, which is an Arsenic derivative of Glutathione, using the Phenix GUI, version 1.6.4-486. > > I have been using the 'Molinspiration' webpage (http://www.molinspiration.com/docu/webme/) to generate a smiles string, which I then feed into ELBOW. Although the structure/chemical restraints of Glutathione should be unchanged by the covalent linkage to arsenic through the cysteinyl sulfur, the resulting restraints file consistently restricts one of the dihedrals to a value that is incompatible with the (quite clear) electron density. This occurs regardless of wether i use AM1 optimization, and is unresponsive to using native Glutathione (which refines into the corresponding density extremely well) as an input geometry file with any of the available 'Use geometry for' options (final geometry, initial geometry, etc). > > I then tried opening the output file in REEL and manually changing the corresponding dihedrals to those of glutathione, however after running simple optimization, the resulting restraints file has the same problem, and upon choosing the 'transer geometry and restraints' option (or any option) midway through running the 'eLBOW optimization' or 'AM1 optimization' options, Phenix consistently crashes. > > Any advice on how to transfer the origional geometry of native Glutathione to my new ligand effectively would be greatly appreciated. I'm a little confused as to the abilities of REEL, and how to affect them. > > Thanks so much in advance. > > Cheers, > > -Joe. > > >

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mlhl refinement
by Florian Schmitzberger 28 Sep '10

28 Sep '10

Dear All, I am running Phenix version 1.6.4.-486 on imac. I just wanted to refine (phenix.refine) a model with MLHL target and experimental phase information. Strange thing is when I load the mtz file, as written out from Phenix Autosol (overall_best_denmod_map_coeffs.mtz) into the GUI, the Phenix refine GUI does not seem to any phase information. Only picks up FP and SIGFP labels; but not the Hendrickson-Lattman coefficients, which are present. The following message comes up when I try to chose mlhl refinement: " You have selected 'mlhl' as the refinement target, but no experimental phases were supplied. If you wish to use phase restraints in refinement, please add or select experimental phases, or choose another target function". I guess it is not such a major problem as I can save the .eff file and manually edit it to include the HL coefficients and then run Phenix (as long as Phenix then recognizes them from the mtz file). I would also like to refine f' and f'', as the data are from a selenomethionine derivatized protein. From what I can see the default in Phenix.Autosol seems to be not to keep the F+/- and Dano labels for the output mtz file? So I suppose I do need to provide the initial mtz file or is there a way to change the output options for the coefficients in Phenix Autosol? Cheers, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

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Does Phenix have the library or program to maintain bond angle and bond length to create an extended chain?
by Rojan Shrestha 28 Sep '10

28 Sep '10

Hello: I am wondering whether Phenix has the library or program to maintain the ideal bond length and bond angle. The torsion angles of residue and xyz of each atoms are already known. I want to juxtapose residue or residues to create an extended chain. Thanks Regards, Rojan

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CCP4 Study Weekend 2011: "Model Building and Refinement and Validation"
by ronan.keegan＠stfc.ac.uk 24 Sep '10

24 Sep '10

Dear All, We're pleased to announce that registration for this coming January's CCP4 Study Weekend meeting is now open. The meeting will take place from January 5th to 7th, 2011 at University of Warwick in the UK. The topic of the meeting will be "Model building and Refinement and Validation". This year's organisers, Roberto Steiner and Bernhard Rupp, have arranged the usual mix of interesting and stimulating lectures from some of the foremost speakers in the field along with the opportunity to see demonstrations of the latest software developments from CCP4 during the lunch-time bytes sessions. For more information on the program and registration details please go to the Study Weekend website: http://www.cse.scitech.ac.uk/events/CCP4_2011/ We look forward to seeing you in Warwick. Best wishes, The CCP4 team -- Scanned by iCritical.

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separate amino acid chains
by Florian Schmitzberger 23 Sep '10

23 Sep '10

Dear All, Quick question regarding the handling of different amino acid chains in the Phenix Autobuild GUI. From the manual I understand that different amino acid chains are separated by > ? I pasted the my amino acid chains in the GUI separated with > ; I don't think in my case Phenix recognizes the different chains as such, but as one contiguous protein. Am I missing anything obvious? Regards, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

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autobuild : use of ncs
by Lepore, Bryan 22 Sep '10

22 Sep '10

i read and see that autobuild finds ncs automatically and uses it. i have one .pdb with one copy of the model for segid's A and B, and chainid's A and B. however, i notice sometimes in density modification that ncs has "NO" flags as to its use, and the output .pdb's have a single chain in them. refinement has sensible .eff's and such for ncs, there's find_ncs_* output, but some .log's suggest it is not specified or used. so just generally, how is ncs used - e.g. is it strict, which would explain a single chain the output .pdb? -bryan

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PDB Tools and CNS formatted structure factors
by Joseph Noel 22 Sep '10

22 Sep '10

Is there anyway with the PDB Tools to renumber protein chains? I have a model that doesn't correspond to the actual sequence, off by a couple of residues and just looking for a quick way to change that. Also, which module in Phenix is used to read in and convert CNS formatted ascii structure factors to the mtz read by phenix other then using ccp4. ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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FYI : autobuild : "refine_pdb_in.mtz is missing" etc.
by Lepore, Bryan 22 Sep '10

22 Sep '10

here's a google-able post of a *solved problem* for the archive : phenix 1.6.4-486 (latest official release as of 21sep2010) building ends (FINISHED) with error messages (see below). some associated job setup details : phenix.autobuild with CL flag refine_eff_file_list=my_refinement_params.eff cartesian or torsion annealing, or start_temperature work OK in building/refinement. two segid's in .pdb, one chain id etc. SOLUTION : use the latest build. i used phenix-dev-533 GNU/Linux 32-bit. and thanks especially to Tom Terwilliger for the solution. [key error messages]: Failed to carry out AutoBuild_multiple_models: Sorry a subprocess has failed... Failed to carry out AutoBuild_build_cycle: Sorry...the file AutoBuild_run_1_/TEMP0/refine_pdb_in.mtz is missing...

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autobuild : annealing
by Lepore, Bryan 21 Sep '10

21 Sep '10

[ phenix 1.6.4-486 ] looks like autobuild annealing is Cartesian. are there any (simple) tricks to get torsion, b/c seems there are no flags for it. -bryan

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deleting jobs in phenix
by Sebastiano Pasqualato 20 Sep '10

20 Sep '10

Hi all, sorry for the maybe silly question, but I don't seem to find a way to delete jobs from a project in phenix (I'm using ver. 1.6.2-473 on a MacBook Pro). The 'job history' tab on the main window does not allow that, so I was wondering if there's an easy way to do it. Thanks a lot for the great software suite, keep it up guys, ciao s. -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990

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Phenix renewal support
by Paul Adams 20 Sep '10

20 Sep '10

Dear Phenix Users, I hope that Phenix has been helpful in your work. We are in the process of submitting a renewal for funding of the Phenix project and I would be most appreciative of your support for our renewal. If you would be willing to write me a short note, before September 18th, in the form of a signed letter (PDF) that indicates how much Phenix has helped your research, that would be incredibly helpful for our renewal. You can send your letter to me at PDAdams(a)lbl.gov Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Kathleen Moody [ KLMoody(a)lbl.gov ] [ 1-510-495-2506 ] --

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R factor
by zhangh1＠umbc.edu 19 Sep '10

19 Sep '10

Hi, I want to calculate Fc based on the PDB file and reproduce the R factor in it. I first tried phenix.model_vs_data. It optimized ksol bsol and b_cart, and the output R factor (0.2143) is close enough to that in PDB (0.215). However, it didn't generate mtz files containing the calculated Fc. Then, I take the optimized ksol bsol and b_cart as the input and tried phenix.fmodel. I wrote my own code to calcuate the R factor. However, I got a lower R factor (0.2078). I think the reason might be my R calculation formula (sigma(fo-fc)/sigma(fo)) is wrong; or model_vs_data did more than just did flat solvent correction and anisotropic scaling. So, I am wondering whether phenix can: (1) Do the similar thing as model_vs_data (hope can be somehow faster:), but generate Fc-containing mtz file; (2) Do a simple R factor calculate to see whether my code is wrong (maybe answered already:) Thanks! Best Regards, Hailiang

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generate Rfree flag for twinned crystals with 3 twin fractions
by Zheng Zhou 19 Sep '10

19 Sep '10

Dear all After reading the informative posts in mailing list, I started to deal with my first twinning dataset. The space group is P3. Xtriage found 3 twin laws. R vs R statistics indicated perfect twinning for two twin laws and one is twin with RPS. I realize that twin-related reflections should be in the same work or free group. Could phenix handle the Rfree flag correctly for me when there are more than one twin fraction identified? By applying one twin law, the Rfree dropped from 37% to 28% using phenix. When I use Refmac, the twin fractions are refined and the Rfree is down to 26%. I copied the Rfree flag from phenix to the ccp4 in this case. When I let ccp4 generate Rfree flag automatically, the Rfree is refined to 26% too. Should I label the Rfree at a higher space group? Thanks for your advice Best, Zheng (Joe) Zhou

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Resolve NCS masks
by Florian Schmitzberger 18 Sep '10

18 Sep '10

Dear All, I would have a question regarding the use of masks in Resolve in Phenix for density modification: Is it possible to output the NCS and/or solvent masks Resolve is using during the Autosol run (similar as the options from the stand alone Resolve version) such as: mask_as_mtz ncs_mask_file mask.mtz protein_mask_file What are the best criteria (other than the final maps of course) within the output from Phenix.resolve to judge if the NCS (and/or solvent) mask was chosen adequately? (NCS_overlap?) I am mostly concerned if the masks chosen do include some of the more peripheral parts of my protein molecule and do not flatten these regions. Secondly, it is possible within Phenix Autosol wizard to supply a pdb file (with dummy atoms) for the mask for Resolve to construct the NCS mask? i.e. similar to set mask_pdb file= dummyatom.pdb Regards, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

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