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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

3 2

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.

3 4

Sulfate at 3-fold axis
by Zhou, Tongqing (NIH/VRC) [E] 24 Jun '14

24 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. ******************************************************************

2 1

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

2 1

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

2 1

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

3 3

Rigid ligand placement into density map
by Phan, Jason 20 Jun '14

20 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

6 5

molprobity coot TODO python script
by wtempel 20 Jun '14

20 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.

2 1

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 19 Jun '14

19 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 19 Jun '14

19 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 19 Jun '14

19 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 19 Jun '14

19 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> <B> 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

2 1

Strange distance in HEM.cif ligands in phenix library
by Yarrow Madrona 17 Jun '14

17 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

2 1

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

2 3

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)

2 2

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

1 0

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 13 Jun '14

13 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 >> > >

2 2

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

2 1

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

2 1

Run PHENIX commands on GUI verison?
by 李翔 10 Jun '14

10 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

3 2

B-factors for some sidechains were not refined well
by Zhou, Tongqing (NIH/VRC) [E] 09 Jun '14

09 Jun '14

Dear colleagues, I am refining one structure at 1.94 A with phenix.refine with individual b, TLS, and xyz. The Rwork and Rfree are now at 16.1 and 19.8%. But when inspecting the maps, I noticed that the sidechain tip of some residues showed positive density and the b-factor for those atoms were very high while those for the other atoms of the same residues were normal; The b-factors for newly added ligands were also not refined well showing high b-value and positive density at the same time; the disulfide bonds also show positive density and high B. The occupancy were all set to 1. Please give suggestions. 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. ******************************************************************

2 1

launching MR jobs from the command line.
by Francis Reyes 05 Jun '14

05 Jun '14

Hi all, For the moment (1.9-1692) phenix.automr still works from the command line but I received a note that it's a 'Deprecated program' . ************************************************************************ WARNING - DEPRECATED PROGRAM Please note: the command-line AutoMR tool and associated GUI have been deprecated and will be removed in future releases. We recommend that you use phenix.mrage or phenix.phaser, both of which are available in the GUI. The program will resume execution in 5 seconds. ************************************************************************ phenix.mrage doesn't resolve to anything, and phenix.phaser runs the phaser binary. Is there a new way to launch MR jobs from the command line (which had all the PHIL friendly goodies that automr had?) ? Thanks, F

2 1

difference map peak in coot not showing all peaks?
by Murpholino Peligro 05 Jun '14

05 Jun '14

In coot I have set the map contour level to 5.0 rmsd and I do Validate -> Difference Map Peaks ... and the new window shows me where the peaks are...but not all of them. For example, see screenshot attached. (there are peaks above sg cys80 and sg cy64, both appear in the visual window in coot but only one of them, cys80, in the listing. If I understand clearly, they should both appear in the visual window and in the listing because I have the same filter (5.0 rmsd). Right? Now...the peaks values are from Phenix doing a Isomorphous Difference Map ... So I do not know if this is from Coot or from Phenix.

2 1

software update
by Edna Patricia Matta, Ms 04 Jun '14

04 Jun '14

Hello everybody, Quick question, do I have to uninstall the old version of the software If I want to have the new one? Thanks a lot, E Edna Patricia Matta, MSc. PhD Postdoctoral Fellow McGill University Goodman Cancer Centre 1160 Pine Avenue West, Room 614 Montreal, Quebec, CANADA, H3A 1A3 [http://www.med.mcgill.ca/nahum/images/tel.png] TEL: 1-514-398-7275 [http://www.med.mcgill.ca/nahum/images/fax.png] FAX: 1-514-398-1287

2 1

Submissions for Comput. Cryst. Newsletter
by Nigel Moriarty 03 Jun '14

03 Jun '14

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the July 2014 issue is 16 June 2014 (with some leeway if you are still working on the text). The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

1 0

Autosol and sequence file
by Stefan Knight 02 Jun '14

02 Jun '14

I don’t seem to have much luck with Phenix these days… Trying to run Autosol from the GUI but the process aborts immediately complaining that a sequence file is required to run Autosol. I have given it a sequence file in fasta format that is recognised as such when added. I’ve also tried instead pasting the sequence into the Crystal info window but that didn’t help. Grateful for any tip on how to convince Phenix it has all it needs to get going ;-). Thanks, Stefan ------------------------------------------------------------------------------------------------------- Stefan D. Knight, PhD Professor of Biology Department of Cell and Molecular Biology, Uppsala University Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala Sweden Voice: +46 (0)18 471 45 54 Fax: +46 (0)18 53 03 96 E-mail: stefan(a)xray.bmc.uu.se ------------------------------------------------------------------------------------------------------- "We trained very hard, but it seemed that every time we were beginning to form into teams, we would be reorganised. I was to learn later in life that we tend to meet any new situation by reorganising - and a wonderful method it can be for creating the illusion of progress while producing confusion, inefficiency and demoralisation." – Gaius Petronius Arbiter (d. AD 66) -------------------------------------------------------------------------------------------------------

2 1

How to add difference map peak value to B-factor column in Phenix-Coot after isomorphous difference map?
by Murpholino Peligro 02 Jun '14

02 Jun '14

Hi all. How to add a difference map peak value to B-factor column in Phenix-Coot after isomorphous difference map? Because what I get (after Phenix Isomorphous Difference Map) is a pdb with the peaks (chain A) and holes (chain B) with their positions given by UNKnown atoms, 1 for occupancy and in the B-column their peak-or-hole value. I would be happy if I could get the actual atoms with positions and the peak-or-hole value in the B-column. Thanks again and again.

1 0

molecular replacement keeping hetatms?
by Murpholino Peligro 27 May '14

27 May '14

Can I do molecular replacement with phenix/phaser, keeping all the waters from the first model from the first data set? >From here ( http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#WATER), I should change all the HOH labels to something like WWW. Then I guess that I should put HOH labels again in the solution model, for the following refinement in phenix.refine. Is that it?... Any suggestions? thanks again!

2 2

(no subject)
by Fulvio Saccoccia 27 May '14

27 May '14

Dear phenix users and developers, in the past I usually used the fix_rotamers=true options to fix some residue issues. Now, this option is lacking (I currently use the dev-1702 version of phenix) but I was wondering if some other option does replace it. In addition, I would like to know better how real_space_refinement works; is there any tutorial or presentation about it? Thanks in advance -- Fulvio Saccoccia, PhD Dept. of Biochemical Sciences Sapienza University of Rome 00185, Rome (Italy) Phone: +39 06 4991 0556 https://www.researchgate.net/profile/Fulvio_Saccoccia/?ev=hdr_xprf

2 1

Workshop announcement @ Inst Pasteur Montevideo - Uruguay : Modern Approaches in Drug Discovery for Neglected Infectious Diseases
by Alejandro Buschiazzo 24 May '14

24 May '14

Dear Colleagues: We are pleased to announce the Workshop: "Modern Approaches in Drug Discovery for Neglected Infectious Diseases" at the Institut Pasteur de Montevideo (Uruguay). *Dates:* November 3rd - 8th, 2014 *Venue**: *Institut Pasteur de Montevideo (Montevideo, Uruguay) *Invited speakers:* Wim Hol (University of Washington, Seattle, USA), Paul Michels (University of Edinburgh, Edinburgh, UK), Celerino Abad-Zapatero (University of Illinois at Chicago, Chicago, USA), Hugo Cerecetto (UdelaR), Marcelo Comini (IP Montevideo), Sergio Pantano (IP Montevideo), Alejandro Buschiazzo (IP Montevideo)* * *Aim:* The general aim of this International Workshop is to train students in state-of-the-art approaches for drug discovery and rational design, with special emphasis on target-based methods. The course will provide with a multidisciplinary view, with invited professors covering a diverse set of subjects : protein crystallography, in silico methods for molecular simulations, medicinal chemistry and biology of neglected infectious diseases.** For details of the activity please see the preliminary program. <http://www.pasteur.edu.uy/images/program_v.5-5-14.2.pdf> The course will be in English. This activity is supported by the /Center for Structural Biology of the MERCOSUR /(CeBEM <http://www.cebem.org.ar/>), jointly with the /United Nations University Biotechnology Programme for Latin America and the Caribbean/ (UNU - BIOLAC <http://unu.edu/about/unu-system/biolac>). * **Applicants:* Graduate students and young research scientists are encouraged to apply. 24 students will be selected among the applications. The Course will provide financial support for the students, covering registration fees, and for the case of those coming from abroad, all local expenses (lodging, per diem and local transportation). /* The application deadline is September 8th, 2014. The results will be announced by September 30th.*/ The application form, activity program, contact information and other details can be found at the web site of the course <http://www.pasteur.edu.uy/index.php/en/teaching/courses/54-ensenanza/cursos…> Please address further inquiries toSBDD_course(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to welcoming you in Montevideo! -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

1 0

Three positions open at the MAX IV Laboratory
by Marjolein Thunnissen 23 May '14

23 May '14

The MAX IV facility, the largest and most ambitious Swedish investment in research infrastructure, will be the brightest source of x-rays worldwide and will replace the existing laboratory, which today consists of the storage rings MAX I, II and III. The new MAX IV facility will become operational in June 2016. To extend the suite of already funded beamlines, MAX IV Laboratory is planning the next set of beam lines. Therefore The MAX IV laboratory in Lund has opened two positions within the life-science division. We are looking for two beamline scientists, one for the biomedical imaging beamline MEDMAX and one for the microfocus beamline MicroMAX. For both these positions the scientist will be overseeing the development, construction and commissioning of the MedMAX, respectively MicroMAX beamline from its conceptual stage to full operation. Both beam lines are planned to be cutting edge beam lines, fully exploiting the excellent properties of the MAX IV 3GeV storage ring. In addition we are also looking for a software engineer to be engaged in the design of the MX software infrastructure at the beamline for protein crystallography which is under construction, BioMAX. More information on these positions can be found at https://www.maxlab.lu.se/positions and the links within this page, or from our Life-Sciences director Tomas Lundqvist . best regards Marjolein Thunnissen [cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC] Marjolein Thunnissen Science Coordinator MX MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se<http://www.maxlab.lu.se/>

1 0

Integrated Structural Biology, PhD program at the IGBMC
by Alexandre OURJOUMTSEV 21 May '14

21 May '14

Dear all, kind reminder for PhD fellowship opportunities at the International PhD program of the IGBMC, notably for Integrated Structural Biology. Deadline for applications is 3rd of june 2014: http://phdprogramme.igbmc.fr/ Interested candidates are invited to visit the home pages of the teams of the Integrated Structural Biology department at http://www.igbmc.fr/research/department/3/ Please feel free to contact the group leaders for further information about the projects. Best regards, Bruno Klaholz Sacha Urzhumtsev

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any idea what is this? (unidentifiable blob in electron density map)
by Murpholino Peligro 21 May '14

21 May '14

1) 2FOFCWT PH2FOFCWT bue map (front1.png) (process: XDS->Aimless within CCP4i->MR with Phaser->Phenix.refine/coot->Phenix-refine-withwaters/coot) 2) FWT PHWT purple map (front2.png) (Output from Aimless and calculate Fs with refmac within coot with last pdb from 1st line) What do I have in the crystal? NaCl, Sodium acetate, water, lysozyme and some complexes (~ 400 daltons) that chelate Cu2+ Is there like a gallery of crazy-looking blobs that are explained with something ....real and possible? (that would be great help for the newb) Thanks in advance. links to screenshots right here: https://www.dropbox.com/s/rzjepvr8genolxi/front1.png https://www.dropbox.com/s/0iycf4lh5y726x4/front2.png https://www.dropbox.com/s/xx5kvgn91p763ei/faraway.png (1.0 rmsd for both maps above and 3.5 for the "red and green maps")

2 1

phenix.rna_validate and the MolProbity web server report different bond angle violations
by Huw Jenkins 21 May '14

21 May '14

Hi, I’ve recently been using phenix.erraser to help correct RNA geometry errors and finding it very useful. However, it appears that the geometry validation statistics reported by phenix.rna_validate with respect to bond angle outliers are very different from those reported by the MolProbity web server. As an example - if I run phenix.rna_validate on 1u8d (as used in the documentation for phenix.erraser) the following outliers are reported: RNA Validation ----------------------------------------------- Pucker Outliers: #residue:delta_angle:is_delta_outlier:epsilon_angle:is_epsilon_outler G A 15 :74.054:no:103.458:yes U A 48 :119.081:yes:283.965:no U A 63 :90.366:yes:74.220:yes ----------------------------------------------- Bond Length Outliers: #residue:atom_1:atom_2:num_sigmas ----------------------------------------------- Angle Outliers: #residue:atom_1:atom_2:atom_3:num_sigmas C A 39 : C5': C4': C3':-5.294 U A 63 : O3': C3': C2':-4.402 ----------------------------------------------- Suite Outliers: #suiteID:suite:suiteness:triaged_angle G A 16 :!!:0.000:epsilon-1 U A 48 :!!:0.000:delta U A 49 :!!:0.000:delta-1 A A 64 :!!:0.000:epsilon-1 The MolProbity web server reports the same pucker and suite outliers but flags up many more angle violations: A 39 C worst is C5'-C4'-C3': 10.588 σ A 63 U worst is O3'-C3'-C2': 8.803 σ A 54 C worst is C5'-C4'-C3': 7.883 σ A 49 U worst is C2'-C1'-N1: 5.416 σ A 62 G worst is C2'-C1'-N9: 4.946 σ A 15 G worst is O3'-C3'-C2': 4.825 σ A 22 U worst is C5'-C4'-C3': 4.785 σ A 64 A worst is C4'-C3'-O3': 4.648 σ A 65 A worst is C2'-C1'-N9: 4.582 σ A 44 A worst is C4'-C3'-C2': 4.395 σ As the number of sigmas for the angle violations are different between phenix.rna_validate and MolProbity I guess they’re using different target distributions (not just reporting at a different sigma cut-off) but I’ve no idea which is more valid. Hopefully there is a simple explanation! Thanks, Huw

2 1

Postdoctoral Fellow: Data Processing and Merging in Serial Crystallography
by Kay Diederichs 19 May '14

19 May '14

The Paul Scherrer Institute PSI is the largest research centre for natural and engineering sciences within Switzerland. We perform cutting-edge research in the fields of matter and materials, energy and environment and human health. By performing fundamental and applied research, we work on sustainable solutions for major challenges facing society, science and economy. PSI is committed to the training of future generations. Therefore about one quarter of our staff are post-docs, post-graduates or apprentices. Altogether PSI employs 1900 people. The Swiss Light Source (SLS) is one of the most advanced radiation sources worldwide. The SLS Macromolecular Crystallography Group operates two high performance undulator beamlines as well as a state-of-the-art bending magnet beamline for protein crystallography. The group is involved in several aspects of protein crystallography including the development of advanced beamline instrumentation and crystallographic methods, as well as structural biology projects in collaboration with the Biomolecular Research Group at PSI and external partners. In collaboration with Prof. Kay Diederichs at University of Konstanz, we are looking for a Postdoctoral Fellow: Data Processing and Merging in Serial Crystallography Your tasks ========== * Serial crystallography with bright micro-focused X-ray beams from both synchrotron and free electron laser sources has brought new opportunities in micro- and nanocrystallography. At the same time, obtaining best diffraction data from hundreds and thousands of crystals presents unprecedented challenges. New statistics based method of multi-crystal merging and analysis need to be developed and validated. * Develop multi-crystal data analysis, processing and merging methods for serial micro- and nanocrystallography at synchrotron radiation (SR) and X-ray free electron laser (XFEL) sources * Actively participate in serial crystallography experiments at both SR and XFEL sources * Implement an automated data merging pipeline at the SLS protein crystallography beamlines Your profile ============ You hold a PhD degree in (bio-)chemistry or physics and have several years of experience in protein crystallography. Working knowledge for data processing programs is a must. Experience in computer programming would be a significant advantage. If you are a good team player with good communication skills and sense of responsibility, this position will offer a great opportunity for you to develop your research career in an exciting and highly multidisciplinary environment. For further information please contact Prof. Kay Diederichs, phone +49 7531 88 40 49 or Dr Meitian Wang, phone +41 56 310 41 75. Please submit your application online (including list of publications and addresses of referees) for the position as a Postdoctoral Fellow (index no. 6112-00) to: Paul Scherrer Institute, Human Resources Management, Miriam Zehnder, 5232 Villigen PSI, Switzerland http://www.psi.ch/pa/offenestellen/0789-1 -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

1 0

Sharing a Phenix project via Dropbox
by Derek Logan 19 May '14

19 May '14

Hi, Has anyone ever successfully shared a Phenix project through Dropbox? I tried Googling for info on this without success. I have tried sharing but it doesn't work because Phenix uses the full path to the project, e.g. /Users/derek/Dropbox/project rather than ~/Dropbox/project, which would work for all users sharing the project. I tried manually editing project.phil in the .phenix directory, but at the end of a run of phenix.refine it was overwritten again. Is there somewhere (job_history.phil?) I can replace /Users/derek with ~ so that it the change will be permanent? I think that this would be a very effective way for me to set up a project being run by one of my PhD students involving people from at least 3 labs that could have opinions on the refinement! /Derek P.S. We are all using Macs.

6 9

phenix.real_space_refine
by Gino Cingolani 16 May '14

16 May '14

Hi all, I'm trying to refine a pdb against an EM map using phenix.real_space_refine using default parameters (e.g. phenix.real_space_refine model1.pdb map.ccp4). The program starts OK but quickly stops with the following output (see below) Any thoughts? Thanks so much! Gino ########################################################################### Add C-beta restraints ********************* Adding C-beta torsion restraints... num c-beta restraints: 11832 ------------------------------------------------------------------------------- Getting target map ****************** Traceback (most recent call last): File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 494, in <module> o = run(sys.argv[1:]) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 273, in __init__ self.caller(func = self.get_target_map, prefix="Getting target map") File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 298, in caller func(prefix=prefix) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 372, in get_target_map number_of_macro_cycles = self.params.refinement.macro_cycles) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 153, in extract_target_map_data_and_crystal_gridding crystal_symmetry = inputs.xray_structure.crystal_symmetry()) File "/usr/local/phenix-dev-1615/cctbx_project/mmtbx/utils/__init__.py", line 3094, in structure_factors_from_map use_sg = True) File "/usr/local/phenix-dev-1615/cctbx_project/cctbx/miller/__init__.py", line 1309, in structure_factors_from_map assert map.focus_size_1d() > 0 and map.nd() == 3 and map.is_0_based() AssertionError ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

2 1

NCS in mr_rosetta
by Stefan Knight 15 May '14

15 May '14

Hi, Is there some way to make mr_rosetta use information about NCS present in the data? I have data from a crystal in sg P21 with a clear 3-fold axis perpendicular to the two-fold screw (as seen in self rotation function), and most likely 6 molecules in the asymmetric unit, but none of the mr_rosetta solutions that have appeared so far show 3-fold symmetry, and it doesn’t seem like the ncs is used in the search. The only info about ncs in mr_rosetta I have been able to find online pertains to extracting NCS from search models or mr_rosetta assembled models. Thanks, Stefan ------------------------------------------------------------------------------------------------------- Stefan D. Knight, PhD Professor of Biology Department of Cell and Molecular Biology, Uppsala University Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala Sweden Voice: +46 (0)18 471 45 54 Fax: +46 (0)18 53 03 96 E-mail: stefan(a)xray.bmc.uu.se ------------------------------------------------------------------------------------------------------- "We trained very hard, but it seemed that every time we were beginning to form into teams, we would be reorganised. I was to learn later in life that we tend to meet any new situation by reorganising - and a wonderful method it can be for creating the illusion of progress while producing confusion, inefficiency and demoralisation." – Gaius Petronius Arbiter (d. AD 66) -------------------------------------------------------------------------------------------------------

4 5

fem command/memory error
by Matteo Colombo 15 May '14

15 May '14

Hi Pavel, I downloaded the last released version of phenix (phenix-1.9-1692) and I would like to run the "feature enhanced map" command. However, when I run it I got the following Memory Error that I didn't have in the previous version of phenix. r_work: 0.1867 r_free: 0.2372 Max B subtracted from atoms and used to sharpen map: 20.0 b_sharp: 25.0 FEM loop: done so far: 10%Traceback (most recent call last): File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", line 120, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", line 99, in run sharp=params.sharp, signal_threshold=params.signal_threshold) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 112, in __init__ progress_counter = progress_counter) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 204, in fem_loop weighted_average_manager = weighted_average_manager) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 276, in fem_loop_ weighted_average_manager = weighted_average_manager) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 234, in one_iteration m = get_map(mc=mc_wa, cg=crystal_gridding) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 20, in get_map fourier_coefficients = mc) File "/usr/local/phenix-1.9-1692/cctbx_project/cctbx/miller/__init__.py", line 4357, in __init__ conjugate_flag=True) MemoryError My OS is Ubuntu precise 12.04 LTS, system 32 bit Thanks in advance Matteo -- Matteo Colombo PhD Groupe Extremophile et grands assemblages moléculaire Institut de Biologie Structural J. P. Ebel 6, rue Jules Horowitz F-38027 GRENOBLE Cedex 1

6 5

Re: [phenixbb] Non bonded contacts
by Mark A Saper 14 May '14

14 May '14

Pavel, Your suggestion of setting the alt-loc the same for the two residues in order to avoid the non-bonded contact restraint is not working yet. Do the residues need to be in the same chain Thanks, Mark On May 12, 2014, at 12:23 PM, Mark A Saper <saper(a)umich.edu> wrote: > Hi Pavel, > > I'll try that. I have a PLP cofactor and a lysine. I refined with them forming a Schiff base but the maps had large delta F indicating that the PLP ring was being pulled out of density. So now I am modeling it as PLP and Lys. But there is some bridging density. I want to see how close the Lys would extend if it didn't see the PLP. > > Thanks, > Mark > > On May 9, 2014, at 8:25 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> Hi Mark, >> >>> Is there a straightforward way to turn off non-bonded restraints between 2 residues? I see the restraints in the .geo file. Thanks. >> >> you can asigne them diferent altloc identifiers and then they will not see each other via non-bonded interactions. >> If these two residues in question are symmetry mates then there is a keyword for this: custom_nonbonded_symmetry_exclusions . >> >> Also, I wonder why you want to do this? >> >> Pavel >> >

3 2

Using command-line Phenix from the Mac graphical installer
by Nathaniel Echols 14 May '14

14 May '14

A public service announcement: the graphical installer gives you access to all of the same tools as the command-line installer. The only differences are a) the location, and b) we remove some of the bulkier data files that are not required for normal operation. (Which means that the graphical installation is actually about 300MB smaller.) Instructions are here: https://www.phenix-online.org/version_docs/1.9-1692/install-setup-run.html#… In general, I recommend that all (64-bit) Mac users run the graphical installer unless you absolutely need Phenix to go somewhere other than /Applications. (I know that some of you are already aware of this, but I've had to make this same suggestion twice already today, and the command-line installer is more work to support, thank you Apple.) -Nat

1 0

Phenix version 1.9 released
by Paul Adams 13 May '14

13 May '14

The Phenix developers are pleased to announce that version 1.9 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights from this version: Significant changes to the content and presentation of documentation, major improvements to HySS and AutoSol for SAD phasing in cases of weak signal, new Phenix/Rosetta refinement program for difficult low resolution refinements, new real space refinement program for refinement against a density map (e.g. cryo-EM), feature enhanced maps (FEM) enhance weak features and reduce noise and bias, new composite omit map program, unified MolProbity validation program (consistent with the MolProbity web server), proximity restraints for group displacement parameter refinement in phenix refine, and option for automated chemical linking in phenix.refine. Graphical interface: ==================== - Rearranged main interface to accompany documentation changes - New Phenix releases may be downloaded directly from the GUI (requires previously registered academic email address or permanent user credentials) - Added command to remove large data files (.geo, .kin, .ccp4, etc.) from a project directory to conserve disk space - Changes to support Mac OS 10.9 ("Mavericks") General: ======== - Re-organized and updated documentation - Binary installers for Ubuntu (10.04 or later) available - Python built as shared library in Linux builds (facilitates Rosetta hybrid) - new commands: phenix.composite_omit_map, phenix.rosetta_refine, phenix.molprobity, phenix.sceds, phenix.fem, phenix.real_space_refine, and many smaller utilities Refinement: =========== - phenix.refine: - similarity restraints for group isotropic B-factor refinement - set by group_b_iso.use_restraints (default=True) - data/restraints targets weight is determined automatically; can be adjusted by setting group_b_iso.restraints_weight (larger value makes restraints stronger) - various rotamer handling bug fixes - Automatic linking generation in phenix.refine and other programs that require restraints can be requested using the parameters link_all=True - handles any appropriate ligand-protein or ligand-nucleic acid covalent bonds, including sugars, amino acid modifications, and other prosthetic groups - behavior can be adjusted by setting maximum bond distances parameters - added "bfactor" and "occupancy" keywords to atom selection syntax (also applies to phenix.pdbtools) - Integration with DivCon suite (http://www.quantumbioinc.com) for QM refinement of ligands (requires separate license and installation) - phenix.rosetta_refine (new command): - Hybrid Rosetta/Phenix refinement of protein X-ray crystal structures for difficult cases at low resolution - reference: DiMaio et al. (2013) Nature Methods - phenix.ensemble_refinement: - enabled use of experimental phases (MLHL target) - phenix.real_space_refine (new command): - tool to refine a model against a map (especially EM maps) - phenix.morph_model: - fixed serious bug present in versions 1449-1626 that resulted in incorrect offset being applied Experimental Phasing and Model Building: ======================================== - HySS (phenix.hyss): - Substructure search much more fully automated: - Search first with Patterson seeds and direct method - If no clear solution, try more seeds, Phaser completion, and varying resolution - Full parallelization makes the search rapid - AutoSol: - Now much more powerful for weak SAD data: - Incorporates new automated Hyss search - Classic solvent flipping density modification after Resolve density modification - Tests several values of smoothing radius for solvent boundary identifcation for weak data - Iterates heavy-atom substructure search with Phaser completion including density after density modification and using model after model-building - Require solutions scored by correlation to be substantially better than altermatives before eliminating alternatives - Building with helices_strands_only set as default for data at lower than 3 Angstroms - AutoSol, AutoBuild, and LigandFit: - You can now specify the value of the test set flag for the free data with test_flag_value=xxxx Molecular Replacement: ====================== - phenix.sceds (new command, formerly phaser.splitter): - implements normal mode-based domain finding method - reference: McCoy et al. (2013) Acta Cryst D69 - phenix.find_alt_orig_sym_mate: - offset the produced MLAD value with log(0.9) to avoid negative values if identical structures were to be compared. Consequently older versions therefore yield MLAD values which are 0.10536 smaller than the current version. New commands: ============= - phenix.rosetta_refine (new command): - Hybrid Rosetta/Phenix refinement of protein X-ray crystal structures for difficult cases at low resolution - reference: DiMaio et al. (2013) Nature Methods - phenix.molprobity (new command): - Unified validation tool for command-line users; similar to existing comprehensive validation in the Phenix GUI - optional output of script for viewing results in Coot, or kinemage file - phenix.composite_omit_map (new command): - Default method uses very fast iterative de-biasing procedure - Can also generate either a simple or composite omit map with refinement and optional simulated annealing - Will generate multiple map types at once - parallelizable on multi-core systems or managed clusters - phenix.sceds (new command, formerly phaser.splitter): - implements normal mode-based domain finding method - reference: McCoy et al. (2013) Acta Cryst D69 - phenix.real_space_refine (new command): - tool to refine a model against a map (especially EM maps) - phenix.fem (new command): - Compute "feature-enhanced" map ("FEM") - this protocol modifies a 2mFo-DFc sigmaA-weighted map such that the resulting map has strengthened weak signal, if present, and a reduced amount of noise and model bias. - combines randomization and averaging, treatment of missing reflections, residual composite omit map, and histogram equalization - resulting maps are more interpretable and have less bias compared to the starting 2mFo-DFc map - very fast procedure, no refinement required - phenix.map_to_structure_factors (new command): - convert map into structure factors (also intended for EM) - phenix.angle (new command): - compute angle between two axes or two atom selections - phenix.model_model_distances (new command): - Given two PDB files compute distances per atom, residue, chain, model and overall. It is assumed (and asserted in the code!) that the amount and order of atoms in both files are identical. - phenix.fab_elbow_angle (new command): - Calculating Fragment Antigen-Binding (Fab) elbow angle - phenix.f000 (new command): - Given PDB file estimate F(0,0,0); includes atomic model and bulk-solvent Ligands: ======== - phenix.ligand_identification: - Now you can use ligand cif files (in addition to .pdb files) to build your own custom ligand library. Just specify "Ligand directory" (GUI) or use keyword "ligand_dir" (command line) to tell the program to use .pdb or .cif files in your own ligand directory. - Bug fix to properly handle mtz labels when using difference maps. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 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: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Re: [phenixbb] HLs not recognised
by Nathaniel Echols 13 May '14

13 May '14

Here is the problem: phenix.mtz.dump resolve_1_190_phenix.mtz ... HLA xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman) HLB xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman) HLC xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman) HLD xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman) We ignore arrays with all zeros, since they're obviously not correct - however, the feedback given to the user is deficient. I am open to suggestions about how we can improve this, but I am reluctant to assault users with pop-ups every time bogus information is detected, especially since this will increase the latency of the GUI. The file from AutoSol you should actually use is probably named overall_best_refine_data.mtz, which contains the original, purely experimental phases (along with data and R-free flags, of course). We don't recommend using the density-modified phases as restraints. (I am not sure why Resolve would output all zeros; that is a question for Tom. I did however notice the same thing in a file generated by AutoSol for a tutorial dataset.) -Nat On Mon, May 12, 2014 at 8:21 AM, Jonathan Grimes <jonathan(a)strubi.ox.ac.uk>wrote: > > hi nat > > i created this mtz file.....by taking a resolve.mtz > and putting it back thru phenix. > > from the GUI and from the command line phenix > doesnt like my HLs coeffs. > > thanks > jon > > Dr. Jonathan M. Grimes, > NDM Senior Reseach Fellow Diamond Research > Fellow > University Research Lecturer Diamond Light > Source > Division of Structural Biology Diamond House > Wellcome Trust Centre for Human Genetics Harwell Science Campus > University of Oxford Didcot > Roosevelt Drive, OX11 0DE > Oxford OX3 7BN, UK > > Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk > Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 > > > > ---- Original message ---- > >Date: Mon, 12 May 2014 07:44:14 -0700 > >From: Nathaniel Echols <nechols(a)lbl.gov> > >Subject: Re: [phenixbb] HLs not recognised > >To: Jonathan Grimes <jonathan(a)strubi.ox.ac.uk> > >Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> > > > > This is a little strange - the GUI should not be > > allowing you to select an array that won't work for > > refinement. Could you please send me (off-list!) > > both MTZ files that you tried using? (I don't > > think I need data or anything else for this.) > > thanks, > > Nat > > > > On Mon, May 12, 2014 at 5:49 AM, Jonathan Grimes > > <jonathan(a)strubi.ox.ac.uk> wrote: > > > > i have now used phenix to read in the mtz file, > > read all the arrays > > and make a new mtz file. > > > > phenix recognised the HLs as Hend/latt coeffs. > > > > i used the eff file to run phenix.refine at the > > command line > > and got this error > > > > Not a suitable array of experimental phases: > > refinement.input.experimental_phases.labels=HLA,HLB,HLC,HL > > > > The phases were orginally derived by Phenix > > using the auto solve GUI. > > Jon > > > > Dr. Jonathan M. Grimes, > > NDM Senior Reseach Fellow > > Diamond Research Fellow > > University Research Lecturer > > Diamond Light Source > > Division of Structural Biology > > Diamond House > > Wellcome Trust Centre for Human Genetics > > Harwell Science Campus > > University of Oxford > > Didcot > > Roosevelt Drive, > > OX11 0DE > > Oxford OX3 7BN, UK > > > > Email: Jonathan(a)strubi.ox.ac.uk, Web: > > www.strubi.ox.ac.uk > > Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - > > 287547 > > > > ---- Original message ---- > > >Date: Mon, 12 May 2014 11:32:39 +0100 > > >From: phenixbb-bounces(a)phenix-online.org (on > > behalf of Jonathan Grimes > > <jonathan(a)strubi.ox.ac.uk>) > > >Subject: [phenixbb] HLs not recognised > > >To: phenixbb(a)phenix-online.org > > > > > > > > > I am trying to refine a structure at low > > resolution and would like to > > > use phase restraints. using the GUI even > > though HLs are present > > > in the MTZ file, and are type > > “A”…checked with CAD…..i am not given > > > the option of selecting them. > > > > > > not clear to me what I’m doing wrong. > > > > > > hints most wellcome > > > thanks > > > jon > > > > > > > > >Dr. Jonathan M. Grimes, > > >NDM Senior Reseach Fellow > > >University Research Lecturer > > >DIAMOND Research Fellow > > > > > >Division of Structural Biology > > >Wellcome Trust Centre for Human Genetics > > >University of Oxford > > >Roosevelt Drive, > > >Oxford OX3 7BN, UK > > > > > >Email: Jonathan(a)strubi.ox.ac.uk, Web: > > www.strubi.ox.ac.uk > > >Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - > > 287547 > > > > > >_______________________________________________ > > >phenixbb mailing list > > >phenixbb(a)phenix-online.org > > >http://phenix-online.org/mailman/listinfo/phenixbb > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb >

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