- phenixbb - phenix-online.org

Phenix-Rosetta integration tests fail with Rosetta MPI on RHEL 6.3
by Sina Masoud-Ansari 12 Sep '14

12 Sep '14

Hi there, I'm wondering anyone has managed to successfully run Phenix with Rosetta MPI on Red Hat Enterprise Linux 6.3 or similar? I currently have a non-MPI build of Rosetta that passes all of the tests in phenix_regression.wizards.test_command_line_rosetta_quick However when running these tests with the MPI build of Rosetta the following tests fail: Running test_relax ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax/test_relax.log test_relax/test_relax_current.log ================================================================= Running test_relax_double ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax_double/test_relax_double.log test_relax_double/test_relax_double_current.log ================================================================= Running test_relax_no_sol ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax_no_sol/test_relax_no_sol.log test_relax_no_sol/test_relax_no_sol_current.log I have attempted to attach an archive of the logs. I'm working with Rosetta 3.5, more recent versions of Rosetta fail other tests in phenix_regression.wizards.test_command_line_rosetta_quick , please see https://www.rosettacommons.org/node/3721 for details. Rosetta 3.5 was compiled with GCC 4.4.6 using OpenMPI 1.6.4 Any help or advice is appreciated. -- Sina Masoud-Ansari Centre for eResearch 409.G21 24 Symonds Street University of Auckland e: s.ansari(a)auckland.ac.nz p: +64 9 3737599 ext 89369 w: http://www.eresearch.auckland.ac.nz

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phenix refine geometry restraints
by George Devaniranjan 12 Sep '14

12 Sep '14

Hi, I was trying to restrain the N-CA-C angle to 110.0 I updated the .def file as follows: angle { action = *add atom_selection_1 = name N atom_selection_2 = name CA atom_selection_3 = name C angle_ideal = 110.0 sigma = 2 I got the following: Sorry: More than one atom selected: "name N" Number of selected atoms: 86 I tried using N in quotes and it doesn't work either but the example in the website had this(below), what am I doing wrong? resname ALA and (name ca or name c or name n or name o) Thank you

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refinement for non-standard DNA base
by John Cheong 11 Sep '14

11 Sep '14

Hi, I have 5-fluoro-Uracil in my DNA:protein complex. I modeled 5-F-dU into the map, ran eLBOW for geometry file and did refinement. After the refinement, 5-F-dU is not connected to the neighboring nucleotides and the phosphate oxygens are rotated to wrong positions. Can anyone teach me how to refine with non-standard DNA base ? Any help or advice would be appreciated. John

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Occupancy refinement of anomalous scatters
by Chen Zhao 08 Sep '14

08 Sep '14

Hi all, I have a question about the occupancy refinement of the anomalous scatters. This is because when I went through all the HA sites, I found that some of them has too high B factor and too high occ. I manually adjusted the occ and fed the model into refinement, but the B factor and occ came back to around their original level again. It seems that those have a stronger peak in the anomalous difference Fourier map has a higher occupancy after refinement, but this does not necessarily equals to a strong density peak in 2Fo-Fc map (some of them even disappear after refinement), and this might be related to their high B factor. Am I doing something wrong in the refinement? I am basically using phenix.refine default setting, but with TLS+isotropic B factor refinement and occupancy refinement of a small region (5-8 residues). The resolution is 3 A, and the refinement is already at the final stage. I am still at the learning stage and your input will be greatly appreciated. Thank you! Sincerely, Chen

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Refinement and Density modification
by Ashu S 08 Sep '14

08 Sep '14

Dear all, I am working on a 3.6A Se SAD data. Autosol followed by autobuild gave a decent map (as expected at this resolution) with a moderate trace. After building poly ala trace and assigning few resides in and around Se positions when I refine the model, all the sharp features of the electron density map are lost. For example, a nice looking helical density becomes a tube. I presume that this happens because wilson B is high (~110 A2) and the map requires modification, sharpening etc. Is there a way to get the map with similar sharp features after model building and refinement as auto build gives? How could I follow exactly the same steps of density modification etc which auto build does? Thanks, Ashu

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Refinement and Density Modification
by Ashu S 08 Sep '14

08 Sep '14

Dear all, I am working on a 3.6A Se SAD data. Autosol followed by autobuild gave a decent map (as expected at this resolution) with a moderate trace. After building poly ala trace and assigning few resides in and around Se positions when I refine the model, all the sharp features of the electron density map are lost. For example, a nice looking helical density becomes a tube. I presume that this happens because wilson B is high (~110 A2) and the map requires modification, sharpening etc. Is there a way to get the map with similar sharp features after model building and refinement as auto build gives? How could I follow exactly the same steps of density modification etc which auto build does? Thanks, Ashu

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refine anomalous
by Andreas Förster 08 Sep '14

08 Sep '14

Dear all, I've solved a structure from a SAD dataset collected at 1.54 Å. The structure contains a good number of sulfurs and also what I think is a potassium ion. To verify, I chose a refinement strategy including "Anomalous groups". This worked well in an important way - R values down by 2 percentage points - but the refined f' and f" values are way off. I start out with these parameters in *.eff: anomalous_scatterers { group { selection = (name SD or name SG) f_prime = 0.319342 f_double_prime = 0.557592 refine = *f_prime *f_double_prime } group { selection = name K f_prime = 0.365562 f_double_prime = 1.06736 refine = *f_prime *f_double_prime } } What I get back is: Anomalous scatterer group: Selection: "(name SD or name SG)" Number of selected scatterers: 15 f_prime: -1.15797 f_double_prime: 0.00577091 refine: f_prime f_double_prime Anomalous scatterer group: Selection: "name K" Number of selected scatterers: 1 f_prime: -4.41689 f_double_prime: 0.00271946 refine: f_prime f_double_prime I thought I'd get close to the book values for S and would be able to identify the other anomalous scatterer by the refined f'/f" values. Naiveté or stupidity? Thank you. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

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Fwd: Re: Sculptor
by Gabor Bunkoczi 08 Sep '14

08 Sep '14

Apologies, this was meant for the BB. -------- Original Message -------- Subject: Re: [phenixbb] Sculptor Date: 2014-09-08 10:41 From: Gabor Bunkoczi <gb360(a)cam.ac.uk> To: Marie Elizabeth Fraser <frasm(a)ucalgary.ca> Hi Marie, please check the extension of your alignment. If it is .pir, the second line is supposed to be a comment line, and it is therefore ignored. You can either change the extension to .ali, or insert an empty line after the ones starting with ">". If this is not the problem, then this is not supposed to happen. Please send me the logfile in the first instance, although I may need the actual alignment and the PDB file as well (you can delete the target sequence if you wish, an alignment with a single sequence is perfectly valid). BW, Gabor On 2014-09-08 01:22, Marie Elizabeth Fraser wrote: > Hello, > I'm running Sculptor from the Phenix GUI, trying to improve a > molecular replacement model. I've given the pdb file and a sequence > alignment. Sculptor does not appear to accept the first residues > aligned in the sequence alignment. In the alignment, these residues > are residue numbers 42 to 60, so they are on the second line of the > fasta file (the first line after the title) and Sculptor starts at > residue 61 (the subsequent line). Residues 42 to 60 of the target are > to match the first residues of the pdb model, so in the alignment, > there are 41 dashes before the beginning of the sequence for the pdb > file. Am I giving an incorrectly formatted sequence alignment, > misinterpreting what Sculptor does or is Sculptor supposed to do this? > Thank you, Marie > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

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Sculptor
by Marie Elizabeth Fraser 07 Sep '14

07 Sep '14

Hello, I'm running Sculptor from the Phenix GUI, trying to improve a molecular replacement model. I've given the pdb file and a sequence alignment. Sculptor does not appear to accept the first residues aligned in the sequence alignment. In the alignment, these residues are residue numbers 42 to 60, so they are on the second line of the fasta file (the first line after the title) and Sculptor starts at residue 61 (the subsequent line). Residues 42 to 60 of the target are to match the first residues of the pdb model, so in the alignment, there are 41 dashes before the beginning of the sequence for the pdb file. Am I giving an incorrectly formatted sequence alignment, misinterpreting what Sculptor does or is Sculptor supposed to do this? Thank you, Marie

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refine structure with mtz file in P212121 or P222?
by Wei Shi 05 Sep '14

05 Sep '14

Hi all, I am working with a protein-ligand complex structure. The data was indexed with XDS and mtz file is generated using Phenix---Reflection tools---Reflection file editor. The space group used was P222. Then, I used the Phenix---Molecular replacement to find a solution (try all possible in same pointgroup), and the MR solution was in space group P212121. And then, I reindexed the data in XDS using space group P212121 and then generate the mtz file in space group P212121. So, I have two mtz file, in space group P212121 and P222. When I refine the MR solution with the different mtz files, the map generated is not same for the ligand. The statisitcs is better with P222 mtz file than P212121 mtz file. I am wondering why the density for the ligand and the statistics is different using mtz file in different space groups and which mtz file should I use to get the final structure model. Thank you so much! Best, Wei

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phenix.refine and R free values
by PC 03 Sep '14

03 Sep '14

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OMIT map
by abhishek jamwal 02 Sep '14

02 Sep '14

Dear phenixbb members, I want to build a SA-OMIT map for a ligand present in xtal structure of a protein. I am using "AutoBuild-create omit map" module of PHENIX ver. 1.8.4-1496 (graphical interface) for this purpose. However, when I run the program after adding requisite input files, it gives an error: " The map file parameter is not supported for omit map calculation" Q: What is this "file parameter" and way to fix this error/parameter ? waiting for answers many thanks in advance Abhishek Jamwal Structural Biology Group ICGEB, New Delhi

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Phasing using CryoEM Map
by Alexander Kintzer 01 Sep '14

01 Sep '14

Hello All, I trying to phase my 4Å data with low resolution cryoEM maps (various 12-18Å). There is some documentation, but not really for dealing with EM data. I am having trouble converting the EM data from mrc to suitable F's for phaser. One would want to try different density contours of the cryoEM map, but I haven't found a good way to accomplish this. I also have been unable to search for Ta6Br12 clusters using Autosol even though the documentation seems to suggest that it is possible using the "TX" or "XX" designation for heavy atom search. Any guidance would be extremely helpful. best, Alex

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Tau angles
by George Devaniranjan 01 Sep '14

01 Sep '14

Hi, Is there a way of extracting the tau (and omega) angles of residues in phenix ? Thank you

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Re: [phenixbb] following on the anomalous map
by Kay Diederichs 29 Aug '14

29 Aug '14

Hi Charles, > Date: Thu, 28 Aug 2014 09:59:30 -0400 > From: CPMAS Chen <cpmasmit(a)gmail.com> > To: Gabor Bunkoczi <gb360(a)cam.ac.uk> > Cc: "PHENIX user mailing list \(phenixbb(a)phenix-online.org\)" > <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] following on the anomalous map > Message-ID: > <CAAU4GKbzA37j=51X4jMOJjq3t4rKW7Jz9+CQrPxO-HN1kFOOiQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > HI, Gabor, > > Thanks for you suggestion. > > I tried this method, it did not give out NO sites for Br. > > why there is apparent anomalous signal and I cannot identify any Br sites? are you sure that your data processing used the correct parameters? E.g. in XDS you should definitively be using "FRIEDEL'S_LAW=FALSE". If you use XSCALE after XDS, it automagically picks up this setting from XDS_ASCII.HKL i.e. you don't have to specify this again. If you, by mistake, use FRIEDEL'S_LAW=TRUE, then the large intensity differences of Friedel pairs will be judged as outliers by XDS, and these reflections will be rejected - that might lead to featureless maps. If the anomalous signal is very strong, and the multiplicity is high, and the Chi^2 values are >1.5, you may also want to use (additionally) "STRICT_ABSORPTION_CORRECTION=TRUE" . But this is rarely necessary. There are similar options in other data processing programs. If you mix and match data processing programs (e.g. XDS integration and aimless scaling) you have to be careful to have the right settings in all programs. best, Kay > > As Nat pointed out, other atoms should have very weak anomalous signal > diffracted at Br absorption peak (3.8e- for Br, versus 0.2e- for the > sulfurs). In the difference map, I can clearly see some peaks at high sigma > (> 6), but the anomalous difference map(they are all generated by > phenix.refine or phenix.maps) is almost featureless, or the peaks has > no overlaps. The anomalous difference gives the possible place of Br while > the difference map gives the possible place of the whole ligand, and I > assume there should be some overlaps between them. Am I right? > > Charles >

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Re: [phenixbb] following on the anomalous map
by CPMAS Chen 29 Aug '14

29 Aug '14

HI, Gabor, Thanks for you suggestion. I tried this method, it did not give out NO sites for Br. why there is apparent anomalous signal and I cannot identify any Br sites? As Nat pointed out, other atoms should have very weak anomalous signal diffracted at Br absorption peak (3.8e- for Br, versus 0.2e- for the sulfurs). In the difference map, I can clearly see some peaks at high sigma (> 6), but the anomalous difference map(they are all generated by phenix.refine or phenix.maps) is almost featureless, or the peaks has no overlaps. The anomalous difference gives the possible place of Br while the difference map gives the possible place of the whole ligand, and I assume there should be some overlaps between them. Am I right? Charles On Wed, Aug 27, 2014 at 6:28 AM, Gabor Bunkoczi <gb360(a)cam.ac.uk> wrote: > Hi Charles, > > I could be totally misunderstanding what you are trying to achieve, but I > think what you need to do is an MR-SAD calculation. First, solve the > structure with MR (use the macromolecule from the non-Br structure, or use > your current model if you have done refinement on it), and use the > Phaser-EP GUI, and select "SAD starting from MR model". This should > highlight any Br you may have, and gives you a PDB-file with all the peaks > (you can also get a proper anomalous map, but this is only useful for > visualization - the peak search will identify any peaks you may have). > > Let me know if you need more details! > > BW, Gabor > > > On 2014-08-26 14:49, CPMAS Chen wrote: > >> Thanks. Nat. >> >> Since I have some MET and CYT in the protein, could I try to supply >> their sulfur as the initial anomalous scatters? >> >> As for the anomalous isomorphous difference map, would it be useful I >> compare the datasets acquired at 1A wavelength and at the Br >> absorption peak (~0.92A)? >> >> Appreciate your help >> >> Charles >> >> On Mon, Aug 25, 2014 at 5:08 PM, Nathaniel Echols <nechols(a)lbl.gov> >> wrote: >> >> On Sun, Aug 24, 2014 at 6:46 AM, CPMAS Chen <cpmasmit(a)gmail.com> >>> wrote: >>> >>> Here is the point I am not clear. If I am using phenix.refine to >>>> generate LLG map, how do I pick the anomalous group since I have >>>> not placed them in the model yet? >>>> >>> >>> You can't. The LLG map only becomes really useful once you have >>> some anomalous scatterers placed and refined - this is how Phaser >>> substructure completion works. If your molecules have no other >>> significant anomalous scatterers other than the expected Br, the LLG >>> map won't do you much good. >>> >>> By the way, when I choose ion_placement and specify Br, the result >>>> comes with no Br. >>>> >>> >>> Not too surprising, since the code is tuned to look for ions, not >>> part of a covalent molecule, and halides also tend to bond >>> non-specifically and we haven't figured out how to deal with that >>> yet. >>> >>> I want to find whether the Br-containing ligand is seen in my >>>> protein which I have a high resolution structure available. >>>> >>>> I have data collected at Br wavelength, peak or higher position. >>>> Phenix.xtriage reported that the anomalous signal is present to >>>> about 4A. However, both AutoSol or MR-SAD cannot identify the Br >>>> position. Simply say, AutoSol or MR-SAD can not generate any >>>> solution. Well, of course, the simple answer would be that there >>>> is no such ligand cocrystallized. >>>> >>> >>> The simplest explanation is that you just don't have enough >>> anomalous signal to determine the substructure, which can be true >>> even if your ligand is bound. Running experimental phasing to >>> figure this out is unnecessary and time-consuming. >>> >>> Anyway, I am trying to see if the anomalous difference map or >>>> LLG(generated by phenix.maps, this would be the initial one I >>>> assume) can tell me anything more useful. >>>> >>>> So, my question on this topic would be what is a better way you >>>> guys would recommend to identify these Br-ligands? By the way, I >>>> did have the native datasets for the same protein with ligand. >>>> >>> >>> I think in this case I would start with the simple anomalous >>> difference map. If you run phenix.find_peaks_holes (it's in the >>> GUI, of course) and give anomalous data as input, it can pick out >>> the highest peaks in the anomalous map. If the ligand really is >>> bound and the Br site is ordered I would expect this to be >>> detectable. Another alternative is to compute an anomalous >>> isomorphous difference map between a dataset collected at or above >>> (in eV) the Br peak, and a dataset collected below the peak. This >>> will allow you to visualize the wavelength-dependent difference in >>> anomalous scattering, and it's going to be specific for elements >>> with absorption edges within that energy range. But I really don't >>> think this should be necessary to answer your question. >>> >>> -Nat >>> >> >> -- >> >> *************************************************** >> >> Charles Chen >> >> Research Associate >> >> University of Pittsburgh School of Medicine >> >> Department of Anesthesiology >> >> ****************************************************** >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> > > -- > ################################################## > > Dr Gabor Bunkoczi > > Cambridge Institute for Medical Research > Wellcome Trust/MRC Building > Addenbrooke's Hospital > Hills Road > Cambridge CB2 0XY > ################################################## > -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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How to tighten ligand geometry in phenix.refine?
by Blankenfeldt, Wulf 28 Aug '14

28 Aug '14

Dear all, I am currently trying to refine a cacodylate ion that partially occupies the phosphate binding site of a PLP cofactor – partially meaning ~90%, in fact I am leaving the PLP out altogether. When I am refining this in phenix. refine, the cacodylate becomes “ugly”: the tetraeder gets slightly squashed and the atoms are flying apart a bit such that they are not automatically connected in Coot any more. I am now wondering if I can tighten the geometry just for the cacodylate to prevent this from happening, either by sending a magical command or by fiddling with the dictionary. Can anyone advise me, please? Regards, Wulf ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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phenix.refine abort
by sujata halder 27 Aug '14

27 Aug '14

Hi, I am trying to refine a protein with 60 chains (a T=1 virus; 5-3-2 symmetry) and each chain has 520 amino acids. I am using version 1.9 (Release tag: 1692). The job stopped midway and gave the error below followed by "Cannot allocate memory". I have run a similar job (i.e using a similar sized protein) before on an older version (version 1.7) and that had worked. Looking at the error I can't really figure out if the problem is related to installation or a missing module or something different about the code. I can share my files off-list. Here is the error: ====================== XYZ individual (reciprocal space) ====================== R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT TARGETS work free delta bonds angl data restr 28.80 29.29 0.49 0.016 1.6 11.9 0.8 7.4 60 none 0.093 160.8996 Traceback (most recent call last): File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/command_line.py", line 163, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/driver.py", line 1577, in run reference_model_manager = self.reference_model_manager).result File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/strategies.py", line 183, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 114, in __init__ self.call(self.xyzrec, "XYZ individual (reciprocal space)") File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 142, in call func(prefix = prefix) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 374, in xyzrec prefix = prefix) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 204, in __init__ call_back=(len(trial_weights)==1)) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 314, in try_weight result = self.show(weight=wt, print_stats=print_stats, call_back=call_back) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 365, in show molprobity_scores = self.main.use_molprobity) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model.py", line 1341, in geometry_statistics molprobity_scores = molprobity_scores) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model_statistics.py", line 99, in __init__ self.clashscore = clashscore(pdb_hierarchy=pdb_hierarchy).get_clashscore() File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 133, in __init__ verbose=verbose) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 257, in __init__ self.run_probe_clashscore(self.h_pdb_string) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 341, in run_probe_clashscore stdin_lines=pdb_string).raise_if_errors().stdout_lines File "/usr/local/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 158, in __init__ close_fds=not subprocess.mswindows) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 709, in __init__ errread, errwrite) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 1222, in _execute_child self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory ------------------------------------------------------------------------------------------------------------- Thanks, Sujata

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Missing sanity check of duplicate resids within one chain?
by Schubert, Carsten [JRDUS] 27 Aug '14

27 Aug '14

Hi, this is a bit of an esoteric issue I just stumbled over, but I'd like to flag this up anyhow. For some reason (most likely boneheaded error on my side) I wound up with duplicate resids for two ion-atoms: TER HETATM 9325 CL CL S 1 10.578 23.153 35.662 1.00 75.71 Cl1- HETATM 9326 CL CL S 2 -6.546 32.210 31.507 1.00 80.31 Cl1- HETATM 9327 CL CL S 3 21.899 28.037 25.883 1.00 86.22 Cl1- HETATM 9328 K K S 3 7.259 -0.149 19.530 1.00 91.09 K1+ TER Phenix (1.9-1692) seemingly happily accepted the input and proceeded with refinement and validation. After upgrading my coot installation to the latest build the error was flagged. I think this sort of mistake should have at least been flagged in the validation stage or is this out of scope for phenix? Cheers, Carsten

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phenix.maps command line arguments
by Ryan McGreevy 26 Aug '14

26 Aug '14

When using phenix.maps from the command line, passing any arguments for the "map" layer of parameters does not seem to work. For example the command: phenix.maps input.pdb_file_name=input.pdb input.reflection_data.file_name=input.mtz works just fine, but parameters under the "map" section don't seem to have any effect, such as: map.file_name=map.ccp4 map.kicked=True Could I be doing something wrong, or does this not actually work? I know I can set these parameters in a maps.params file, but I would like to be able to pass them on the command line for scripting and automation purposes.

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following on the anomalous map
by CPMAS Chen 26 Aug '14

26 Aug '14

Hi, All Phenix users, I am following this topic. http://www.phenix-online.org/pipermail/phenixbb/2014-April/020622.html. Here is the point I am not clear. If I am using phenix.refine to generate LLG map, how do I pick the anomalous group since I have not placed them in the model yet? By the way, when I choose ion_placement and specify Br, the result comes with no Br. Let me make my situation clear first. I want to find whether the Br-containing ligand is seen in my protein which I have a high resolution structure available. I have data collected at Br wavelength, peak or higher position. Phenix.xtriage reported that the anomalous signal is present to about 4A. However, both AutoSol or MR-SAD cannot identify the Br position. Simply say, AutoSol or MR-SAD can not generate any solution. Well, of course, the simple answer would be that there is no such ligand cocrystallized. Anyway, I am trying to see if the anomalous difference map or LLG(generated by phenix.maps, this would be the initial one I assume) can tell me anything more useful. So, my question on this topic would be what is a better way you guys would recommend to identify these Br-ligands? By the way, I did have the native datasets for the same protein with ligand. Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Header accuracy after only refining ligands
by Katherine Sippel 25 Aug '14

25 Aug '14

Hi all, I was trying to prep a structure for PDB deposition. All the protein atoms were good, but I needed to correct some ADP and ligand issues. I ran coordinate refinement only on the ligands and subsequent ADP refinement. Everything was good, except the RSMD values output are clearly only for the ligands. Now I am wondering which values in the header I can trust as far as deposition goes. I tried to do a workaround where I ran refine with 0 macrocycles to see if I could get the proper values, but obviously the bulk solvent is different and I get higher R values. I am wondering if I can run validation to get the correct RMSD values or if there are other header values that might have been affected by not refining all the coordinates? Cheers, Katherine -- "Nil illegitimo carborundum"* - *Didactylos

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DEN refinement
by marinabb phenix 25 Aug '14

25 Aug '14

Dear all, I am trying to use DEN refinement as implemented in the Phenix-1.9 release to refine a structure at 3.6 Angstrom resolution. The asu consists of 8 copies of hetero-dimers (of roughly 40 KDa sunbunits each). The structure of one of the subunits has already been solved at about 2 Angstrom, whereas for the other no homologous model is available. After automatic + manual building, I have now a model with Rfree = 28 / R = 23, with some protomers better built than others. I have used this pdb model as input for DEN refinement, adding the known higher-resolution structure as a (partial) reference model, and ncs restraints previously found (and run a DEN parameters optimisation). The final DEN Rfee got significantly worse. I would appreciate any advise for a better DEN strategy to be adopted in this case, if possible. In particular I was wondering whether it can be worth building a model for the missing subunit (or part of it) based on structural similarity of the current unrefined 3D structure. I thank you in advance for the suggestions. With kind regards, Marina ----- Marina Mapelli, PhD Department of Experimental Oncology European Institute of Oncology Via Adamello 16, 20139 Milan, Italy tel: +39-02-94375018 email: marina.mapelli(a)ieo.eu web: http://www.ifom-ieo-campus.it/research/mapelli.php -----

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overlapping electron density maps
by 李翔 25 Aug '14

25 Aug '14

Hi everyone, I am working on a series of crystals with overall same framework structure plus a different extra part which attaches to the framework. I want to compare the electron density maps of the crystals by overlapping the frameworks and see how the extra parts differ from each other. Is there a way I can do it? Thank you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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table_one
by Andreas Förster 24 Aug '14

24 Aug '14

Dear all, I encounter the following error when running phenix.table_one from the command line (RHEL 6.3 64-bit, phenix-dev-1769): andreas@csbstereo in blah: phenix.table_one Traceback (most recent call last): File "/csb/soft/Linux64/share/phenix-dev-1769/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/table_one.py", line 6, in <module> phenix.automation.table_one.run(sys.argv[1:], auto_extract_labels=True, AttributeError: 'module' object has no attribute 'run' Aunt Google insists that this is "a circular import issue". What do the developers say? Thanks. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

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Low resolution refinement
by Appu kumar 23 Aug '14

23 Aug '14

Hello All, I have a data from a crystal which we can process to 4.5A, and we are able to get a good molecular replacement model and it is a tetramer in ASU. I tried refining structure with phenix.refine but Rfree stuck at 0.41. I read a paper published by David Baker and phenix developer in 2013 about the low resolution refinement using a combination of rosseta and phenix. I would appreciate if i get a help on the refinement in rosseta along with phenix. This paper convince me that its worth trying the rosseta and phenix together for low resolution structure refinement. Thank you Appu

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Re: [phenixbb] Phenix Webserver Down?
by Chen Zhao 22 Aug '14

22 Aug '14

Thank you all for the info. It is been like this for me for a week, and it might just be some local issues. On Fri, Aug 22, 2014 at 4:20 PM, Paul Adams <pdadams(a)lbl.gov> wrote: > > Appears to be okay from the Bay Area. > > On Aug 22, 2014, at 1:00 PM, Chen Zhao <c.zhao(a)YALE.EDU> wrote: > > > Dear all, > > > > I am sorry to bother you, but I have problems connecting to > www.phenix-online.org. Does anybody have similar problem? > > > > Thank you, > > Chen > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > -- > 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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Phenix Webserver Down?
by Chen Zhao 22 Aug '14

22 Aug '14

Dear all, I am sorry to bother you, but I have problems connecting to www.phenix-online.org. Does anybody have similar problem? Thank you, Chen

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mr_rosetta
by Felipe Trajtenberg 20 Aug '14

20 Aug '14

Dear all I am trying to perform MR of a multidomain protein using phenix.mr_rosetta and building each domain sequentially. The first search works perfect and I have a potential solution. In the second search I am having some troubles in setting up the process. When I fixed the best first model and look for a second domain I found that rosetta only rebuilds the chain A, which was the one that already was fixed and chain B disappears. how can I fix one domain and build the second without loosing any information thanks in advance Felipe

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Stereo Microscope
by jens j birktoft 20 Aug '14

20 Aug '14

Hi: I would be grateful for suggestion regarding stereo microscopes suitable for protein/dna crystal viewing and manipulation. We would need a system that fulfull all of the criteria: 1) Two polarizers one for below the sample holder and one above 2) A fully rotatable stage 3) A camera option, either one that comes included with the unit (the best) or one with a universal camera mount Thanks Jens +++++++++++++++++++++++++++++++++++++++++++++++++++ Jens J. Birktoft Director of Crystallography Structural DNA Nanotechnology New York University e-mail: jens.knold(a)gmail.com; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++++++++++++++++++++++++++++++++++++++++++++++++++

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Composite Omit Map with Parallel Processing
by Whitley, Matthew J 19 Aug '14

19 Aug '14

Hello all, I am trying to calculate a simulated annealing composite omit map via parallel processing in Phenix 1.9-1692. Our computer cluster uses a PBS que, and jobs are submitted using the 'qsub' command. In the 'Processes' tab under Phenix Preferences, the queueing system is set to PBS, and the queue submit command is set to qsub + additional flags (walltime, etc). All the usual boxes are checked to indicate to Phenix that jobs should be run in parallel when possible. However, when I actually run the composite omit map calculation, the specified qsub flags do not get carried over into the calculation parameters. If I click on Settings-->View all settings in the Composite Omit map calculation window, the qsub_command parameter under 'parallel' is set to None. Because my desired walltime is not being carried over with the qsub command when the calculation starts, the calculation for each individual box is aborting prematurely when it reaches the default process time limit set by our cluster administrator. In the composite omit map calculation in previous versions of Phenix, when clicking "Run" you used to be able to then click "edit parameters and run" in order to check all settings one last time before starting the job. This option does not seem to be available in Phenix 1.9-1692, and thus I can't verify and/or edit the qsub command directly before firing off the job. Any ideas on how to overcome this? Am I missing something? Thanks, Matthew

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Error: "cannot allocate memory"
by sujata halder 19 Aug '14

19 Aug '14

Hi, I am trying to refine a protein with 60 chains (a T=1 virus; 5-3-2 symmetry) and each chain has 520 amino acids. I am using version 1.9 (Release tag: 1692). The job stopped midway and gave the error below followed by "Cannot allocate memory". I have run a similar job (i.e using a similar sized protein) before on an older version (version 1.7) and that worked. Looking at the error I can't really figure out if the problem is related to installation or a missing module or something different about the code. I can share my input and output files off-list. Here is the error: ====================== XYZ individual (reciprocal space) ====================== R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT TARGETS work free delta bonds angl data restr 28.80 29.29 0.49 0.016 1.6 11.9 0.8 7.4 60 none 0.093 160.8996 Traceback (most recent call last): File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/command_line.py", line 163, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/driver.py", line 1577, in run reference_model_manager = self.reference_model_manager).result File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/strategies.py", line 183, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 114, in __init__ self.call(self.xyzrec, "XYZ individual (reciprocal space)") File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 142, in call func(prefix = prefix) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 374, in xyzrec prefix = prefix) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 204, in __init__ call_back=(len(trial_weights)==1)) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 314, in try_weight result = self.show(weight=wt, print_stats=print_stats, call_back=call_back) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 365, in show molprobity_scores = self.main.use_molprobity) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model.py", line 1341, in geometry_statistics molprobity_scores = molprobity_scores) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model_statistics.py", line 99, in __init__ self.clashscore = clashscore(pdb_hierarchy=pdb_hierarchy).get_clashscore() File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 133, in __init__ verbose=verbose) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 257, in __init__ self.run_probe_clashscore(self.h_pdb_string) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 341, in run_probe_clashscore stdin_lines=pdb_string).raise_if_errors().stdout_lines File "/usr/local/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 158, in __init__ close_fds=not subprocess.mswindows) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 709, in __init__ errread, errwrite) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 1222, in _execute_child self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory ------------------------------------------------------------------------------------------------------------- Thanks, Sujata

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Phenix.refine with Ir
by Chen Zhao 15 Aug '14

15 Aug '14

Dear all, I am sorry for bothering you with this dumb question, but it occurs to me that phenix cannot refine a model with Ir, giving the error message of atoms with unknown nonbonded energy type symbols. Since this is my first time really working on the refinement, I have no clue of how to fix it. Would anybody give me a hint? Thanks a lot in advance! Sincerely, Chen

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maps for PDB without SF's
by PC 15 Aug '14

15 Aug '14

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van der Wall's radii
by Rituparna Sengupta 15 Aug '14

15 Aug '14

Hi! I'm new to the list. This might be a naive question to ask, but I'm looking for information about the set of van der Waal's radii popular with most protein crystallographers. Is there a certain list that phenix uses for building from the x-ray structures. If so, where can I find it. I shall be grateful for any thoughts or inputs on this. Thanks, Ritu Rituparna Sengupta Graduate Student Biophysics Graduate Program Record Lab Department of Biochemistry Biochemical Sciences Building University of Wisconsin-Madison

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Computational Crystallography Newsletter - Volume 5, Number 2
by Nigel Moriarty 13 Aug '14

13 Aug '14

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. Articles Details of the Conformation-Dependent Library <http://phenix-online.org/newsletter/CCN_2014_07.pdf#page=12> Short Communications Connectivity analysis tools in CCTBX <http://phenix-online.org/newsletter/CCN_2014_07.pdf#page=4> phenix.fab_elbow_angle: Fragment Antigen-Binding elbow angle calculation tool <http://phenix-online.org/newsletter/CCN_2014_07.pdf#page=8> Fitting tips #8 – Acetyl Groups are like Peptides: Planar and trans <http://phenix-online.org/newsletter/CCN_2014_07.pdf#page=2> 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

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PSDI 2014, Registration and Abstract Info
by Anna Gardberg 13 Aug '14

13 Aug '14

*[image: Inline image 1]PROTEIN STRUCTURE DETERMINATION IN INDUSTRY 2014* The 22nd PSDI will take place at the Hotel Miragem in Cascais, Portugal, a coastal town located 30 kilometers west of Lisbon, Portugal. The meeting will start with registration and an opening reception on Sunday, 2nd November. This will be followed by two and a half days of scientific program starting Monday morning and finishing at noon on Wednesday, 5th November. A half day excursion to Lisbon is scheduled as a part of the meeting. The scientific program will include the following sessions: · Drug Discovery Stories · Challenging Targets · Biophysics Supporting Structural Biology · Binding Kinetics in Drug Discovery · Structural Biology of Biopharmaceuticals Registration for participants and exhibitors is open at the website: www.psdi2014.org *Please note the deadline for registration and payment: 31 Aug 2014* If you are interested in speaking in any of the scientific sessions, please contact the organizers at psdi2014(a)merckgroup.com with an abstract. Abstracts for “Binding Kinetics in Drug Discovery” are particularly encouraged. Additional information concerning the conference and further updates can be found at the PSDI2014 website <http://www.psdi2014.org/>. Vendor/Sponsor opportunities are available. If you have any questions, please contact the organizers at psdi2014(a)merckgroup.com. Please feel free to forward this announcement to anyone who may be interested in participating. We look forward to a great conference this fall. With kind regards, The PSDI 2014 organizing committee: · Tiago Bandeiras, IBET, Portugal · Anna Gardberg, EMD Serono, USA · Theresa Johnson, EMD Serono, USA · Beate Matlok, Merck KGaA, Germany · Djordje Musil, Merck KGaA, Germany psdi2014(a)merckgroup.com http://www.psdi2014.org

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random half data sets
by Michael Thompson 12 Aug '14

12 Aug '14

Hello All, I'm interested in doing some comparisons of random half data sets, inspired by statistics like CC1/2, CC*, etc. Does phenix contain some tool to split unmerged data into 2 random sets? Thought I would ask before trying to write my own script. Thanks, Mike -- Michael C. Thompson Postdoctoral Scholar Institute of Genomics and Proteomics University of California, Los Angeles miket(a)chem.ucla.edu

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Alternate sequence
by Mullins, Elwood A. 12 Aug '14

12 Aug '14

Hello all, I'm having trouble refining a protein-DNA complex in which one of the DNA strands has a mixture of two different nucleotides at one position. Both are non-standard and require CIF files. I tried assigning each nucleotide the same chain identifier and the same residue number but unique alternate location identifiers. This didn't work. Phenix refined the model but only linked one of the nucleotides with the rest of the chain, pushing the 3' OH and 5' phosphate out of the density for the other nucleotide. Coot won't even open the model output by Phenix. I assume there's some way to do this. Thanks in advance, Elwood Elwood A. Mullins, Ph.D. <> elwood.mullins(a)vanderbilt.edu<mailto:[email protected]> <> tel 615.936.5234 <> fax 615.343.6707

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Calculate F (model)
by PC 12 Aug '14

12 Aug '14

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Re: [phenixbb] pdb_redo
by Nathaniel Echols 12 Aug '14

12 Aug '14

> > From: "Lenin Domínguez" <acheron24(a)gmail.com> > Subject: Re: [phenixbb] pdb_redo > I was wondering about PDB_REDO too. Your command line is priceless, Nat. > > I have one further question: Using phenix.fetch_pdb --maps shouldn't I be > able tro reproduce a figure from a paper showing the electron density of a > ligand? > Well, yes, usually. But: http://www.ncbi.nlm.nih.gov/pubmed/23385452 The one caveat is that there are a few legitimate manipulations that could make the figure look slightly different from how it appears in e.g. Coot: 1. Use of a finer FFT grid (d_min/5 or smaller, versus d_min/4 or d_min/3 which are the defaults for Phenix and Coot respectively) 2. Maximum entropy treatment (removes Fourier artifacts, extends coefficients to high resolution without actually adding information) 3. Map sharpening (2) and (3) should really be explicitly mentioned, however. And I have yet to see a case where these would make the difference between a ligand being detectable or not by eye. (Maximum entropy can sometimes improve the performance of LigandFit but the density is still pretty obvious to a human.) The maps from PDB_REDO shouldn't be hugely different from the maps that come out of phenix.maps, so looking at those results would be another control. I have tried using phenix.fetch_pdb, PDB_REDO (conservative and aggresive > refinement) as well as the data straight from EDS. > > Any thoughts? > Send me the PDB ID (and ligand name) off-list and I'll take a look. -Nat

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Re: [phenixbb] pdb_redo
by Ed Pozharski 11 Aug '14

11 Aug '14

I believe the intent is to provide electron density maps at the end of pdb_redo re-refinement process. Recent versions of coot allow direct download of pdb_redo maps and there are also pymol plugins. You could ask Robbie Joosten directly whether your specific intended use of pdb_redo output is kosher. Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: Nathaniel Echols <nechols(a)lbl.gov> </div><div>Date:08/11/2014 11:06 AM (GMT-05:00) </div><div>To: PC <patrick.cossins(a)inbox.com> </div><div>Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> </div><div>Subject: Re: [phenixbb] pdb_redo </div><div> </div>On Mon, Aug 11, 2014 at 10:50 AM, PC <patrick.cossins(a)inbox.com> wrote: I was wondering what the community thought of the use of PDB_REDO for MTZ files? I see that they have easy to download MTZ files but has anyone actively used them? Unless we're looking at something different, these are output from Refmac, and do not include all of the data contained in the original deposition. I am not sure if the data will have undergone other changes as well. For instance, the deposited structure factors for PDB ID 2whz include both the fully processed anomalous differences (DANO) and the anomalous intensities (I+/I- and sigmas). The MTZ file I found on PDB_REDO has neither, just FP with Friedel mates merged. This throws out important information. Personally, I just do this: phenix.fetch_pdb --mtz 2whz or this: phenix.fetch_pdb --maps 2whz (Perhaps someday we'll have a server for this.) I should mention however that this will fail on a significant fraction of PDB entries that do not adhere to the CIF standard, at least as implemented in CCTBX. -Nat

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pdb_redo
by PC 11 Aug '14

11 Aug '14

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Two ions at same position
by Eric Girard 08 Aug '14

08 Aug '14

Dear phenixbb members, I am refining a structure that contains Ca2+ atoms. The structure was determined in presence of lanthanide ions. Thus, the resulting density clearly indicates that a part of each Ca2+ sites is substituted with Eu3+ (let's say 75% Ca2+ and 25% Eu3+ per sites). How can I deal with such situation? Indeed phenix.refine complains when I try to put a Ca2+ ion and a Eu3+ one with the same coordinates (and with the occupancies mentionned above) and stop. Thanks for your help. Eric. -- **************************************************************** Eric Girard Extremophiles and Large Macromolecular Assemblies (ELMA) group Institut de Biologie Structurale UMR 5075 CEA-CNRS-UJF-PSB 71 avenue des Martyrs CS 10090 38044 Grenoble Cedex 9 Phone: +33 (0)4 57 42 86 45 Fax: +33 (0)4 76 50 18 90 Web site: http://www.ibs.fr/ *****************************************************************

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command line
by PC 08 Aug '14

08 Aug '14

3 3

RNA 5' end needs 2 PO4s
by Phoebe A. Rice 07 Aug '14

07 Aug '14

I'm trying to model the first residue of an RNA, which has a di (maybe tri) phosphate on the 5' end I'm sure someone has already worked this out ... should we call the 1st residue GDP or GTP, and somehow tell phenix about the bond to residue #2 (how?) or should we add pyrophosphate to the default 5' phosphate? PS - as a side point, elbow generates GMP with no phosphate thanks, Phoebe

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CIF for Thiol-substituted DNA
by Mark A. White 06 Aug '14

06 Aug '14

Hello, I have a diThiol substituted phosphate on a CYT residue (C2S: S1P & S2P in place of O1P & O2P). So far I have tried using phenix.elbow to produce a CIF, but with limited success. First, the links to the neighbouring nucleotides are not created. I could just add a links.cif to the input, but this would not include the DNA angle restraints. Second, the sugar-base chirality is not preserved, although it is listed in the CIF file. Is there a better way to produce a substituted DNA, similar to the example of adding the O5T to 5pho GUA? Also, why is the sugar-base chirality not preserved if it is in the CIF? C2S chir_03 C1' O4' N1 C2' positiv the comand: phenix.elbow --do-all dt15_C.pdb produced: elbow.C2S.dt15_C_pdb.001.cif Thanks, Mark -- Yours sincerely, Mark A. White, Ph.D. Associate Professor of Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (281) 734-3614 Fax. (409) 747-1404 mailto://[email protected] http://xray.utmb.edu QQ: "All opinions are not equal. Some are a very great deal more robust, sophisticated and well supported in logic and argument than others." - Douglas Noel Adams (2002)

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elbow, how to get partial charges in mol2 output file?
by Florian Nachon 06 Aug '14

06 Aug '14

Dear phenixbbers, The partial charges are not written in mol2 output files generated by elbow. Is there any way to change that behavior? Probably by editing tripos_mol2_writer.py? Thanks for helping. Florian -- La chance ne sourit qu'aux esprits bien préparés. Louis Pasteur

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Re: [phenixbb] PEG dependent structural changes in crystal structure
by shivendra singh 05 Aug '14

05 Aug '14

Dear Dr. Van Raaji and Dr. Domínguez, Thank you very much for your reply. The salt and pH of crystallisation recipe were same except PEG avg. mol wt. I agree, it may be due to different crystal packing but i am wondering whether disorderedness observed was intrinsic to the protein under PEG1500 or induced by different crystal packing. Also, is it possible that it may be the molten globule state of this protein? I read somewhere that its almost impossible to crystallise molten globule of any protein due to its transient nature. Is it possible that under the PEG1500 environment this collapsed state is more stable? Also looking at its active site, we are sure that it cant be in active form so i am not sure what may be its significance. Also if its a different conformation of active enzyme so is it possible to find out that whether its prior or later state of native form. The function of this enzyme is not related to polyols but hydrolyze cyclic amide substrate. Kind regards Shiv On 6 August 2014 00:23, shivendra singh <shivendra22(a)gmail.com> wrote: > Dear All, > I have been working on a protein which initially got crystallised in > condition having PEG1500 as precipitant. The space group was P21 and got > solved with reasonable Rfree. Analysis of its structure showed large > deviation and very distinct active site architecture along with > disorderedness in one of its long loop (no density) in comparison with the > expected result, based on related homologous structures. The structure does > not seem to be active with one of its active site residue moved apart from > other catalytic amino acids. Also the substrate entry tunnel looks > distorted. The purified enzyme used for crystallisation showed optimum > activity in vitro. This led us to screen it again for some other > crystallisation condition and got another crystal hit in condition having > PEG3350 as precipitant. Rest of the components of crystallisation cocktail > were same. The data belonged to P212121 space group. The regions which were > disordered or distorted in earlier case were observed to be ordered and in > their expected orientation and position. The enzyme is not reported to be > in different structural or functional states as observed. > I am wondering how the protein from the same batch showed two distinct > structural organizations in conditions with varying PEGs. > What may cause it to follow such transition. > Whether it has some significant functional aspect or just a result of > improper crystal packing. > > Thanks. > > Shiv >

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Phenix/DivCon: IUCr & ACS conferences
by Lance Westerhoff 05 Aug '14

05 Aug '14

Hello all- If you are attending the International Union of Crystallography conference in Montreal this week, be sure to stop by our booth and say hello (we are sharing booth #229 with CCG). We will be there to discuss QuantumBio’s quantum mechanics plugin to Phenix, and we will also be presenting results from some of our recent work with Phenix/DivCon. If you would like more information on our activities at the conference, please take a look at the following link: http://www.quantumbioinc.com/news/show/IUCr-2014 And for those of you planning to attend the American Chemical Society meeting in San Francisco next week, we’ll be there as well (yeah, this will be a busy couple of weeks!). I will be presenting a talk on the subject of quantum mechanics based refinement and its impact on drug discovery efforts. More information is available here: http://www.quantumbioinc.com/news/show/ACS-2014-CA Incidentally, we have a new release of our Phenix plugin coming out. If you are not yet a user and you would like to check it out, certainly feel free contact me for more information. Release Notes: http://www.quantumbioinc.com/news/show/Update-6.0.8 We look forward to seeing you! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909

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