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Re: [phenixbb] refine .log : loggraph flags
by Lepore, Bryan 06 Oct '10

06 Oct '10

On Wed, 6 Oct 2010, Nathaniel Echols wrote: > > loggraph [...] OR am i just missing something (CL flag, GUI...) > The GUI already does this nifty - does the entire gui have to be run? i.e. is that a "smaller" plotter you used?

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refine .log : loggraph flags
by Lepore, Bryan 06 Oct '10

06 Oct '10

[ thanks for the comments on sigma-A ] a related thread : its nice how xtriage puts loggraph specifications ($TABLE etc.) in the output. what is the source file that writes this? or is it more complicated than that? the .log can be hacked, but its a miserable thing to do. e.g. to incorporate such lines into phenix refine output - esp. a ln(sigma-A) plot - would be handy in such a format. then the course of refinement or all the dmin-dependent stats can be graphed. OR am i just missing something (CL flag, GUI...) -bryan

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refinement / alpha_beta
by Kay Diederichs 06 Oct '10

06 Oct '10

Dear Phenix developers, I'd like to refine (using phenix.refine) a _very_ incomplete model (obtained by molecular replacement with one subunit of the complete structure) against the native amplitudes, with the goal to obtain meaningful phases and figures_of_merit which should serve to find heavy atom sites in derivative datasets. If I "just refine" in phenix.refine, then the R-factors are in the 50s and the program estimates the coordinate error to be very large. Thus I would like to tell phenix.refine that the coordinates are actually quite accurate, but that a lot of the model is simply missing. I found alpha_beta free_reflections_per_bin= 140 number_of_macromolecule_atoms_absent= 225 n_atoms_included= 0 bf_atoms_absent= 15.0 final_error= 0.0 absent_atom_type= "O" method= *est calc estimation_algorithm= *analytical iterative verbose= -1 interpolation= True fix_scale_for_calc_option= None number_of_waters_absent= 613 sigmaa_estimator kernel_width_free_reflections= 100 kernel_on_chebyshev_nodes= True number_of_sampling_points= 20 number_of_chebyshev_terms= 10 use_sampling_sum_weights= True in the documentation but I have trouble understanding its meanings and defaults - but I do think this should be used. Maybe I should switch to method=calc and specify number_of_macromolecule_atoms_absent= as well as bf_atoms_absent= ? Can anyone advise me, please? thank you, Kay

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best strategy using two datasets?
by Manoj saxena 05 Oct '10

05 Oct '10

Hi , I have data 2.4 A for a protein ( Se-Met derivative) unit cell dimensions. 53.098,60.207,142.382. I have used this data to solve the partial structure with phenix.autosol and phenix.autobuild. The model from this data was then used as MR model in phaser with another data set from a crystal at 2.2 A (group P212121 ) .unit cell dimensions are 53.86,61.47,142.49. Currently my R free is 23%. My question is 1) Is there a a better way to use the two datasets. can I merge the reflection files from two datasets and does using a merged reflection file have an advantage over the strategy I used. 2) Although not directly related to phenix I was wondering can we use the merged reflection file for PDB depositions? Thanks . I will greatly appreciate any suggestions and guidance in this regard Manoj

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Re: [phenixbb] Help on multi-start-simulated-annealing sigmaA-weighted 2fofc map - WORKING EXAMPLE
by Pavel Afonine 03 Oct '10

03 Oct '10

Hi Fengyun, no problems, here is the updated script and inputs files to illustrate how it works: http://cci.lbl.gov/~afonine/mssa2/ All it needs is a bunch of PDB files and corresponding map coefficients. Let me know if you have any questions. Pavel. On 9/9/10 7:48 PM, fn1(a)rice.edu wrote: > Hi Pavel, > > The script works fine. I hope you could slightly revise the script for > me. > > Since right now, I could run the multi-sa on different nodes at the > same time. So I could get the refined models in the name of sa-#.pdb > within a short time. > > So I could begin with the different models and combine them to > "all.pdb" and calculate the average map after that. But I don't know > how to revise the run.py to do that. > > Wait for your help. > Thanks! > Fengyun > > 引用 Pavel Afonine <pafonine(a)lbl.gov>： > >> Hi Fengyun, >> >> my previous email actually doens't answer your question - I realized >> this after I pushed Sent button -:) >> >> To really answer your question I just wrote a Python script that does >> the following: >> - run multi-start Simulated Annealing, >> - combine all refined models into one multi-model PDB file (models >> separated by MODEL-ENDMDL records), and >> - compute averaged 2mFo-DFc map. >> >> The complete working example is here: >> >> http://cci.lbl.gov/~afonine/mssa/ >> >> You have two options at this point: >> >> - take this example, slightly change inputs by editing the run.py >> file (change input data and model file names, number of SA runs, etc) >> and run it as following: >> >> phenix.python run.py >> >> (since I spent 15 minutes on writing this script it's obviously not >> thoroughly tested or parameter-optimized, although I believe it >> should do the job right) >> >> or >> >> - wait a few days for one of the next PHENIX nightly builds where the >> above script will be available as a user-friendly either >> phenix.multi_start_sa command or an option of phenix.maps (I haven't >> decided yet what is better). >> >> Let me know if you have any questions. >> >> Pavel. >> >>> I read on the paper that they use CNS (model_map.inp) to calculate >>> the avarage sigmaA-weighted 2fofc map. Right now I have set up the >>> simulated annealing with different random seeds. I wonder whether >>> phenix could calculate the average map with the multiple coordinates >>> from different starts? >> >> >> > > >

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Job Opening Announcement
by Lance Westerhoff 01 Oct '10

01 Oct '10

Hello All- We have a number of computational chemist and computational crystallographer post doc positions available. One has a significant focus on x-ray refinement method development, and the other one will explore computational chemistry method research and development. We are excited to fill these openings with talented individuals, so if you think you would be a good fit, we invite you to take a look at our careers website below and submit your CV (along with cover letter) to careers(a)quantumbioinc.com http://www.quantumbioinc.com/careers/ Thank you for your time! -Lance ____________________ Lance M. Westerhoff, Ph.D. 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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using custom_param file from the gui
by Sebastiano Pasqualato 01 Oct '10

01 Oct '10

Hi all, I have a custom parameter file that I used to use running phenix.refine from the command line. Is there a way to use it from the gui? ciao, s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990

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question on the weight for adp
by fn1＠rice.edu 30 Sep '10

30 Sep '10

Hi everyone, I have some questions the weight for adp. My case is that some part of the model will be refined to large B values (about 100) if the default value of wxu_scale (1.0) is used. The other part of the model will have average B value of about 40, which the wilson B is about 35. The corresponding 2FOFC map has very poor density for the region with large B values. If the value of wxu_scale set to be 0.1, that part with large B will be refined to about 80 for B. The corresponding 2FOFC map has some better (but not good enough) density for this region. My question is that can I keep the wxu_scale at the small value for the refinement? Or finally do I need to loose this value? Thanks! Fengyun

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Seeking Postdoctoral Researcher
by Francois Berenger 29 Sep '10

29 Sep '10

Laboratory: Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, Japan. (Unit Leader: Dr. Kam Zhang) Job title and Job description: Postdoctoral Researchers Job description: We are seeking a highly motivated and experienced computational structural biologist to join the Zhang Initiative Research Unit at RIKEN. The successful candidate will use computational tools to tackle problems in the area of protein folding, structure prediction, and structure-based drug design. Our ability to predict the structure of proteins from their primary sequences will greatly facilitate our understanding of the important biological functions that proteins play in their host systems. The 3D structure information will also facilitate the rationale design of drugs for the treatment of various diseases with unmet medical needs. Qualifications: This position requires a PhD in areas related to biophysics, biochemistry, computational chemistry, bioinformatics, or structural biology with experience in employing computational tools to solve biological or chemical problems. Experiences in protein folding, protein structure prediction, protein structure analysis, protein crystallography, or structure-based drugs are highly desired. Proficiency in object-oriented programming such as C++, Java, scripting languages such as Python, Perl are also desired. Experiences in high performance computing, network computing, or grid computing would be a plus. The ideal candidate should possess a track record of accomplishments demonstrating technical proficiency, independent thinking, and scientific creativity. The research environment will be international and hence communication in English is encouraged. The complete job ad, as well as how to apply can be viewed here: http://www.riken.jp/engn/r-world/info/recruit/k100817_s_asi.html Best regards, Francois.

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Ligand restraints editing with REEL -summary
by Joseph Brock 28 Sep '10

28 Sep '10

Hi all, I just wanted to post a quick summary of how my problem was resolved. I later realised that the 'native glutahione' molecule I was transferring ligand restraints from was actually produced by eLBOW released under the Phenix package v1.4, and was therefore defined differently to those restraints created by v1.6.4-486. I was advised by Nigel (author of eLBOW and REEL) to download the latest nightly build (dev-541) and create a clean subdirectory. Copying my model.pdb and data.mtz file into this, running phenix.ready_set on these files and running phenix.refine with the resulting .pdb and .cif files, resulted in a ligand that was correctly restrained to refine into the density extremely well. Hope this is of help to anyone with a similar problem. Cheers, Joe. > From: phenixbb-request(a)phenix-online.org > Subject: phenixbb Digest, Vol 58, Issue 18 > To: phenixbb(a)phenix-online.org > Date: Sat, 18 Sep 2010 12:00:01 -0700 > > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Ligand restraints editing with REEL (Joseph Brock) > 2. Re: Ligand restraints editing with REEL (Ralf W. Grosse-Kunstleve) > 3. Resolve NCS masks (Florian Schmitzberger) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 18 Sep 2010 08:09:23 +0000 > From: Joseph Brock <joeylives2ride(a)hotmail.com> > To: <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Ligand restraints editing with REEL > Message-ID: <SNT120-W580E16EA4DC524ED59A3209B7C0(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi all, > > I'm working on a 1.5A structure that contains a novel ligand within the active site, which is an Arsenic derivative of Glutathione, using the Phenix GUI, version 1.6.4-486. > > I have been using the 'Molinspiration' webpage (http://www.molinspiration.com/docu/webme/) to generate a smiles string, which I then feed into ELBOW. Although the structure/chemical restraints of Glutathione should be unchanged by the covalent linkage to arsenic through the cysteinyl sulfur, the resulting restraints file consistently restricts one of the dihedrals to a value that is incompatible with the (quite clear) electron density. This occurs regardless of wether i use AM1 optimization, and is unresponsive to using native Glutathione (which refines into the corresponding density extremely well) as an input geometry file with any of the available 'Use geometry for' options (final geometry, initial geometry, etc). > > I then tried opening the output file in REEL and manually changing the corresponding dihedrals to those of glutathione, however after running simple optimization, the resulting restraints file has the same problem, and upon choosing the 'transer geometry and restraints' option (or any option) midway through running the 'eLBOW optimization' or 'AM1 optimization' options, Phenix consistently crashes. > > Any advice on how to transfer the origional geometry of native Glutathione to my new ligand effectively would be greatly appreciated. I'm a little confused as to the abilities of REEL, and how to affect them. > > Thanks so much in advance. > > Cheers, > > -Joe. > > >

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