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on phenix.real_space_refine
by Smith Liu 05 May '15

05 May '15

Dear All, If I only want to refine resi 30-50 in Chain A by phenix.real_space_refine, and my protein contains A, B, C chains of a identical sequence of 800 aas, will you please let me know how can I specify "residue 30-50 of Chain A" in the phenix.real_space_refine command? Smith

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neutron refinement of protonated Glu and residues with alternate conformation
by crystallogrphy 05 May '15

05 May '15

Hi, I am doing joint X-ray and neutron refinement for my structure. I found a few residues with two alternate conformations. After I generated alternation conformations, I used phenix.readyset to generate hydrogen and deuterium atoms for D/H atoms. However, phenix.readyset only gives H atoms for exchangable H atoms, such as the amide H atoms. The reason is that A and B letters have been assigned for the alternate conformation, not for the D/H atoms for particular conformations. Could anyone know how to solve this problem? The second question is that I found one Glu residue is protonated at OE1 atom of its carboxylate side chain. How could I generate protonated Glu? Do I need a strain file for this? Thanks! Qun

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SA
by Irina PROKHOROVA 01 May '15

01 May '15

Hello, I am trying to run coordinate refinement 5 cycles with first cycle of simulated annealing (torsion) via command line. Here is a part of my params file that I adapted from my colleges: refinement.main { number_of_macro_cycles = 5 target = *ml mlhl ml_sad ls simulated_annealing_torsion = True } simulated_annealing { mode = every_macro_cycle second_and_before_last once *first first_half } refinement.refine { strategy = *individual_sites individual_sites_real_space rigid_body \ individual_adp group_adp tls occupancies group_anomalous sites { individual = segid *A individual = segid *B } As a result I get the Error Unused parameter definitions: simulated_annealing.mode (file "refine.params", line 26) Could you help me with the syntax, please. Should I include sites definition for simulated annealing? Irina

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Phenix.real_space_refine and B-factor
by Smith Liu 30 Apr '15

30 Apr '15

Dear All, By Phenix.real_space_refine if is very nic to fit a PDB into an EM map, and we can get a fitted PDB. However no matter what is the run strategy (default, morphing, local grid search, etc), in the got PDB the B-factors for each atom in the coordinates were always those from the original input PDB, which may make the B-factors in refined PDB meaningless. As finally we need to deposit the refined PDB and EM to the database, will you please explain how to settle the B-factor issues in the refined PDB related to Phenix.real_space_refine? Smith

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on B-factor refine
by Smith Liu 29 Apr '15

29 Apr '15

Dear All， If in the Phenix refine GUI, I only want to refine based on individual B-factors, can I only click "individual B-factors" without cliking any other items in the "Strategy" and without clicking any items in the "Targets and weighting" and "other options"? Further, if I only click "XYZ cordinates" without cliking any other items in the "Strategy" and without clicking any items in the "Targets and weighting" and "other options", what the Phenix refine realy do? Smith

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extra density for phosphorylated Thr
by Ursula Schulze-Gahmen 29 Apr '15

29 Apr '15

I have a structure with a phosphorylated Thr (TPO). As far as I can see, phenix recognizes the TPO residue, but the electron density maps have a large positive density around the side chain of this residue. Any suggestion what is wrong? Do I need a special definition file for the TPO? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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Number of reflections
by Ana Ramos 28 Apr '15

28 Apr '15

Dear all, I am finishing with the refinement of my structure and I noticed that the number of observed reflections used for refinement 36720 is less than 80 percent of observed reflections for data collection (172551). I am aware that the data collection statistics should be calculated in the same resolution range of refinement. Do you know the reason of this difference? I just followed the instructions from HKL where I indexed and scaled and then used Phenix for MR and refinement. Ana

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on phenix.real_space_refine
by Smith Liu 28 Apr '15

28 Apr '15

Dear All, If with phenix.real_space_refine, I got a model (with PDB), in which there is a fragment containing several residues (not in continuation in the fragment), with side chains not fitting to the corresponding side chain density (or out of the density, but close to the density), which function(s) of phenix.real_space_refine (for example,minimization_global or local_grid_search?) can improve the fitting of the sidechains to the density? I am looking forward to getting your reply. Smith

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Autobuild on parallel
by Kaushik Hatti 28 Apr '15

28 Apr '15

Hi, What is the best way to run Autobuild if I need to run it on hundreds of datasets (through command-line)? I have a single machine with 24 cores and access to a cluster with 128 cores (on parallel; accessible only through PBS script). Each Autobuild job with nproc=4 on a single core machine takes ~12 hours to run (nproc > 4 wouldn't make any difference in the speed of computation?!). However, I read that I could set nproc=10 (or more) and run on parallel ( https://www.phenix-online.org/documentation/reference/autobuild.html#parall…). When I tried the same through PBS script, I got the following error, XXXXXXXXXXXXXX Running up to 1 jobs in parallel... with total of 3 jobs Splitting work into 3 jobs and running with 1 processors using qsub background=False nproc=20 background=False in ~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0 Final job will be run with sh with background=True Starting job 1...Log will be: ~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1.log Traceback (most recent call last): File "~opt/phenix-1.9-1692/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "~opt/phenix-1.9-1692/phenix/phenix/autosol/AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 2364, in AutoBuild_build_cycle self.AutoBuild_rebuild_cycle_run() File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 4647, in AutoBuild_rebuild_cycle_run always_reuse_model=always_reuse_model) File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 7452, in AutoBuild_build_refine mtz_file=mtz_file,mtz_ref_file=mtz_ref_file) File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 7696, in run_standard_build_in_parallel r.run(out=sys.stdout) File "~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line 294, in run self.start_run(run_file,last=is_last) File "~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line 604, in start_run cmd+" "+self.add_double_quote(run_file,escape_space=False)).raise_if_errors() File "~opt/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 37, in raise_if_errors raise Error(msg) RuntimeError: child process stderr output: command: 'qsub background=False nproc=20 "~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1"' /bin/sh: qsub: command not found XXXXXXXXXXXXXX Please let me know if I can share eff and log files of the run. Please advice, Kaushik -- People living deeply have no fear of death - Anais Nin Caution: I am still the dumbest person I have ever known :-)

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FEM map calculation without model?
by Oliver Clarke 28 Apr '15

28 Apr '15

Hi all, Is there any way to apply the local map sharpening and histogram equalization procedures described as part of the FEM map generation procedure (described in “FEM: feature-enhanced map”, Afonine et al,mActa D71 2015) to an MTZ containing amplitudes and phases only, without a model (e.g. as generated by phenix.map_to_structure_factors)? I would like to see if these different approaches to map modification are useful for improving maps derived from cryoEM. I guess there is no way to do the random map perturbation part of the FEM procedure without a model, but the sharpening and histogram equalization seem like they might be applicable? Best, Oliver.

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