- phenixbb - phenix-online.org

Long Distant Restraints
by Bradley Hintze 18 Jul '14

18 Jul '14

Hey PHENIX, I am wondering if I can define a distant restraint longer that 3A in a custom restraint file? The conventional way of doing this is to provide : refinement.geometry_restraints.edits { C8_C1=chain C and resid 8 and name C1' D10_C1=chain D and resid 10 and name C1' bond { action = *add atom_selection_1 = $C8_C1 atom_selection_2 = $D10_C1 distance_ideal = 9.1 sigma = 0.02 slack = 0.5 } Obviously this is a distant and not bond restraint. 9.1 exceeds the allowed length of 3 for a bond. Is there a different type of restraint that allows longer distances? Thanks! -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry

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Refinement cycles
by George Devaniranjan 17 Jul '14

17 Jul '14

Hi, I was wondering if there is a reason for setting the default number of refinement cycles to 3 in Phenix refine? is there a number of cycles at which point it becomes unacceptable to run so many ? Thank you, George

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B factors too high for low resolution data refinement
by 李翔 15 Jul '14

15 Jul '14

Hi everyone, I am working on my low-resolution data (~6.5 A). When I was doing refinement with PHENIX, the B factors remain pretty high (~400, not sure whether it is normal for the data with such resolution.) And B factors further increased after group B factor refinement (~500). Does it mean the group B factors refinement not working or is there a way I can somehow define a limit for B-factors? (I read one previous topic a few years ago which indicates the B factor can not be controlled. Not sure whether it is available now). Thank you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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So what is unique?
by Kenneth A. Satyshur 15 Jul '14

15 Jul '14

There is some disagreement on terms used to deposit data. We need a definition and an algorithm for each definition. "Unique Reflections" My definition is all the possible reflections out to the highest resolution reported not related by symmetry. Where can I find this? The .mtz contains a list of all HKL calculated to the highest resolution. Usually, we are not able to measure all these diffraction spots due to limits of the detector, mechanical limits, crystal orientation, etc. 'Total reflections' The depositions server asks for total reflections. I assume it wants only those unique reflections we were able to collect, regardless of the sigma cut off. These are called 'observed'. The total we use in refinement will be a subset of the 'unique observed' that are cut on sigma. However, some crystallographers believe that we should not cut on sigma since some of the intensities may in fact be zero. Is this a question for the Refmac and Phenix people? Please give us some guidance and maybe a reference or two that we can use. thanks -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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cifs still in pdb v2
by Guenter Fritz 14 Jul '14

14 Jul '14

Dear Pavel and Nat, can you include in future phenix versions the FAD.cif, NAD.cif and data_NAI.cif / NAI.cif in pdb v3? Currently both are still pdb v2. I usually simply copy the cifs pdb v3 into the mon_lib directory , but sometimes I forget it and stumble over it. Thanks and best wishes, Guenter

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Maximum-likelihood score calculation
by Jouko Virtanen 12 Jul '14

12 Jul '14

Hi all, I would like to calculate the maximum-likelihood score given an input structure and an mtz file. How can I do that? Thanks in advance. Best regards, Jouko

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Real space implementation of DEN refinement?
by Oliver Clarke 11 Jul '14

11 Jul '14

Hi all, Just wondering whether there is any capacity to include DEN restraints in phenix.real_space_refine, e.g. as implemented in the program DireX (see ref below), or any possibility of implementing such in a future release of PHENIX? This would be very handy for refinement of models into low resolution maps (particularly EM maps). Also, on a different but related topic, does anyone have any suggestions as to how to handle model validation (local and global) at low resolution in real-space? It seems as though there is not a solid consensus on how to handle this. Many thanks, Oliver. 1. Schröder, G. F., Brünger, A. T. & Levitt, M. Combining Efficient Conformational Sampling with a Deformable Elastic Network Model Facilitates Structure Refinement at Low Resolution. Structure 15, 1630–1641 (2007).)

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Twinning in data reduction and phenix.refine
by Chen Zhao 11 Jul '14

11 Jul '14

Dear all, I am now dealing with a pseudo-merohedral twin (3.2 A, P1 twinned into C2), and I have a couple of questions concerning the data reduction and refinement: 1) R-free flag in refinement a) For twin refinement, I know the reflections related by the twin law should have the same R-free flag. If I process my data in P1, and generate the R-free flag by phenix.refine using the key word xray_data.r_free_flags.use_lattice_symmetry=True, can phenix generate the R-free flags considering the 2-fold point group symmetry and deal with the twinning properly? b) I read that the R-factor could go down to around 40% in twin refinement in the presence of twinning even if the model is completely wrong. For my understanding, this could be due to the fact that the reflections are correlated by the twin law. If the R-free flags are chosen in the highest lattice symmetry, will the R-free still suffer from this problem? 2) Twin fraction In phenix.xtriage, the predicted twin fraction is about 30%. However, in phenix.refine, the twin_fraction is always between 46% to 50%. Why could this happen? 3) Data reduction I am not very clear about this point, since I just started dealing twinning. But what I am thinking is whether it is a good idea to merge the Friedel pair in the presence of twinning. Since the two twin domains have different hkl index if considering one as the reference, is the Friedel law still valid? This might be a very simple mathematical problem. I really appreciate your answers! Sincerely, Chen

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Anomalous or not?
by CPMAS Chen 10 Jul '14

10 Jul '14

Hi, Phenix Users, I recently collected data at SSRL. I used autoxds and multiscale to merge couple of datasets and hoped to see some anomalous signals. Now comes the questions. 1. if I use the default sigma(=2), then autoxds will report weak anomalous signals and leave the friedel flag off. If I lower sigma to 1.5, it will report strong anomalous signals. 2. when I used Xtriage under Phenix to check the data quality, it reported weak anomalous signal or at above 10A. 3. I used aimless (in CCP4) to merge data, it also reported weak anomalous signal. Which result should I trust? By the way, how can I view/display the ***.anamplot file, which is apparently xmgr format file, but I can not display in CCP4i. Thanks! -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Re: [phenixbb] Anomalous or not?
by Ryan Spencer 10 Jul '14

10 Jul '14

The question then becomes how do you know the bromine is in the crystal? Is it covalent on the protein? Is it covalent on the ligand? How do you know if the ligand is in the structure? We have seen rapid crystal degredation with Br at its edge. Do you see the resolution significantly degrade after a few frames? I don't think it's a processing issue with xds or with phenix. Ryan -------- Original message -------- From: CPMAS Chen <cpmasmit(a)gmail.com> Date: 07/10/2014 9:52 AM (GMT-08:00) To: Ryan Spencer <rspencer(a)uci.edu> Cc: Francis Reyes <Francis.Reyes(a)colorado.edu>,phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Anomalous or not? Well, let me make this clear. 1. I am using Br anomalous signal to identify the potentially bound ligand. 2. I do shoot the crystals at 0.92A. 3. the different crystals have different resolution, but anomalous signal was weak as reported by autoxds. Charles On Thu, Jul 10, 2014 at 12:25 PM, Ryan Spencer <rspencer(a)uci.edu> wrote: So I assume you were not able to shoot the crystal at ~0.92 A at SSRL or are the crystals sensitive? If you were limited to the single wavelength beam which is around 1A you’re dealing with a really low f” of 0.5322. There have been crystals solved with Sulfur using an in-house Cu sources (takes a lot of merged sets and anomalous is stronger at certain crystal angles) which gives about the same anomalous scattering as Br. Is the bromine covalent or is it soaked ion? Alternatives – soak with potassium iodide and get a dataset from an in-house source (iodine f” 6.6 at 1.54), or at least the anomalous locations. You may get a partial model to use for replacement at that point. Did each processed dataset have the same level of anomalous signal when processed individually? Ryan From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of CPMAS Chen Sent: Thursday, July 10, 2014 8:55 AM To: Francis Reyes Cc: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Anomalous or not? Francis, My anomalous plot for Br is more like your Cobalt 1 site less redundancy. Ryan, As my Br anomalous signals are weak, I merged signals from multiple crystals. Meanwhile I am looking into the detail about the autoxds processing as suggested by Tim. Thanks, On Thu, Jul 10, 2014 at 10:02 AM, Francis Reyes <Francis.Reyes(a)colorado.edu> wrote: In addition to Tim's comments above, using loggraph to see the anomalous CC plot from scala is a good qualitative indicator of whether you have anomalous signal.. Some data points for what reasonable plots (and their corresponding XDS SigANO's) look like: https://dl.dropboxusercontent.com/u/19558536/AnomalousCC.pdf F On Jul 10, 2014, at 9:03 AM, CPMAS Chen <cpmasmit(a)gmail.com> wrote: > > Which result should I trust? By the way, how can I view/display the ***.anamplot file, which is apparently xmgr format file, but I can not display in CCP4i. > -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ****************************************************** -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Postdoctoral Position in Membrane Protein Structural Biology
by Noinaj, Nicholas (NIH/NIDDK) [E] 07 Jul '14

07 Jul '14

Two postdoctoral positions in structural biology are available starting in August in my new laboratory within the Biological Sciences department at Purdue University. As part of the Markey Center for Structural Biology, my lab will integrate electron microscopy and X-ray crystallography with biochemical methods to study the biogenesis of beta-barrel membrane proteins in Gram-negative bacteria with a focus on eventual therapeutic development against pathogenic strains of bacteria (See Noinaj et al., Structure (in press, 2014), Nature, 501:385-390 (2013), and Nature, 483:53-58 (2012)). The Markey Center for Structural Biology at Purdue is recognized worldwide for its leadership in structural biology of viruses, membrane proteins, receptors, signaling proteins and enzymes in addition to methods development in crystallography, NMR and electron microscopy. My lab is located within the Hockmeyer Hall of Structural Biology which boasts state-of-the-art shared resources including a Titan Krios cryo-TEM, Bruker Avance-III 800 MHz NMR, Rigaku X-ray generators and detectors, and other advanced instrumentation available at the Bindley Bioscience Center, the Birck Nanotechnology Center, and the new Center for Drug Discovery. In addition, Purdue is in close proximity to the Advanced Photon Source at Argonne National Lab for convenient access to synchrotron data collection. The successful candidate(s) should be highly motivated, have strong written and communication skills, have (or expect) a recent PhD in structural biology, biophysics, biochemistry, or other related field of study and have previous experience in working with membrane proteins and/or X-ray crystallography or electron microscopy. Applicants should send a CV, names of three referees and a statement describing your interests and relevant work experience to Nicholas Noinaj at nicholas.noinaj(a)gmail.com<mailto:[email protected]>. Nicholas Noinaj Purdue University Department of Biological Sciences 333 Hockmeyer Hall 915 W State St West Lafayette, IN 47907

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Autobuiold from polyalanine model
by Chieh Yin 07 Jul '14

07 Jul '14

Dear Phenix Users, I am doing the molecular replacement to solve a membrane protein structure(transmembrane and soluble domain). The structure of the soluble domain is known, 200AAs. And there is a homology structure of transmembrane domain, 350AAs. I used the polyalanine model of the homologous model of transmembrane domain to do the first search. I got a solution with TFZ 16. Then used the partial solution to do the second search with the soluble domain as the model.I also got a solution with TFZ about 15. The density map showed I got the right solution. And the simple rigid body refinement yielded a Rfactor/Rfree 0.29/0.32. Then I used the polyalanine model and the soluble domain as the starting model to do the phenix autobuild. But it seemed that Autobuild didn't replace the alanine with the real sequence AAs. I tried to set the rebuild in place to false but I still got the same result. The Autobuild even didn't change any amino aside reside from the starting model. I hope you could figure out the problem for me. Thank you in advance! Best regards, Jie

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distinguish between metals
by Aleksandar Bijelic 01 Jul '14

01 Jul '14

Dear phenix developers and users, I wanted to ask if there is a possibility to considerably distinguish betwenn two/three metals. I crystallized an iron-binding protein (transferrin in apo form) with a Ru- and Ga-compound. I see density in the metal-binding site which should come from the Ru/Ga metal since crystallization was done with the apo-form, but nevertheless I need to prove this. The wavelength of the X-ray was 1.02 Angstrom and the respective f''and f' values for the metals are +1.66e/+0.30e (Fe), +1.62/-0.5 (Ru) and +2.95/-0.76 (Ga). Is it possible to distinguish between Ru/Ga and Fe and thus to prove that Fe was not bound? The resolution is moderate with 3.1 angstrom and all metals are able to exhibit the same coordination geometry, thus you cannot distinguish according to the geometry. Unfortunately, I was also not able to measure the crystal with multiple wavelenghts because the crystals were very fragile. I hope you can help me and give me some advice. Thank you in advance. Best Regards, Aleks -- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 1090 Wien Tel: +43 1 4277 52536 e-Mail:[email protected]

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mailing list
by Aleksandar Bijelic 01 Jul '14

01 Jul '14

aleksandar.bijeli(a)univie.ac.at -- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 1090 Wien Tel: +43 1 4277 52536 e-Mail:[email protected]

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select sphere syntax
by Tanner, John J. 28 Jun '14

28 Jun '14

Is there a way to select a sphere of residues in the phenix.superpose_pdbs command, analogous to the "around" syntax in cns? I tried "within" and "around" in phenix.superpose_pdbs but got "Atom selection syntax error". Thanks. Jack Tanner John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 email: tannerjj(a)missouri.edu<mailto:[email protected]> phone: 573-884-1280 fax: 573-882-2754 http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

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Coot DNA names
by Bradley Hintze 27 Jun '14

27 Jun '14

Hey Folks, Does anybody know a quick way to convert DNA atom names back to PDB standard after coot modifies them to match the ccp4 dictionary? Thanks -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry

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quick R-value calculation
by Patrick Loll 27 Jun '14

27 Jun '14

I have a structure pulled from the PDB that contains a gnarly, complex ligand, for which I don't have a library. I just want to do a quick R-value calculation +/- ligand, and I don't want to go to the trouble of building and testing a library just for this purpose. Is there some way to induce phenix.refine or phenix.model_vs_data to do the R-value calculation even if it doesn't recognize the nonbonded energy type symbols? Thanks for any tips. Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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seeking help about running SCALEPACK2mtz
by chen c 26 Jun '14

26 Jun '14

Dear PHENIXBBers: I'e got a problem about data processing when running SCALEPACK2mtz. Hope you can give me some advice on that. Here's my problem: I have an .sca file processed by HKL2000 about 4 years ago, I just ran the Scalepack2mtz program in order to transform it into .mtz file. However, the program keeps running. To ensure that the Scalepack2mtz program is ok, I use another .sca file for verification and it turns out that this file for verification is successfully transformed into .mtz file within seconds. I checked the .log file, the program keeps running when there are the following messeages: "Mean acentric moments I from input data: <I^2>/^2 = 2.360 (Expected = 2.000, Perfect Twin = 1.500) <I^3>/^3 = 9.187 (Expected value = 6.000, Perfect Twin = 3.000) <I^4>/^4 = 52.348 (Expected value = 24.000, Perfect Twin = 7.500) Mean acentric moments I from anisotropically corrected data: <I^2>/^2 = 3.121 (Expected = 2.000, Perfect Twin = 1.500) <I^3>/^3 = 12.788 (Expected value = 6.000, Perfect Twin = 3.000) <I^4>/^4 = 57.952 (Expected value = 24.000, Perfect Twin = 7.500) " does this means that the .sca file isn't processed properly? I also checked the scale.log file, and there are the following messages: " Shell Summary of observation redundancies: Lower Upper % of reflections with given No. of observations limit limit 0 1 2 3 4 5-6 7-8 9-12 13-19 >19 total 50.00 5.60 5.9 6.1 18.0 15.1 26.9 19.7 8.3 0.0 0.0 0.0 94.1 5.60 4.45 7.9 9.4 13.0 12.9 23.2 27.5 6.1 0.0 0.0 0.0 92.1 4.45 3.88 19.2 5.6 13.3 13.5 20.4 21.9 6.0 0.0 0.0 0.0 80.8 3.88 3.53 31.9 6.5 11.6 11.3 14.9 17.9 5.8 0.0 0.0 0.0 68.1 3.53 3.28 2.4 4.7 11.3 15.3 23.5 34.1 8.7 0.0 0.0 0.0 97.6 3.28 3.08 0.2 3.6 7.0 15.4 23.7 40.1 9.9 0.0 0.0 0.0 99.8 3.08 2.93 0.4 4.4 8.7 16.8 21.1 41.3 7.2 0.0 0.0 0.0 99.6 2.93 2.80 4.2 8.0 12.7 15.2 20.3 33.7 6.0 0.0 0.0 0.0 95.8 2.80 2.69 15.4 9.1 14.0 13.8 19.2 25.2 3.3 0.0 0.0 0.0 84.6 2.69 2.60 31.6 16.2 11.7 14.2 13.7 10.6 2.0 0.0 0.0 0.0 68.4 All hkl 11.8 7.3 12.2 14.4 20.8 27.1 6.4 0.0 0.0 0.0 88.2 " This clearly indicates an ice ring problem in the data-collection process. However, the ice ring problem shouldn't have caused the error during the .sca to .mtz process. In fact, I have use it for structure-solvement, and currently the two R factor is around 30%. However, the large deviation of <I^3>/^3 or <I^4>/^4 do means something wrong. Would you tell me what exact mistakes did I make? Can I use this .sca file for subsequent structure solving and refinement? Great thanks for your help! best regards chen

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Anisotropic B-factor restraints
by Elke De Zitter 26 Jun '14

26 Jun '14

Dear All I'm refining a protein structure with a resolution of 1.25 A, using Phenix GUI version 1.9. I am refining the B-factors for the protein atoms anisotropic and those for the water molecules isotropic. How can I restrain the anisotropic B-factors so that bonded atoms have similar ellipsoids (like the SIMU and DELU commands in Shelx making the atoms moving similarly in direction and amount)? Thanks Elke Elke De Zitter PhD student, KU Leuven Biochemistry, Molecular and Structural Biology Celestijnenlaan 200f - bus 2404, 3001 Leuven Room 00.84, +32 16 3 26530

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Combining phases?
by Yuri 26 Jun '14

26 Jun '14

Dear All, Im struggling with a structure. I have a good native data set with resolution 2.1A and a data set with ok stats collect at low energy trying to extract some anomalous signal from intrinsic sulphur atoms (6/ASU/400aa). Using a model of one of the domains I got a MolRep solution that has somewhat convincing features in the electron density maps some portions of the structure but not in others. I also ran HySS and obtained some coordinates for the 6 sulphur atoms but the map here is uninterpretable. Xtriage suggests the anomalous is only good until about 8A so I am not that surprised. Is there any way I can try to combine my putative MolRep model and phases with the sulphur anomlaous signal and maybe get better maps to build into? If so, how would I do that using PHENIX? thanks for the help -- Yuri Pompeu, Ph.D.

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GRC/GRS Diffraction Methods
by Anastassis Perrakis 26 Jun '14

26 Jun '14

Dear all, I am sorry to send one more post to the already overloaded bb, but please let me remind you for the last time that the deadline for applications for the GRC and the GRS is approaching, and is only three days from now. http://www.grc.org/programs.aspx?id=11654 We are all looking forward to welcome you at Bates College in a month from now, and we do hope for a few more last minute participations: we need all of you to make it as exciting and fun as possible! Best regards, Tassos

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Multiple Metal Sites in Autosol
by Ryan Henry Gumpper 24 Jun '14

24 Jun '14

??Hello All, ?I have a question regarding the metal assignments when using Autosol to process SAD datasets. I am new to field and I want to make sure that I am doing things correctly. My enzyme should contain 2 metal sites, one with Cu and one with Fe. We collected data at the Fe-edge, the Cu-PreEdge, and the Cu-Edge for a comparison. When I tell Autosol to search for 1 Cu site, using the Cu-Edge data, and another heavy atom Fe, it finds 33 sites all Cu with 2 being Fe. Likewise, using the same dataset, when I include S as an additional anomalous scattering moiety, it will find 1 Cu in the correct position and 32 S atoms--my protein does not contain 32 S atoms. Finally, when I include every possibility that was in my crystallization buffer, this includes a fairly high concentration of MgCl2, and I tell it to search for 1 Cu site with the additional heavy atoms being Fe, S, Mg, and Cl, it seems that it is able to assign the Cu correctly, however it now gives Mg coordinated with Cu instead of H2O molecules, and this is not possible. Should I include Mg and Cl in the search? And S? Also, why would it not be finding the Fe? Furthermore, and most importantly, why is it assigning so many heavy atom sites? I am having similar problems with the other two data sets as well. Thank you very much in advance! Regards, Ryan Gumpper

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Re: [phenixbb] Iron (FE2) metalloprotein
by Nathaniel Echols 24 Jun '14

24 Jun '14

On Tue, Jun 24, 2014 at 1:11 AM, Egor Tchesnokov < etchesnokov(a)chemistry.otago.ac.nz> wrote: > Thank you for the comment. > The model I use for Phaser is coming from Sculptor, so it does not have > heteroatoms. > I introduce heteroatom (Fe) only after Phaser. I use Phaser-EP to find it, > eventhough it is obvious from the density. Then I merge Fe and Phaser.pdb > in Coot after which I feed it to ReadySet. So the pdb that I give to Refine > either have Fe with occupancy of 1, <1 or >1 (I tried both). I use PDB > editor to add charge, but the outcome is still the same. After refinement > Fe occupancy is either 1 or very close. > My apologies, I misinterpreted your message. Is this just a case of "name that blob?" If so, I suggest posting images of the density around the iron to the list (and probably ccp4bb as well) asking for suggestions. It's very likely that someone will have encountered similar density before. -Nat

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Iron (FE2) metalloprotein
by Egor Tchesnokov 24 Jun '14

24 Jun '14

Hello, Active site contains iron (FE2) coordinated by three histidines. After Phaser the active site does not contain un-explained green density. After Refinement blobs of various shapes appear in the vicinity and upto 3-4A of active site iron. Refinement is done using occupancy and anomalous of iron options. Buffers do not contain molecules that could fit in those blobs. Any suggestions? Thank you Egor

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Geometry problems
by Yarrow Madrona 24 Jun '14

24 Jun '14

Hello, I have a ligand bound to a heme and I have supplied a CIF for phenix in refinement. I did not include all atoms just, those close to the iron. Unfortunately, I am getting very large reported bond deviations for other atoms. For example I get: bond pdb="FE HEM A 410 " pdb=" N3 CPZ A 500 " ideal model delta sigma weight residual 2.100 4.054 -1.954 2.00e-01 2.50e+01 9.54e+01 N3 and FE are not bonded and not expected to be close to one another. it is not supported by the structure. I suspect that this is causing my overall bonds deviations to be ~0.03 even if I greatly reduce the weight of wxc. Is it necessary to enter all of these outliers into the .cif file or is there an easier way? Thank you.

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Sulfate at 3-fold axis
by Zhou, Tongqing (NIH/VRC) [E] 23 Jun '14

23 Jun '14

Dear Colleagues, I am refining a structure and there is a SO4 on the 3-fold axis. What I did was to put atom S and O1 on the 3-fold with occ=0.33, and O2 with occ=1, and no O3 and O4 in the pdb (O3 and O4 will be the symmetry of O2). But when I refine it, Phenix complains close non-bounded distances for both S and O1. Is there a way to refine this sulfate? Thanks! Best regards, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

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after updating my system 1.9 1692
by Afshan Begum 23 Jun '14

23 Jun '14

Dear Developers, I am wondering why my system is getting too much slow after update the phenix new version??? before that its take few mints to finish my job but now its take more than 7 hour just finish one job .could you help me regarding this. Many thanks Best Regards AFSHAN

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Update waters and chain ID
by Scott Lovell 20 Jun '14

20 Jun '14

Hi All, I'm refining a structure (dev-1726) that contains 24 protein subunits which are assigned to chains A-X in the PDB file. Chains Y and Z are assigned to a couple of ligands and the ordered solvent molecules are chain w (lower case). I decided to give the "Update waters" option a try during refinement but it seems that the chain ID of the ordered solvent is changed to chain S by default. Since I already have a protein subunit assigned to chain S, the following error is obtained when I try to open the model in Coot (ERROR 39 READ: Duplicate sequence number and insertion code.). To enable visualization of the model in Coot, I can of course manually change the chain ID for the ordered solvent in the output PDB file using a text editor. However, is there a way to override the ordered solvent default chain ID in Phenix to prevent duplication? Thanks, Scott __________________________________ Scott Lovell Ph.D., Director Protein Structure Laboratory University of Kansas Del Shankel Structural Biology Center

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More problems with HEM.cif?
by Yarrow Madrona 20 Jun '14

20 Jun '14

Hello, The HEM.cif in $Phenix/chem_data/mon_lib has ideal angles of 1.337 for single bonds on the vinyl groups. HEM CAC CBC coval 1.337 0.02 HEM CAB CBB coval 1.337 0.02 As far as I know these are single bonds and the ideal bond angles should be around 1.5. -Yarrow

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Rigid ligand placement into density map
by Phan, Jason 19 Jun '14

19 Jun '14

Hi All, Is there an option or flag in Phenix LigandFit to place the ligand rigidly with pre-generated conformations without torsional adjustments? Would setting "conformers = 1" and "refine_ligand = false" work? Coot Find Ligand with the "flexible" option unchecked seems to work but it won't tell you which original conformer (SD file) the "fitted ligand" comes from since all the conformers have the same residue name and number. Coot doesn't write out SD format either so any ID associated with the original conformer is lost. Jason

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molprobity coot TODO python script
by wtempel 19 Jun '14

19 Jun '14

Hello, I noticed the following when loading a phenix-created python TODO script using the 4730 and 5100 Linux-x86_64-ubuntu-12.04.3-python-gtk2 coot builds. A "MolProbity to-do list" window opens. GUI functions such as "Show Probe dots" and "Overlap only" are working as expected. Clicking anywhere within the "C-beta outliers" or "Severe clashes" areas of the window moves the display center to problem areas of the structure. But: no text is visible in any of the columns ("Chain", "Residue", "Name", etc. of the "C-beta outliers area"; "Atom 1", Atom 2", "Overlap" of the "Severe clashes"). As a result, I cannot select a specific problem spot for centering. Any ideas? Another molprobity related question: us there a phenix script that produces a list of NQH flip candidates? Thank you, Wolfram Tempel Attached image: Clicking in the white areas on the window in the attached screen grab will move the center of the coot display, but labels for the problem areas are not shown in the window's columns.

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GUI program to calculate effective resolution of a data set
by Alexandre OURJOUMTSEV 19 Jun '14

19 Jun '14

Dear All, Recently, there was a ccp4bb conversation concerning the definition of a ‘real’ (effective) resolution of (incomplete) diffraction data sets. I am happy to announce that a corresponding GUI program EFRESOL is available now and you may download it from the Web site: http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/efresol/Efresol.html http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Sites.html The method is described in L.Urzhumtseva, B.P.Klaholz, A.Urzhumtsev (2013) Acta Cryst., D69, 1921-1934. We would like to thank Joel Bard, Tom Peat, Rajan Prabu and especially Boaz Shaanan for testing the original version of the program. With best wishes, Sacha Urzhumtsev

1 1

Re: [phenixbb] special positions
by Yarrow Madrona 18 Jun '14

18 Jun '14

Hi Pavel, It turns out I do have some special positions. Waters sit near a 2 fold axis. I have given them 0.5 occupancy. No error comes up but they simply get kicked out of the electron density. Maybe I should turn off rigid body refinement since I don't need it? Below is a link to a screen shot. https://www.dropbox.com/s/lt3hqzjmygin9l8/special_position.png On Wed, Jun 18, 2014 at 8:49 AM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Yarrow, > > oh good! I'm glad you solved the problem -:) > > All the best, > Pavel > > > On 6/18/14, 8:02 AM, Yarrow Madrona wrote: > > Hi Pavel, > > Thanks for your quick response. It turns out that after I reprocessed a > data set in a higher symetry space group I forgot to use a reference mtz so > the orientation was completely off. I just re-ran phaser and everything > worked fine. I didn't run rigid body refinement after phaser. > > The original error message didn't list the atoms and I am not sure how > it could have any atoms on special positions with the solution being > completely wrong. Probably nothing to worry about. > > -Yarrow > > On Tuesday, June 17, 2014, Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> Hi Yarrow, >> >> ok, I wish that error message (that I put a while ago, in 2009 to be >> precise) lists those atoms... Can you send me the file so I can tell you >> what these atoms are? >> >> In general, if at rigid-body refinement stage you have atoms at special >> positions it is unlikely to be right. >> >> Pavel >> >> On 6/17/14, 12:56 PM, Yarrow Madrona wrote: >> >>> Hi, >>> >>> I am trying to do rigid body refinement, however I get an error in >>> phenix telling me that there are atoms at special positions. >>> >>> I am not sure how to determine which atoms are at special positions so >>> that I can exclude them from rigid body refinement. Can someone help me >>> with this? Thank you. >>> >>> -Yarrow >>> >> >> >

2 3

Calculate F (model) + Calculate Map Correlation
by George Devaniranjan 18 Jun '14

18 Jun '14

Hi, I am trying to use phenix and I was trying to do the following: Take a PDB, generate a MTZ file using Calculate F (model) and lets call it native.mtz then change a few phi and psi values of the pdb (so its slightly different from the native), run Calculate F (model) model.mtz Now I tried to calculate the CC of the two MTZ using Calculate Map Correlation. I get the following: "Missing at least one map file or label" What am I doing wrong? Thank you, George

3 3

Calculation of RSR for a fragment of PDB
by George Devaniranjan 18 Jun '14

18 Jun '14

Hi everyone, I apologize at the beginning itself as I am new to using PHENIX/X-ray crystallography so this question might not make the most sense but I will try and explain it well. I cut out a part of a map for a PDB fragment using phenix map cut out density resulting in a MTZ file. Now I changed the fragment (changed its phi and psi externally) and want to calculate the RSR [real-space R -factor] for the model based on the old density (to check if I have made things worse or not). how can I go about this? I tried using phenix.refine couldn't get it to work. I have attached the MTZ fragment, the original PDB fragment and the modified PDB fragment. native: nativeFragment.pdb model: modelledFragment.pdb MTZ: cut_out_density.MTZ (I can see mine is worse but I want to quantify that "badness") Thank you, George

2 4

Re: [phenixbb] special positions
by Yarrow Madrona 18 Jun '14

18 Jun '14

Hi Pavel, It turns out I do have some special positions. Waters sit near a 2 fold axis. I have given them 0.5 occupancy. No error comes up but they simply get kicked out of the electron density. Maybe I should turn off rigid body refinement since I don't need it? Below is a link to a screen shot. https://www.dropbox.com/s/lt3hqzjmygin9l8/special_position.png -Yarrow On Wed, Jun 18, 2014 at 8:49 AM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Yarrow, > > oh good! I'm glad you solved the problem -:) > > All the best, > Pavel > > > On 6/18/14, 8:02 AM, Yarrow Madrona wrote: > > Hi Pavel, > > Thanks for your quick response. It turns out that after I reprocessed a > data set in a higher symetry space group I forgot to use a reference mtz so > the orientation was completely off. I just re-ran phaser and everything > worked fine. I didn't run rigid body refinement after phaser. > > The original error message didn't list the atoms and I am not sure how > it could have any atoms on special positions with the solution being > completely wrong. Probably nothing to worry about. > > -Yarrow > > On Tuesday, June 17, 2014, Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> Hi Yarrow, >> >> ok, I wish that error message (that I put a while ago, in 2009 to be >> precise) lists those atoms... Can you send me the file so I can tell you >> what these atoms are? >> >> In general, if at rigid-body refinement stage you have atoms at special >> positions it is unlikely to be right. >> >> Pavel >> >> On 6/17/14, 12:56 PM, Yarrow Madrona wrote: >> >>> Hi, >>> >>> I am trying to do rigid body refinement, however I get an error in >>> phenix telling me that there are atoms at special positions. >>> >>> I am not sure how to determine which atoms are at special positions so >>> that I can exclude them from rigid body refinement. Can someone help me >>> with this? Thank you. >>> >>> -Yarrow >>> >> >> >

1 0

(no subject)
by Orpheus Mandal 18 Jun '14

18 Jun '14

Hi, Is there any way to perform unrestrained refinement on some selected residues in phenix GUI? Thanks, Orpheus

2 1

Rotamer Selection in Low Resolution Data
by Antony Oliver 18 Jun '14

18 Jun '14

Dear Crystallographic Community, Apologies for the cross-posting, but I *do* routinely use programs from all three software packages. I find myself refining a relatively low resolution structure (3.5 Angstrom) - with 8 molecules in the asymmetric unit. Is there a *simple* automated way to place “optimal-fit to electron density" side-chain rotamers into my model? Preferably in an NCS-independant manner? With thanks, Antony. - - - - - - - - - - - - - - - - - - Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ - - - - - - - - - - - - - - - - - - email: antony.oliver(a)sussex.ac.uk<mailto:[email protected]> tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 http://www.sussex.ac.uk/lifesci/oliverlab http://tinyurl.com/aw-oliver - - - - - - - - - - - - - - - - - -

1 0

special positions
by Yarrow Madrona 18 Jun '14

18 Jun '14

Hi, I am trying to do rigid body refinement, however I get an error in phenix telling me that there are atoms at special positions. I am not sure how to determine which atoms are at special positions so that I can exclude them from rigid body refinement. Can someone help me with this? Thank you. -Yarrow

2 1

coot -> fetch pdb & map using EDS
by Murpholino Peligro 17 Jun '14

17 Jun '14

Hi all How to proceed when Coot -> File -> Fetch PDB and Map using EDS does not work?

4 6

strange increase of R/Rfree in the last tow steps of a macrocycle
by Christian Roth 17 Jun '14

17 Jun '14

Dear Phenix-Team, I did a refinement of 5 macrocycles and it worked really well for 4 cycles, but in the last cycle the R/Rfee increased by nearly 1 percent. Specifically in the last ADP refinement. I don't really understand why. Do you have any comments what might be the problem. it seems that the as optimal chosen weight is not the optimal weight at all. I have copied the relevant part of the logfile in. Thanks in advance for your help. Best Regards Christian ----------Individual ADP refinement---------- R-FACTORS <Bi-Bj> WEIGHT TARGETS work free delta data restr 22.88 25.57 2.69 7.305 69.519 0.356 1.056 25.57 27.18 1.61 5.329 75.682 0.005 1.128 24.30 26.40 2.10 6.197 74.591 0.021 1.087 23.56 26.22 2.66 10.610 72.524 0.082 1.065 23.95 27.03 3.08 14.233 73.918 0.165 1.082 23.67 26.53 2.86 15.745 73.489 0.247 1.073 23.55 26.04 2.49 15.268 73.145 0.329 1.067 23.46 26.14 2.68 17.052 73.654 0.412 1.065 23.25 26.16 2.91 17.712 73.655 0.494 1.061 23.17 26.26 3.09 18.359 73.638 0.576 1.061 22.80 26.15 3.35 15.697 72.615 0.659 1.051 22.73 26.19 3.46 15.989 72.549 0.741 1.050 22.63 26.20 3.57 15.613 72.287 0.823 1.048 max suggested <Bi-Bj> for this run: 10.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.0 Best ADP weight: 0.021 Accepted refinement result: 24.30 26.40 2.10 6.197 74.591 0.021 1.087 |-ADP statistics (Wilson B = 38.175)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 22327 10961 22.54 481.16 74.59 0.25 0.84 0.33 | | all(noH): 11454 10961 22.73 481.16 70.40 0.25 0.84 0.33 | | Sol. : 410 0 24.44 104.66 49.01 None None None | | Mac. : 11044 10961 22.73 481.16 71.19 0.25 0.84 0.33 | | Hyd. : 10873 0 22.54 389.64 79.01 None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 22.735 - 68.577: 7910 | 5: 251.946 - 297.788: 42 | | 1: 68.577 - 114.419: 1983 | 6: 297.788 - 343.631: 25 | | 2: 114.419 - 160.262: 941 | 7: 343.631 - 389.473: 19 | | 3: 160.262 - 206.104: 407 | 8: 389.473 - 435.315: 5 | | 4: 206.104 - 251.946: 113 | 9: 435.315 - 481.157: 9 | | =>continue=> | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of anisotropy: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 0.250 - 0.309: 6325 | 5: 0.546 - 0.605: 227 | | 1: 0.309 - 0.368: 1851 | 6: 0.605 - 0.664: 110 | | 2: 0.368 - 0.428: 1094 | 7: 0.664 - 0.723: 49 | | 3: 0.428 - 0.487: 801 | 8: 0.723 - 0.783: 15 | | 4: 0.487 - 0.546: 474 | 9: 0.783 - 0.842: 15 | | =>continue=> | |-----------------------------------------------------------------------------| =========================== Idealize ADP of riding H ========================== r_work=0.2430 r_free=0.2640 r_work=0.2440 r_free=0.2645 ----------X-ray data---------- |--(resolution: 2.20 - 48.79 A, n_refl.=183093 (all), 5.00 % free)-----------| | | | r_work= 0.2440 r_free= 0.2645 coordinate error (max.-lik. estimate): 0.29 A | | | | x-ray target function (ml) for work reflections: 1.088996 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 48.7982 - 6.8296 0.99 5785 298 0.2106 0.2093 2.1338 2.1779| | 2: 6.8296 - 5.4232 1.00 5818 342 0.2291 0.2632 1.8091 1.8784| | 3: 5.4232 - 4.7383 1.00 5733 351 0.1950 0.2248 1.8106 1.9715| | 4: 4.7383 - 4.3053 1.00 5810 297 0.1865 0.2091 1.8418 1.9422| | 5: 4.3053 - 3.9969 1.00 5770 351 0.1947 0.2125 1.7965 1.8123| | 6: 3.9969 - 3.7614 1.00 5854 317 0.2059 0.2273 1.7389 1.8541| | 7: 3.7614 - 3.5730 1.00 5807 315 0.2165 0.2248 1.6958 1.7279| | 8: 3.5730 - 3.4175 1.00 5743 309 0.2116 0.2532 1.6098 1.7535| | 9: 3.4175 - 3.2860 1.00 5844 333 0.2255 0.2873 1.5248 1.6889| | 10: 3.2860 - 3.1726 0.99 5763 329 0.2437 0.2678 1.4283 1.4634| | 11: 3.1726 - 3.0735 1.00 5828 271 0.2467 0.2763 1.2886 1.403| | 12: 3.0735 - 2.9856 1.00 5803 326 0.2456 0.2590 1.179 1.2299| | 13: 2.9856 - 2.9070 1.00 5782 340 0.2506 0.2807 1.1218 1.155| | 14: 2.9070 - 2.8361 1.00 5762 305 0.2575 0.3100 1.0497 1.0718| | 15: 2.8361 - 2.7716 1.00 5892 309 0.2555 0.2665 0.96762 1.1343| | 16: 2.7716 - 2.7127 1.00 5681 293 0.2698 0.3171 0.92297 1.0768| | 17: 2.7127 - 2.6584 0.99 5948 246 0.2877 0.2608 0.86751 0.93978| | 18: 2.6584 - 2.6082 1.00 5814 297 0.2929 0.2990 0.79337 0.80596| | 19: 2.6082 - 2.5617 0.99 5806 266 0.3032 0.3671 0.75287 0.77999| | 20: 2.5617 - 2.5182 1.00 5886 261 0.3065 0.2973 0.73691 0.83083| | 21: 2.5182 - 2.4776 1.00 5777 298 0.3082 0.3174 0.68817 0.79164| | 22: 2.4776 - 2.4395 0.99 5758 274 0.3293 0.3626 0.64915 0.72304| | 23: 2.4395 - 2.4036 1.00 5864 337 0.3385 0.3388 0.62574 0.73292| | 24: 2.4036 - 2.3698 1.00 5791 322 0.3418 0.3387 0.59163 0.66116| | 25: 2.3698 - 2.3377 0.99 5667 329 0.3491 0.3861 0.55553 0.58025| | 26: 2.3377 - 2.3074 0.99 5876 285 0.3572 0.3901 0.55473 0.60051| | 27: 2.3074 - 2.2785 1.00 5813 305 0.3605 0.3906 0.51979 0.59044| | 28: 2.2785 - 2.2511 0.99 5738 303 0.3831 0.3878 0.48079 0.53204| | 29: 2.2511 - 2.2249 0.98 5716 289 0.4042 0.4574 0.49415 0.54579| | 30: 2.2249 - 2.1999 0.98 5810 256 0.4013 0.4243 0.43974 0.41396| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 48.7982 - 6.8296 5785 298 0.83 22.51 0.97 0.01 10.98| | 2: 6.8296 - 5.4232 5818 342 0.80 26.62 0.97 0.01 6.91| | 3: 5.4232 - 4.7383 5733 351 0.84 22.92 1.00 0.01 6.67| | 4: 4.7383 - 4.3053 5810 297 0.86 20.63 1.00 0.01 6.47| | 5: 4.3053 - 3.9969 5770 351 0.85 21.50 1.00 0.01 5.76| | 6: 3.9969 - 3.7614 5854 317 0.84 22.93 1.01 0.01 5.36| | 7: 3.7614 - 3.5730 5807 315 0.83 24.02 1.02 0.01 4.81| | 8: 3.5730 - 3.4175 5743 309 0.81 26.14 1.02 0.01 4.72| | 9: 3.4175 - 3.2860 5844 333 0.77 29.41 0.98 0.01 4.39| | 10: 3.2860 - 3.1726 5763 329 0.75 31.32 1.01 0.01 3.58| | 11: 3.1726 - 3.0735 5828 271 0.77 29.32 1.06 0.01 2.56| | 12: 3.0735 - 2.9856 5803 326 0.79 28.13 1.04 0.01 1.97| | 13: 2.9856 - 2.9070 5782 340 0.79 28.31 1.02 0.01 1.76| | 14: 2.9070 - 2.8361 5762 305 0.76 30.59 1.00 0.01 1.65| | 15: 2.8361 - 2.7716 5892 309 0.75 31.96 0.99 0.01 1.55| | 16: 2.7716 - 2.7127 5681 293 0.76 31.00 0.98 0.01 1.34| | 17: 2.7127 - 2.6584 5948 246 0.75 32.10 1.01 0.01 1.16| | 18: 2.6584 - 2.6082 5814 297 0.76 31.04 1.12 0.01 0.99| | 19: 2.6082 - 2.5617 5806 266 0.74 33.23 1.09 0.01 1.00| | 20: 2.5617 - 2.5182 5886 261 0.74 32.81 1.08 0.01 0.94| | 21: 2.5182 - 2.4776 5777 298 0.73 33.99 1.06 0.01 0.92| | 22: 2.4776 - 2.4395 5758 274 0.68 38.36 1.05 0.01 0.95| | 23: 2.4395 - 2.4036 5864 337 0.68 37.76 1.05 0.01 0.87| | 24: 2.4036 - 2.3698 5791 322 0.68 37.81 1.04 0.01 0.81| | 25: 2.3698 - 2.3377 5667 329 0.66 40.12 1.02 0.01 0.82| | 26: 2.3377 - 2.3074 5876 285 0.66 40.04 1.02 0.01 0.80| | 27: 2.3074 - 2.2785 5813 305 0.64 41.52 1.00 0.01 0.80| | 28: 2.2785 - 2.2511 5738 303 0.61 43.75 0.96 0.01 0.75| | 29: 2.2511 - 2.2249 5716 289 0.61 43.65 1.00 0.01 0.72| | 30: 2.2249 - 2.1999 5810 256 0.62 43.45 0.97 0.01 0.68| |alpha: min = 0.01 max = 0.01 mean = 0.01| |beta: min = 0.67 max = 12.97 mean = 2.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.74| |phase err.(work): min = 0.00 max = 90.00 mean = 31.89| |phase err.(test): min = 0.00 max = 89.95 mean = 31.57| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r_work=0.2440 r_free=0.2645 n_reflections: 183093 start: r_work=0.4676 r_free=0.5197 (reset all scales to undefined) cycle 0: bulk-solvent and scaling: r_work=0.2443 r_free=0.2670 HD scattering refinement: r_work=0.2436 r_free=0.2671 k_h=-0.50 b_h=68.00 cycle 1: bulk-solvent and scaling: r_work=0.2431 r_free=0.2659 HD scattering refinement: r_work=0.2429 r_free=0.2661 k_h=-0.80 b_h=76.00 remove outliers: r_work=0.2429 r_free=0.2661 correct solvent mask: r_work=0.2403 r_free=0.2646 final: r_work=0.2403 r_free=0.2646 n_reflections: 183093 overall anisotropic scale matrix: V0: 0.7884,-1.3407,1.0850,-0.6410,0.0941,-0.9208 V1: -0.0081,-0.0224,0.0112,0.0027,0.0051,0.0136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso kani kmask 48.786-25.095 95.24 97 3 0.4187 1086.912 945.454 1.000 0.978 0.333 25.084-20.829 96.12 93 6 0.3183 823.323 739.609 1.000 1.069 0.332 20.816-17.332 95.77 128 8 0.2779 830.776 766.444 1.000 0.984 0.330 17.254-14.349 96.37 278 14 0.2092 778.625 740.522 1.000 0.771 0.303 14.321-11.898 98.22 469 29 0.1781 880.823 854.378 1.000 0.825 0.300 11.885-9.873 99.07 806 50 0.1587 839.382 814.201 1.000 0.810 0.300 9.866-8.193 99.54 1447 65 0.1797 706.818 683.600 1.000 0.854 0.300 8.191-6.800 99.78 2564 127 0.2032 565.003 544.081 1.000 0.859 0.275 6.798-5.642 99.96 4380 260 0.2212 465.483 447.550 1.000 0.842 0.270 5.641-4.682 99.85 7661 461 0.1911 532.250 514.206 1.000 0.869 0.225 4.682-3.885 99.91 13619 747 0.1911 546.495 530.277 1.000 0.970 0.220 3.885-3.224 99.84 23640 1298 0.2156 401.920 389.232 1.000 1.053 0.125 3.224-2.675 99.61 41527 2193 0.2543 219.824 208.597 1.000 1.027 0.020 2.675-2.200 99.31 77230 3893 0.3355 120.901 104.169 1.000 1.008 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9148 b_overall=-2.3712 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.4542 0.5034 0.014 1.36 22.3 139.6 58.4 410 0.000 1_bss: 0.2297 0.2604 0.014 1.36 21.8 139.1 57.9 410 0.000 1_settarget: 0.2297 0.2604 0.014 1.36 21.8 139.1 57.9 410 0.000 1_addcbetar: 0.2297 0.2604 0.014 1.36 21.8 139.1 57.9 410 0.000 1_weight: 0.2297 0.2604 0.014 1.36 21.8 139.1 57.9 410 0.000 1_nqh: 0.2297 0.2605 0.014 1.36 21.8 139.1 57.9 410 0.000 1_xyzrec: 0.2249 0.2590 0.006 0.97 21.8 139.1 57.9 410 0.052 1_regHxyz: 0.2250 0.2591 0.006 0.97 21.8 139.1 57.9 410 0.057 1_adp: 0.2316 0.2642 0.006 0.97 21.9 185.5 60.4 410 0.057 1_regHadp: 0.2334 0.2657 0.006 0.97 21.9 185.5 60.4 410 0.057 2_bss: 0.2326 0.2642 0.006 0.97 21.1 184.8 59.7 410 0.057 2_settarget: 0.2326 0.2642 0.006 0.97 21.1 184.8 59.7 410 0.057 2_weight: 0.2326 0.2642 0.006 0.97 21.1 184.8 59.7 410 0.057 2_nqh: 0.2326 0.2642 0.006 0.97 21.1 184.8 59.7 410 0.058 2_xyzrec: 0.2316 0.2632 0.005 0.85 21.1 184.8 59.7 410 0.061 2_regHxyz: 0.2316 0.2632 0.005 0.85 21.1 184.8 59.7 410 0.064 2_adp: 0.2308 0.2605 0.005 0.85 19.8 213.7 61.5 410 0.064 2_regHadp: 0.2310 0.2604 0.005 0.85 19.8 213.7 61.5 410 0.064 3_bss: 0.2307 0.2610 0.005 0.85 18.9 212.8 60.6 410 0.064 3_settarget: 0.2307 0.2610 0.005 0.85 18.9 212.8 60.6 410 0.064 3_weight: 0.2307 0.2610 0.005 0.85 18.9 212.8 60.6 410 0.064 3_nqh: 0.2307 0.2610 0.005 0.85 18.9 212.8 60.6 410 0.064 3_xyzrec: 0.2337 0.2598 0.004 0.83 18.9 212.8 60.6 410 0.057 3_regHxyz: 0.2337 0.2597 0.004 0.83 18.9 212.8 60.6 410 0.060 3_adp: 0.2354 0.2563 0.004 0.83 26.0 194.2 62.6 410 0.060 3_regHadp: 0.2357 0.2564 0.004 0.83 26.0 194.2 62.6 410 0.060 4_bss: 0.2341 0.2571 0.004 0.83 20.0 188.2 56.6 410 0.060 4_settarget: 0.2341 0.2571 0.004 0.83 20.0 188.2 56.6 410 0.060 4_weight: 0.2341 0.2571 0.004 0.83 20.0 188.2 56.6 410 0.060 4_nqh: 0.2341 0.2571 0.004 0.83 20.0 188.2 56.6 410 0.060 4_xyzrec: 0.2328 0.2564 0.004 0.83 20.0 188.2 56.6 410 0.056 4_regHxyz: 0.2328 0.2564 0.004 0.83 20.0 188.2 56.6 410 0.060 4_adp: 0.2344 0.2569 0.004 0.83 19.3 325.3 63.8 410 0.060 4_regHadp: 0.2353 0.2576 0.004 0.83 19.3 325.3 63.8 410 0.060 5_bss: 0.2321 0.2580 0.004 0.83 19.3 324.6 63.1 410 0.060 5_settarget: 0.2321 0.2580 0.004 0.83 19.3 324.6 63.1 410 0.060 5_weight: 0.2321 0.2580 0.004 0.83 19.3 324.6 63.1 410 0.060 5_nqh: 0.2321 0.2580 0.004 0.83 19.3 324.6 63.1 410 0.060 5_xyzrec: 0.2325 0.2588 0.004 0.82 19.3 324.6 63.1 410 0.056 5_regHxyz: 0.2325 0.2588 0.004 0.82 19.3 324.6 63.1 410 0.060 5_adp: 0.2430 0.2640 0.004 0.82 22.7 481.2 70.4 410 0.060 5_regHadp: 0.2440 0.2645 0.004 0.82 22.7 481.2 70.4 410 0.060 end: 0.2403 0.2646 0.004 0.82 22.7 481.2 70.4 410 0.060 ------------------------------------------------------------------------ CPU time actual refinement: 10207.44 ============================== Exporting results ============================== Writing refined structure to PDB file: /y/people/christian/projects/BtGH84/John/phenix/Refine_18/BtGH84activator_refine_18.pdb n_use = 22327 n_use_u_both = 10961 n_use_u_iso = 11366 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 22327 =============================== Detailed timings ============================== Micro-tasks: mask = 0.00 f_calc = 0.00 alpha_beta = 26.67 target = 5.80 gradients_wrt_atomic_parameters = 0.00 fmodel = 0.00 r_factors = 273.36 phase_errors = 132.42 foms = 1.54 TOTAL for micro-tasks = 439.79 NUMBER OF MASK CALCS= 0 Time per interpreted Python bytecode instruction: 1.763 micro seconds Total CPU time: 2.87 hours from_scatterers_fft: 988 calls, 348.82 s gradients_fft: 534 calls, 461.04 s =========================== phenix.refine: finished =========================== # Date 2014-06-16 Time 21:27:40 BST +0100 (1402950460.37 s) wall clock time: 12291.21 s Start R-work = 0.2297, R-free = 0.2604 Final R-work = 0.2403, R-free = 0.2646

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Strange distance in HEM.cif ligands in phenix library
by Yarrow Madrona 16 Jun '14

16 Jun '14

Hello, After validating a PDB for deposition I received a message that the HEME ligand C2D-C3D distance was longer than ideal. It was 1.52 angstroms, while it was 1.35 for C2A-C3A, C2B-C3B and C2C-C3C. The ideal bond length is listed as 1.544 vs. 1.337 for the other bonds in $PHENIX/chem_data/mon_lib/h/HEM.cif Is there a reason for this? If not, I am inclined to edit it. -Yarrow

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Occupancy refinement of secondary conformation doesn't add up to 1.00
by Benjamin Stauch 15 Jun '14

15 Jun '14

Hi Phenix, I do a refinement of a glycoprotein that has a NAG-NAG attached to an Asn. The data set is very high resolution and I am positive there is indication of a secondary conformation of the entire attachement. I modeled a second conformation in Coot and run my refinement, with the "adjust occupancy" option checked. After initially setting both occupancies to 0.5, I am puzzled to see one of the NAGs to be refined to 0.45 (conformer A) and 0.75 (conformer B) occupancy .. For the other NAG, and indeed all amino acid residues, things always add up like they should. Additionally to this, I was wondering if there was an easy option to restrain each conformer of the entire Asn-NAG-NAG group to have uniform occupancies -- i.e. the Asn and both NAGs of conformer A to have identical occupancy. Thanks and best Ben

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Prime and switch crashing
by Oliver Clarke 13 Jun '14

13 Jun '14

Hi all, I’m getting an error running phenix.prime_and_switch_map that I can’t figure out. It crashes shortly after F(model) initialization. The last part of the log and traceback is appended below - if anyone can figure out what I’m doing wrong I’d be very grateful! I’m running dev-1702 on a Mac (not sure whether this is a mac specific issue though). This happens with multiple different pdb/mtz combinations, so I don’t think it is something specific to my files. Best, Oliver. Command: phenix.prime_and_switch_map model_rs6_refine_001.pdb model_rs6_refine_001.mtz debug=true Error: ----------F(model) initialization---------- Twinning will be detected automatically. |--(resolution: 3.00 - 71.59 A, n_refl.=26875 (all), 5.48 % free)------------| | | | r_work= 0.2683 r_free= 0.3402 coordinate error (max.-lik. estimate): 0.58 A | | | | x-ray target function (ml) for work reflections: 5.858242 | |-----------------------------------------------------------------------------| End of input processing Traceback (most recent call last): File "/Applications/PHENIX-dev-1702/Contents/phenix-dev-1702/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/prime_and_switch_map.py", line 160, in <module> run(sys.argv[1:]) File "/Applications/PHENIX-dev-1702/Contents/phenix-dev-1702/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/prime_and_switch_map.py", line 68, in run map_coeffs = fmodel.electron_density_map().map_coefficients( TypeError: electron_density_map() takes exactly 2 arguments (1 given)

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GRC and GRS on Diffraction Methods in Structural Biology 7/27/2014 - 8/1/2014
by Anastassis Perrakis 13 Jun '14

13 Jun '14

Dear all, As I did give the full promotional message for why these are just outstanding meetings to attend, I will only invite you to look at the latest programs GRC (http://www.grc.org/programs.aspx?id=11654) GRS (http://www.grc.org/programs.aspx?year=2014&program=grs_diff). and also remind you that the registration is closing in 15 days (June 29). There are still spots available for selected abstracts to be presented towards the end of the meeting, and participant places are filling up soon (especially after a wave of 15 new registrations only yesterday!) We hope to see you all at Bates college and promise you two exciting meetings and a great time! On behalf of the GRC and GRS organizers, Tassos

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pdb file with duplicate atom names (Hydrogens)
by Rex Palmer 13 Jun '14

13 Jun '14

I have taken over a high resolution set of protein data which has H atoms built in. For non-H atoms having 2 or three H atoms these H atoms each carry the same atom number in the pdb file. Phenix will not accept this format. Should I delete all H-atoms and reassign them in the next Phenix refinement run? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com

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Re: [phenixbb] NAG-NAG link definition seems to have no effect
by Benjamin Stauch 12 Jun '14

12 Jun '14

Thanks for your quick reply! However now I get the following error message, "Fatal problems interpreting model file: NUmber of atoms with unkown nonbonded energy type symbols: 3 Please edit the model file to resolve the problems nd/org supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Alternatively, to continue despite this problem use: stop_for_unknown=False" the log file says, Monomer Library directory: "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib" Total number of atoms: 11298 Number of models: 1 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain A and resname NAG and resid 401 residue_selection_2: chain A and resname ASN and resid 74 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain A and resname NAG and resid 401 residue_selection_2: chain A and resname NAG and resid 402 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain B and resname NAG and resid 401 residue_selection_2: chain B and resname ASN and resid 74 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain B and resname NAG and resid 401 residue_selection_2: chain B and resname NAG and resid 402 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5075 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 319, 4675 Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1} Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1} Classifications: {'undetermined': 2, 'peptide': 317} Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, 'NH3': 1} Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} Not linked: pdbres="ALA A 317 " segid="A " pdbres="NAG A 401 " segid="A " Not linked: pdbres="NAG A 401 " segid="A " pdbres="NAG A 402 " segid="A " Conformer: "B" Number of residues, atoms: 319, 4675 Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1} Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1} Classifications: {'undetermined': 2, 'peptide': 317} Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, 'NH3': 1} Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} Not linked: pdbres="ALA A 317 " segid="A " pdbres="NAG A 401 " segid="A " Not linked: pdbres="NAG A 401 " segid="A " pdbres="NAG A 402 " segid="A " bond proxies already assigned to first conformer: 4309 Chain: "B" [...] Chain: "C" [...] Residues with excluded nonbonded symmetry interactions: 26 residue: [...] Number of atoms with unknown nonbonded energy type symbols: 3 "ATOM 5046 HO4 NAG A 401 .*.A H " "ATOM 6215 HD22 ASN B 74 .*.B H " "ATOM 10057 HO4 NAG B 401 .*.B H " Time building chain proxies: 4.05, per 1000 atoms: 0.36 Deleting these atoms (NAG HO4 and ASN HD22) manually doesn't seem to do the trick - as I explicitly want to refine hydrogens I reckon they are added back on. Also it seems BETA1-4 wants to desperately link NAG O4 to NAG O1 which doesn't exist .. Shuld I manually define my NAG-NAG link instead of using the BETA1-4? Thanks again! B 2014-06-12 10:54 GMT+02:00 Benjamin Stauch <bs448c(a)gmail.com>: > Thanks for your quick reply! However now I get the following error message, > > "Fatal problems interpreting model file: NUmber of atoms with unkown > nonbonded energy type symbols: 3 Please edit the model file to resolve the > problems nd/org supply a CIF file with matching restraint definitions, > along with apply_cif_modification and apply_cif_link parameter definitions > if necessary. Alternatively, to continue despite this problem use: > stop_for_unknown=False" > > the log file says, > > > > Monomer Library directory: > "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib" > Total number of atoms: 11298 > Number of models: 1 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain A and resname NAG and resid 401 > residue_selection_2: chain A and resname ASN and resid 74 > apply_cif_link: > data_link: BETA1-4 > mod_id_1: DEL-HO4 > mod_id_2: DEL-O1 > residue_selection_1: chain A and resname NAG and resid 401 > residue_selection_2: chain A and resname NAG and resid 402 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain B and resname NAG and resid 401 > residue_selection_2: chain B and resname ASN and resid 74 > apply_cif_link: > data_link: BETA1-4 > mod_id_1: DEL-HO4 > mod_id_2: DEL-O1 > residue_selection_1: chain B and resname NAG and resid 401 > residue_selection_2: chain B and resname NAG and resid 402 > Model: "" > Number of chains: 4 > Chain: "A" > Number of atoms: 5075 > Number of conformers: 2 > Conformer: "A" > Number of residues, atoms: 319, 4675 > Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1} > Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1} > Classifications: {'undetermined': 2, 'peptide': 317} > Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, > 'NH3': 1} > Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} > Not linked: > pdbres="ALA A 317 " segid="A " > pdbres="NAG A 401 " segid="A " > Not linked: > pdbres="NAG A 401 " segid="A " > pdbres="NAG A 402 " segid="A " > Conformer: "B" > Number of residues, atoms: 319, 4675 > Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1} > Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1} > Classifications: {'undetermined': 2, 'peptide': 317} > Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, > 'NH3': 1} > Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} > Not linked: > pdbres="ALA A 317 " segid="A " > pdbres="NAG A 401 " segid="A " > Not linked: > pdbres="NAG A 401 " segid="A " > pdbres="NAG A 402 " segid="A " > bond proxies already assigned to first conformer: 4309 > Chain: "B" > [...] > Chain: "C" > [...] > Residues with excluded nonbonded symmetry interactions: 26 > residue: > [...] > Number of atoms with unknown nonbonded energy type symbols: 3 > "ATOM 5046 HO4 NAG A 401 .*.A H " > "ATOM 6215 HD22 ASN B 74 .*.B H " > "ATOM 10057 HO4 NAG B 401 .*.B H " > Time building chain proxies: 4.05, per 1000 atoms: 0.36 > > > Deleting these atoms (NAG HO4 and ASN HD22) manually doesn't seem to do > the trick - as I explicitly want to refine hydrogens I reckon they are > added back on. Also it seems BETA1-4 wants to desperately link NAG O4 to > NAG O1 which doesn't exist .. Shuld I manually define my NAG-NAG link > instead of using the BETA1-4? > > Thanks again! > > B > > > > 2014-06-12 2:12 GMT+02:00 Nathaniel Echols <nechols(a)lbl.gov>: > > On Wed, Jun 11, 2014 at 5:05 PM, Benjamin Stauch <bs448c(a)gmail.com> wrote: >> >>> I want to refine a model that has two NAGs linked to an Asn - the sugars >>> are already part of my initial coordinate file, but upon refinement the >>> link between the NAGs gets lost. I have defined a cif_link file as follows >>> that I load (using the GUI), >>> >>> apply_cif_link { >>> data_link = "NAG-ASN" >>> residue_selection_1 = "chain A and resname NAG and resid 401" >>> residue_selection_2 = "chain A and resname ASN and resid 74" >>> } >>> apply_cif_link { >>> data_link = "BETA1-4" >>> residue_selection_1 = "chain A and resname NAG and resid 401" >>> residue_selection_2 = "chain A and resname NAG and resid 402" >>> } >>> >> >> Okay, I think this may be part of the problem - you are missing the outer >> "scope" for these parameter blocks, so they are not processed correctly. >> If you change "apply_cif_link" to >> "refinement.pdb_interpretation.apply_cif_link" in both places it may fix >> the problem. >> >> Refinement doesn't crash or produce errors as far as I can see, however >>> when checking the MolProbity output after refinement, it complains of >>> missing atoms O1 in NAG 401 and 402. (Not sure if this is relevant) >>> >> >> Sorry, this is actually my bug (those atoms should not be included in >> covalently linked sugars), and I think I still have an email complaining >> about this in my inbox from late 2012. I need to overhaul that bit of code >> anyway so I will see if Nigel and I can come up with something smarter. >> >> -Nat >> > >

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NAG-NAG link definition seems to have no effect
by Benjamin Stauch 12 Jun '14

12 Jun '14

Hi Phenix, apologies for the beginner question, and I do realise that there are some related threads already but nothing so far has helped me to solve this problem. I want to refine a model that has two NAGs linked to an Asn - the sugars are already part of my initial coordinate file, but upon refinement the link between the NAGs gets lost. I have defined a cif_link file as follows that I load (using the GUI), apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = "chain A and resname NAG and resid 401" residue_selection_2 = "chain A and resname ASN and resid 74" } apply_cif_link { data_link = "BETA1-4" residue_selection_1 = "chain A and resname NAG and resid 401" residue_selection_2 = "chain A and resname NAG and resid 402" } when checking the .geo file phenix.refine outputs, I do not see any restraints between Asn and NAG, nor NAG and NAG. There might be some clues in the refine.log file: Build ligand and use monomer library to name atoms : NAG Using monomer library entry NAG as template which I guess looks good, and then something like this which could be where things are going wrong: Monomer Library directory: "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib" Total number of atoms: 11298 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5075 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 319, 4675 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2, 'peptide': 317} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} Not linked: pdbres="ALA A 317 " segid="A " pdbres="NAG A 401 " segid="A " Not linked: pdbres="NAG A 401 " segid="A " pdbres="NAG A 402 " segid="A " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Refinement doesn't crash or produce errors as far as I can see, however when checking the MolProbity output after refinement, it complains of missing atoms O1 in NAG 401 and 402. (Not sure if this is relevant) Furthermore there's still a HO4 attached to the O4 of NAG ... while the BETA1-4 should care to delete it .. however the mon_lib reads BETA1-4 . DEL-HO4 pyranose . DEL-O1 pyranose glycosidic_bond_beta1-4 which doesn't seem entirely relevant for my case? Any help would be appreciated Thanks! Ben

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Using .fcf file with Phenix
by Rex Palmer 10 Jun '14

10 Jun '14

Can I run Phenix with a .fcf file and a .pdb file? If not how can I convert .fcf to the correct format? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com

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Run PHENIX commands on GUI verison?
by 李翔 09 Jun '14

09 Jun '14

Hi, I currently can only access to PHENIX with my laptop which has a Windows system (GUI). I want to run some commands for generating restraints for my models such as: iotbx.show_distances MR.1.pdb > contacts.distances, phenix.secondary_structure_restraints model.pdb Is there a way I can run commands in GUI version or can I run the above commands in the GUI version? Thanks for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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