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ERRASER fails to run on ribosome model
by #AHMED TOFAYEL# 11 May '17

11 May '17

Dear PHENIX and ERRASER developers, While ERRASER is running fine (command line) when I use a small PDB file, it fails repeatedly on a complete ribosome model giving following error: Starting erraser Date: Tue May 9 17:53:20 2017 Directory: /home/tofayel/Desktop/test HOSTNAME: localhost.localdomain Log file will be /home/tofayel/Desktop/test/erraser.log Splitting output to /home/tofayel/Desktop/test/erraser.log Running ERRASER Rosetta app... ################################### Path to ERRASER: /usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER ERROR: Unique best command line context option match not found for -fixed_res. Possible matches include: -willmatch:fixed_res -stepwise:fixed_res -rna:farna:erraser:fixed_res Either specify namespace from command line; or in code, use add_relevant() to register option. Traceback (most recent call last): File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/erraser.py", line 14, in <module> erraser_run=phenix.erraser.erraser.erraser(args=sys.argv[1:]) File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/erraser/erraser.py", line 349, in __init__ self.run(params,out=out) File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/erraser/erraser.py", line 459, in run erraser(option) File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 92, in erraser full_struct_slice_and_minimize( minimize_option ) File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 662, in full_struct_slice_and_minimize erraser_minimize( minimize_option ) File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 488, in erraser_minimize subprocess_call(command, sys.stdout, sys.stderr) File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_util.py", line 101, in subprocess_call subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel) File "/usr/local/phenix-1.11.1-2575/base/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/usr/local/rosetta_src_2016.32.58837_bundle/main/source/bin/erraser_minimizer.linuxgccrelease -database /usr/local/rosetta_src_2016.32.58837_bundle/main/database/ -s /home/tofayel/Desktop/test/test-model-coot-19_erraser_temp/minimize_0_full_minimize_temp/before_min_temp_rs.pdb -score:weights stepwise/rna/rna_hires_elec_dens_FCC2012 -score:rna_torsion_potential FCC2012_RNA11_based_new -rna::corrected_geo true -rna::rna_prot_erraser false -rna::vary_geometry true -constrain_P true -attempt_pyrimidine_flip false -rna:farna:erraser:skip_minimize false -chemical:enlarge_H_lj false -in:guarantee_no_DNA false -scale_d 100 -scale_theta 10 -stepwise:rna:o2prime_legacy_mode true -use_2prime_OH_potential false -fixed_res 78 79 100 101 102 106 107 108 109 110 115 116 -edensity:mapfile /home/tofayel/Desktop/test/test-map.ccp4 -edensity:mapreso 3.3 -edensity:realign no -graphics false -skip_connect_info true ' returned non-zero exit status 255 Please suggest some fixes. Thanks in advanced. Best regards, Tofayel

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error when running the tutorials?
by Murpholino Peligro 10 May '17

10 May '17

[murphy@eva00 tut-phenix]$ phenix.run_example gene-5-mad Examples to be run: gene-5-mad Running PHENIX example: gene-5-mad Wed May 10 21:24:26 CDT 2017 Working directory: /home/murphy/X-Rays/tut-phenix/gene-5-mad Starting run now ... please wait a moment Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] Traceback (most recent call last): File "/home/murphy/X-Rays/phenix/phenix-dev-2747/build/../ modules/cctbx_project/site.py", line 48, in <module> import os ImportError: No module named os tutorial files look ok. ps running phenix dev2747 happens the same thing with p9-sad

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how to run Rosetta using phenix GUI interface on windows
by chen c 08 May '17

08 May '17

Hi, everyone, Can anybody tell how to run Rosetta using phenix GUI interface on windows system? Thank you so much! Best regards Chen -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China Tel:+86-10-62772291 Fax:+86-10-62773145 E-mail:[email protected] 北京市海淀区清华大学生命科学馆201-212室邮编：100084

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phenix real space refine & free R reflections
by Hillen, Hauke 05 May '17

05 May '17

Dear Phenix bb, I have a rather conceptual question regarding the treatment of free R flags in phenix.refine and phenix.real_space_refine. I am refining an xray structure using phenix.refine (but not using the real space refinement implemented there) and at some point decided to play a bit with the standalone program phenix.real_space_refine. In particular, I was interested in testing real space refinement against different maps (experimental map vs. model-phased). Being used to the excellent handling of free R flags in Phenix, I assumed giving phenix.real_space_refine the output MTZ of a previous phenix.refine run as a map would be safe to do. But I then saw the phenix.refine FAQ states the following: "Are R-free flagged reflections included in the maps used for real-space refinement? No, this is almost guaranteed to bias R-free; these reflections are removed internally prior to map calculation. However, the output maps will include these reflections unless you explicitly request otherwise.” While it makes sense to me that including the free reflections in the maps used for real space refinement will bias R-free, I wonder why the default behavior of phenix.refine is to output maps which include these reflections. I assume most users will use these output maps (for example via the OPEN IN COOT button in the GUI) to iteratively improve their model by local real space refinement in Coot. Conceptually, how is real space refinement performed by phenix.refine (where the free R reflections are not used to calculate the map to refine against) different from manual local real space refinement in Coot? Will the latter not also bias R-free when the default output maps from phenix.refine are used? Best, Hauke

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Different stats with different number of macrocycles
by Patrick Loll 05 May '17

05 May '17

Hi, I have an odd observation. I am finishing a refinement at 2.5 Å, using the Phenix GUI. I performed a three-macrocycle refinement, and saw that the geometry (RMS bonds/angles) and R/Rfree all got better in the first macrocycle, and then worsened in the subsequent two macrocycles. OK, fine. So I repeated the refinement, except I performed only a single macrocycle (starting from the exact same input coordinates). However, the statistics after this one-macrocycle job did not match the stats seen after 1 macrocycle in the 3-macrocycle job (?!). This doesn’t make sense to me; if you’re starting from the exact same coordinates, shouldn’t the first macrocycle always wind up at the same place, regardless of whether or not the program goes on to do additional macrocycles of refinement? In case this isn’t clear: In the 3-macrocycle job, after the first macrocycle, RMS bonds/angles = 0.005 Å/0.9 deg, R/Rfree = 0.208/0.236 (by the end of the third macrocycle, these numbers have changed to 0.009 Å/1.41 deg and 0.212/0.244) At the end of the 1-macrocycle job, RMS bonds/angles = 0.008 Å/1.4 deg, R/Rfree = 0.209/0.240 This is Phenix version 1.11.1-2575-000. Any insights welcome. Cheers, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology 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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Phenix Generate Table 1 Tool for twin-refinement statistics
by Xiao Lei 04 May '17

04 May '17

Dear All, I am using Windows Phenix Version 1.11.1. I'd like to generate table 1 for journal using Phenix "Generate Table 1 tool". In the input column, I input pdb model, data mtz, and data unmerged mtz, it gives me output statistics without twin refinement. But I'd like to show the results of twin refinement because I used Refmac5 to do twin refinement. Even I put the pdb from the output after twin refinement, the tool still gives me without twin refinement statistics. Thanks ahead for any input.

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TLS refinement
by Reza Khayat 02 May '17

02 May '17

Hi, I'm having difficulty with performing TLS refinement on a highly symmetric system. The difference between the R_work and R_free increases with TLS refinement (16.5/21.4 changes to 14.4/22.2). The TLS tensors for some of the group are not sensible (if I understand the literature correctly) -there are some negative numbers for the T and L tensors (see below). The TLS groups were identified with phenix.find_tls_groups. Any suggestions would be appreciated. REMARK 3 SELECTION: chain 'A' and (resid 38 through 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.6459 -23.5648 -59.0695 REMARK 3 T TENSOR REMARK 3 T11: 0.2105 T22: 0.2895 REMARK 3 T33: 0.0962 T12: 0.0829 REMARK 3 T13: 0.0473 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.0446 L22: 0.0120 REMARK 3 L33: 0.0096 L12: 0.0246 REMARK 3 L13: 0.0209 L23: 0.0106 REMARK 3 S TENSOR REMARK 3 S11: 0.0228 S12: -0.0268 S13: -0.0023 REMARK 3 S21: -0.0507 S22: 0.0526 S23: -0.0287 REMARK 3 S31: -0.0296 S32: -0.0137 S33: 0.0534? The data set is complete at 2.3Å resolution and there are no strange crystal phenotypes. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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starting model using phenix.map_to_model
by Chang Sun 01 May '17

01 May '17

Hi there, I am currently using the phenix.map_to_model for model building from a cryo EM electron density map. One thing I am wondering is whether the starting model should be aligned with the original map or the shifted map produced in the process? Because in my case, most of the starting model is not retained in the final "map_to_model.pdb". BTW, Dr Terwilliger, thanks for devoloping this wonderful tool! Thanks, Chang Postdoctoral Research Associate , Gennis Lab Department of Biochemistry, University of Illinois A306 CLSL 600 S. Goodwin Ave Urbana, IL 61801 Phone: 217-333-4939

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FSC curve between experimental cryo EM map and model
by #AHMED TOFAYEL# 28 Apr '17

28 Apr '17

Dear all, If I want to calculate FSC curve between experimental cryo EM map and model, what is the correct procedure to do so? I will explain what I have tried so far. Although I have variable local resolution in my map, according to FSC=0.143 criterion I have a 4 Ang map (say 1.mrc), I have used 'molmap' command in Chimera to generate a simulated map at 4 Ang. Then I used "vop resample" to take care of the pixel and box values ( then saved as 2.mrc). Thereafter, I have used "e2proc3d.py 1.mrc fsc.txt --calcfsc=2.mrc and plotted the fsc.txt file to get the curve. I am not sure if I am on the right track. My pixel size is 1.28. Best regards, Tofayel

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radiation damage-induced phasing (RIP) tutorial
by Murpholino Peligro 28 Apr '17

28 Apr '17

Hi lads... Do you know if there is a good tutorial for doing RIP somewhere on the internet? What programs can do RIP? -SHELX -AutoRickShaw -? Thanks

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