Search results for "look through"

Re: [phenixbb] Refining partially occupied DNA on top of itself

by Pavel Afonine

Hi Bryan, when you place them one on another with the occupancy 0.5, you need to treat them as "alternative conformations", that is set altloc identifiers A and B. In this case they will not "see" each other through non-bonded interactions term and therefore will not be pushed apart. Their relative occupancies will also be refined. Please let me know if you have any difficulty with this. I do not understand why xyz refinement is off. If you send me the inputs (data+model+commands), I will be happy to have a closer look. Pavel. On 5/7/09 8:25 AM, bschmidt(a)berkeley.edu wrote: > Hello, > I am having difficulty using Phenix to build and refine a DNA duplex. The > issue is that my asymmetric unit consists of one protein monomer bound to > DNA, but the protein is a dimer and the DNA is not palindromic, so each > monomer is bound to a different sequence of DNA. As such, the density for > the two different DNA half-sites is averaged out in the asymmetric unit. I > have tried to place two duplexes directly on top of one another, each with > 0.5 occupancy, and then refine. But I have noticed two problems. The first > is that when xyz refinement is off, and I look at the output files, the > density for DNA is awfully green, as if there were only *one* helix with > 0.5 occupancy there. The other problem I noticed is that when I turn xyz > refinement on, and look at the output files, one of the two half-sites > gets moved several angtroms, so that it is in a region that generally has > no density. I expect that, if done properly, the backbone of both > half-site DNAs ought not to move. Any advice would be greatly appreciated. > Thanks, > Bryan Schmidt > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

16 years, 1 month

[phenixbb] Trouble refining following molecular replacement

by Tyler Liban

Hello all, We are currently working with a dataset for a trimeric protein complex at 3A that is giving us some issues. The space group seems to be P21 ( 59.5, 61.6, 99.6 , 90, 98, 90) and the Mathews coefficient (2.6) suggests 2 copies of this 35kDa complex in the ASU. We are using a homolog as the search model that is 80% identical, and Phaser is able to find 2 molecules in P21 when searching in the same point group and gives good TFZ scores (TFZ = 9 or 10). However, these solutions do not refine well following Phaser (Rfree ~.50), and after removing parts of the model that look incorrect the Rfree still stays between .46 and .50. We ran the data through Xtraige and saw no signs of twinning based on the L-test, and the Patterson map has one small off-origin peak that is only 5%, indicating that there is no significant pseudotranslation. We have also tried finding MR solutions in P1, but haven’t had much luck. Any ideas on where to go from here would be greatly appreciated. Tyler

9 years, 6 months

[phenixbb] merging in hires data in AutoBuild

by Desiree Ho-Chi Fong, Ms

Hello all, I am using PHENIX 1.7.3-928 and I am trying to merge a high resolution native data set with a MAD data set in AutoBuild. I have run AutoBuild through the GUI as well as on the command line. Here is the command I used: phenix.autobuild data=AutoSol_run_1_/exptl_fobs_phases_freeR_flags_1.mtz hires_file=hires.mtz model=AutoSol_run_1_/overall_best.pdb rebuld_in_place=True The data file, exptl_fobs_phases_freeR_flags.mtz from AutoBuild only includes data to the resolution of the MAD data set. The higher resolution native data was not incorporated into this mtz file. Looking at the log file, the hires data was merged with expel_fobs_phases_freeR_flags_1.mtz from AutoSol (with AutoBuild after) and followed by anisotropy correction. This was then used for density modification. However, the high resolution data was never included in the mtz file for refinement in AutoBuild. My understanding is that if hires data is specified in AutoBuild, the phases would be extended and included in map calculation as well as subsequent refinement. The output exptl_fobs_phases_freeR_flags.mtz from AutoBuild would also include the hires data for subsequent refinement. Is this correct? Thank you for your help. Desiree

13 years, 3 months

Re: [phenixbb] Judging AutoSol Output

by Tom Terwilliger

Hi Angela, Peter makes several excellent points. Here are a few more notes... The file to look at first is "AutoSol_summary.dat" The final lines in your AutoSol.output are the same as that file. Here are the useful lines and how to interpret them >>Solution # 1 SCORE:110.810151796 Dataset #1 FOM: 0.34 ---------------- 110 means 110 sigma above random -> very likely correct >>Solution 1 using HYSS on ec6046s-peak.sca_ano_1.sca. Dataset #1 >>Dataset number: 1 >>Dataset type: sad >>Datafiles used: ['ec6046s-peak.sca'] >>Sites: 16 (Already used for Phasing at resol of 2.22) Refined Sites: >>16 Sites in each NCS group: 4 NCS correlation: 0.661541164 >>Experimental phases in: solve_1.mtz_0 >>Density-modified phases in: resolve_1.mtz_0 >>HA sites (PDB format) in: ha_1.pdb_0 >>Model in: resolve_1.pdb >> Residues built: 362 Out of 588, this is reasonably good >> Side-chains built: 11 >> Overall model-map correlation: 0.49 Not that great a correlation, but ok at this stage >>Scaling logfile in: dataset_1_scale.log >>HYSS logfile in: ec6046s-peak.sca_ano_1.sca_hyss.log >>Phasing logfile in: solve_1.prt_0 >>Density modification/build logfile in: resolve_1.log_0 >> >> Score Type: Resolve CC Resolve R Skew NCS >>Raw scores: 0.655 0.492 0.157 0.662 >>Z-scores: 38.788 24.380 14.565 33.077 all Z-scores are very high -> strong solution. Particularly convincing is the NCS correlation of 0.66 and Z-score of 33. Why didn't solve find all 16 sites? Solve uses a patterson-based method for sites, AutoSol uses direct methods. Could be that in this case the patterson method didn't work well. I hope that helps! -Tom T At 04:18 PM 4/24/2006 -0600, agb838(a)mail.usask.ca wrote: >I have some basic questions about the output from Phenix. Basically I >have a data set that gave a solution, but I am not exactly sure how to >tell about the quality of the solution from the outputs. The overall >score is 110. I am not sure exactly what that refers to or how good/bad >it is. I have attached the AutoSol.output file. Any basic suggestions at >what I should be looking at, or if this is even the right file, would be >helpful. The resolve.mtz and resolve.pdb look alright. They are a good >start, but much improvement is needed. If anyone has some suggestions as >to how to improve the output, that would also be helpful. > >I have also run the data through solve/resolve through the command >prompt and it repeatedly locates four heavy atom sites (the data set is >SAD). Yet, when Phenix is used, 16 sites are found. Why the difference >and how do I tell what is working better and why. > >Thank you, >Angela Hoffort > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

19 years, 2 months

[phenixbb] Problems placing second component in Phaser

by Morten Groftehauge

Hi guys, So I have a solution that covers some of target and I ran it through phenix.mr_rosetta and I am actually kinda happy with the output from there. However, while I can place both (NCS=2) with the original model I only seem to be able to place one of the rosetta models, even with 'packing function' set to 'all' or 'allow'. Original model - Refinement after placing component 1: LLG 175 Refinement after placing component 2: LLG 620 Rosetta model (packing 'all') - Refinement after placing component 1: LLG 295 Refinement after placing component 2: LLG 390 Rosetta model (packing standard) - Refinement after placing component 1: LLG 295 Refinement after placing component 2: LLG 350 More notably there is little to no increase in TFZ with the placement of the second component... There are more residues in the Rosetta model and I would expect more clashes but this looks weird. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

12 years, 4 months

Re: [phenixbb] Refinement versus intensities?

by Pavel Afonine

Hi Ulrich, phenix.refine refines only against Fs. We don't have intensity based refinement targets in phenix.refine. If your input file has Is, it will convert them automatically into Fs (to make sure that it actually did it, please look for corresponding message lines in log-file). Pavel. Ulrich Baumann wrote: > Dear Phenix, > > I came across the following: my .mtz reflection file contains columns IMEAN > SIGIMEAN F SIGF. phenix.refine picks the IMEAN SIGIMEAN columns (column types > are properly assigned, by the way) -- does it per default refine against > intensities, e.g. like SHELX? This would probably mean that we better should > feed reflection files before TRUNCATE or similar programs, right? > > > Thank you very much, > > Ulrich > > ------------------------------------------------------ > This mail was sent through IMP at http://mail.unibe.ch > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

18 years, 3 months

Re: [phenixbb] Running Autobuild after Autosol

by Folmer Fredslund

Dear Tom, 2009/8/14 Thomas C. Terwilliger <terwilliger(a)lanl.gov>: > Hi Katya, > > AutoBuild will look through all the autosol runs and choose the solution > with the highest final score, and use that one. You can see this near the > beginning of the AutoBuild run: > > Appending solution 4060.75360229 1 75.3602294036 > exptl_fobs_phases_freeR_flags_1.mtz solve_1.mtz > Appending solution 59.3469818876 2 59.3469818876 None solve_2.mtz > Best solution 4060.75360229 1 75.3602294036 > exptl_fobs_phases_freeR_flags_1.mtz solve_1.mtz AutoSol_run_2_ > If I understand correctly solve_1.mtz and solve_2.mtz both originate from the AutoSol_run_2_ directory? How did AutoBuild choose to go with that solution in the first place? What about the scores for solution from eg AutoSol_run_1_ or AutoSol_run_3_? > In this case it took run 2 with the solution solve_1.mtz with score of > 4060.7 over the solution solve_2.mtz with score of 59. > > If you want to choose a different AutoSol solution, then you will need to > explicitly tell AutoBuild all the files that you want to use. > > All the best, > Tom T > Best regards, Folmer Fredslund

15 years, 10 months

Re: [phenixbb] Multistart simulated annealing refinement

by Pavel Afonine

Hi Joe, to do this you can simply compose a script in whatever language you prefer, which prototype looks like this: for random_seed in random_seeds: phenix.refine model.pdb data.mtz main.simulated_annealing=true main.random_seed=random_seed output.prefix=str(random_seed) where random_seeds is the array of random seeds, containing ~100 elements. If you have multiple CPUs then you can obviously split it among them. I'm not sure we have GUI for this and I guess this kind of task is best run from the command line anyway. Pavel. On 12/8/10 10:47 AM, Joseph Noel wrote: > Hi All, > > I'm sure this has already been addressed but is there a way through the PHENIX GUI to carry out multistart simulated annealing refinement either with different starting seeds (velocities) or temperatures automatically or does one have to start a fresh run each time? > > Thanks! > > Joe > > P.S. Similar procedure as described in the PNAS paper: "Multistart simulated annealing refinement > of the crystal structure of the 70S ribosome"

14 years, 6 months

Re: [phenixbb] anomalous difference map

by Nathaniel Echols

On Sat, Mar 26, 2011 at 9:45 AM, Jason <phenix.upitt(a)gmail.com> wrote: > I was hoping to identify the ligand binding position by resolving the > anomalous map first. Shouldn't this be the procedure to locate ligand? It depends on the ligand, I guess. If it's large enough and actually bound, it should be detectable in the Fo-Fc map - this would be a good sanity check to make sure that the anomalous map generation is working properly. > I know CCP4 can also generate anomalous difference map. But I myself have > never done it (I googled online and found it not that straight forward). Can > anybody go through it for me please, or there are other handy programs that > can make anomalous difference map? You don't need to use CCP4 to make the map, just to process the data - i.e. use MOSFLM/SCALA (xia2 will automate this), or you could also try HKL2000, then use that as input for Phenix. But I doubt this is going to give you a different answer. Also: run Xtriage and look at the plot of anomalous signal vs. resolution. -Nat

14 years, 3 months

Re: [cctbxbb] rna3p error

by Haiguang Liu

Dear Pavel and others, After looking through the files, I found that the error is due to the missing dna_rna cif files in the geostd folder. mmtbx/monomer_library/pdb_interpretation.py calls to mmtbx/monomer_library/server.py then read the structure information from geostd folder. In the release I obtained from server using bootstrap.py, the information about chem_data was not downloaded (maybe it is in a different location?). After copying a chem_data to modules, the program works fine. Best, Haiguang On Wed, Aug 30, 2017 at 11:35 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Haiguang, > > please send us PDB file and we will investigate. > > Thanks, > Pavel > > > On 8/30/17 07:23, Haiguang Liu wrote: > > Dear All, > > I recently run into an error while processing DNA molecules using > pdb_interpreter. The error message is as the following: > > File "/Users/hgliu/test/cctbx/modules/cctbx_project/mmtbx/ > monomer_library/pdb_interpretation.py", line 5419, in __init__ > restraints_loading_flags=restraints_loading_flags) > File "/Users/hgliu/test/cctbx/modules/cctbx_project/mmtbx/ > monomer_library/pdb_interpretation.py", line 3221, in __init__ > log=log, > File "/Users/hgliu/test/cctbx/modules/cctbx_project/mmtbx/ > monomer_library/pdb_interpretation.py", line 2507, in __init__ > m_j=mm, > File "/Users/hgliu/test/cctbx/modules/cctbx_project/mmtbx/ > monomer_library/pdb_interpretation.py", line 1693, in get_lib_link > return mon_lib_srv.link_link_id_dict["rna3p"] > KeyError: 'rna3p' > > After searching through the threads, I found the same error has been > reported, but no solution posted. Any suggestion is appreciated. > > Best, > haiguang > > > _______________________________________________ > cctbxbb mailing [email protected]://phenix-online.org/mailman/listinfo/cctbxbb > > >

7 years, 10 months

Search results for query "look through"