- phenixbb - phenix-online.org

real space refinement or fix rotamers
by helene.krueger＠staff.uni-marburg.de 14 Oct '10

14 Oct '10

Hi, I want to fit bad fitting residues into electron density of my 2.0 A dataset. To do so should I use the "real space" option or the "fix bad sidechain rotamers" option? or both? Thanks Helene -- Helene Köster Philipps-Universität Marburg Institute of Pharmaceutical Chemistry AG Klebe Marbacher Weg 6 35032 Marburg, Germany Phone: +49-6421-28-25908 Mail: helene.krueger(a)staff.uni-marburg.de www.agklebe.de

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How to eliminate or decrease negative electron density at ligand position
by J J 14 Oct '10

14 Oct '10

Hello everyone, I have fine electron density 2Fo-Fc around a small ligand (~20 atoms) binding to my protein (at 1sigma level, all of the ligand atoms are surround by electron density, resolution=3 angstrom). However, I also see some negative electron density Fo-Fc surrounding some of the ligand atoms. My question is should I care about these negative electron density? If I should, what should I do in order to decrease or eliminate these negative electron density? I have tried occupancy refinement. It does help to decrease the negative density. However, it also makes 2Fo-Fc weaker. Another method I tried is to use tls refinement only for the ligand. It also helped to decrease the negative electron density. But since the data resolution is only 3 angstrom, I do not know if I am even allowed to do tls refinement? Thank you all in advance. Jason University of Pittsburgh

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Average B-factors when using TLS
by Phil Jeffrey 13 Oct '10

13 Oct '10

I'm having a discussion with a colleague here about what we expect to see on a model with and without TLS being used. I had the expectation that if you'd compared both models the Biso values reported in the ATOM line for the same atom w/ and w/o TLS would be somewhat comparable. Not the same, because the ADP model is different, but similar. However in the case of the TLS-refined model the average B-factors are systematically higher over the whole structure (86 A^2 vs 69A^2 for one polypeptide chain). Is this reasonable ? Expected ? Phil Jeffrey Princeton

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Re: [phenixbb] When to freeze crystal?
by miket＠chem.ucla.edu 13 Oct '10

13 Oct '10

Just last week I had crystals on Friday, then by Monday they dissolved back into the drop. I don't really understand how or why this happens, but it does. After experiencing this and complaining about it, I heard several other similar stories from around the department. Lesson learned: if you think you have a decent crystal, freeze it. Having said this, I've also heard of good data being collected from a crystal that was over a year old. Like Bert said, I think that occasionally a crystal survives or even improves over time, but those cases are much more rare than cases where the crystal deteriorates. Do how many crystals do you have? You might try freezing some and saving the others in the drop, then you can see for yourself. Good luck, Mike ----- Original Message ----- From: "Nathaniel Echols" <nechols(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Wednesday, October 13, 2010 8:44:42 AM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] When to freeze crystal? On Wed, Oct 13, 2010 at 4:16 PM, J J <phenix.upitt(a)gmail.com> wrote: > Hi everyone, > Sorry to ask a question that is not really related to phenix. I hope someone > here will be able to help me out. > I have a few crystals at hand right now, but I will not be able to look at > them for at least another month or so due to beamline schedule. Do you think > I should freeze them now or wait till I have my beamtime, or it is crystal > dependent? Thanks in advance. (Bert meant to send this to the list, but since he's using the wrong email address, it went to the list admin instead:) From: "Van Den Berg, Bert" <Lambertus.VandenBerg(a)umassmed.edu> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Date: Wed, 13 Oct 2010 11:27:32 -0400 Subject: Re: [phenixbb] When to freeze crystal? It is crystal dependent, but if they are big enough I would freeze them now. I have seen many crystal forms deteriorate over time and wouldn’t take the risk of that happening. It can happen though that old crystals get better (presumably due to slow dehydration of the drop), but I think these cases are fairly rare. Bert _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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When to freeze crystal?
by J J 13 Oct '10

13 Oct '10

Hi everyone, Sorry to ask a question that is not really related to phenix. I hope someone here will be able to help me out. I have a few crystals at hand right now, but I will not be able to look at them for at least another month or so due to beamline schedule. Do you think I should freeze them now or wait till I have my beamtime, or it is crystal dependent? Thanks in advance. Jason University of Pittsburgh

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Merging low resolution mtz file with high resolution sca file with phenix_reflection_file_editor
by Pei-Chun Lin 13 Oct '10

13 Oct '10

Hi, If I merge my low resolution mtz file with the high resolution sca file with phenix.reflection_file_editor GUI, is it the same as : Merge in hires data phenix.autobuild data=solve_2.mtz hires_file=w1.sca seq_file=seq.dat in Phenix Autobuild? PC

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secondary structure restraints question
by Peter Grey 12 Oct '10

12 Oct '10

Dear Phenix community, I have a very large model with many chains (due to NCS and complexity of model) where chain-id is not unique (e.g. there are several chain A) but segid is. All atom selections (for rigid body refinement, ncs restraints, tls etc...) are defined by segid. When I look at the output of phenix.secondary_structure_restraints I see that these restraints are defined by chain-id and residue number. Does this mean I must have unique chain-id names to correctly apply these secondary structure restraints or am I missing something ? Thank you for your time, Peter

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refine : annealing and bulk solvent
by Lepore, Bryan 12 Oct '10

12 Oct '10

[ phenix 1.6.4-486 ] from the program output, it appears that prior to annealing ( e.g. torsion ), a bulk solvent grid search is run using the initial model. after that ends, all the annealing steps are carried out on the model using the initially optimized bulk solvent. When annealing is done, another search is conducted on the final model. i.e. there are no bulk solvent changes during annealing. is this right? -bryan

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DNA base pairing restraints work for GC only
by Phoebe Rice 07 Oct '10

07 Oct '10

We're trying to refine a large, low-resolution protein-DNA complex structure (4A in the good direction), and we need every restraint we can get, so I'm trying to use secondary structure restraints (in addition to ncs and 3 known substructure models). I found this from the newsletter: phenix.secondary_structure_restraints model.pdb > ss.eff ran it, editted it, and plugged into the gui, where it seems to be taken into account if I also say "yes" to "find automattically". Then I ran torsion angle dynamics to see if things were restrained as requested. It only seems to be restraining G:C pairs - the ATs fly apart! The log file makes a very suspicious set of remarks under "secondary structure": No entry for base pair AT with type WWT (H=False). (repeated about the same # of times as we have AT pairs). I thought maybe it was a nomenclature problem, but if "Gd" is OK I don't see what's wrong with "Ad", and the usual suspect, the thymine methyl, stays coplanar with the rest of its base, so the program must be recognizing our base/atom names. Question 2 is that I wanted to view the restraints in pymol, but this command, also cribbed from the newsletter: phenix.secondary_structure_restraints partry1noss.pdb ss_manual.eff format=pymol > h_bonds.pml seems to overwrite the manual editing in my .eff file. Help? I'm new to phenix, so please be explicit about where I've gone wrong. thanks, Phoebe ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alph… http://www.rsc.org/shop/books/2008/9780854042722.asp

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maps : scattering corrections
by Lepore, Bryan 07 Oct '10

07 Oct '10

i'd like to define anomalous scattering corrections for phenix.maps, it looks like i'm not doing it right. it appears that simply pasting in various adjustments of : anomalous_scatterers { group { selection = element = Ni f_prime = 2.4 f_double_prime = -0.1 refine = *f_prime *f_double_prime # not sure about this one } in various places in maps.params mostly causes phenix.maps to report "unused parameter", e.g: maps.anomalous_scatterers.group.selection this should work, right? what am i missing here - is there a scope missing, what scope does this go in, did i miss this in the docs... -bryan

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Phenix.refine stops running in the background
by José Trincão 07 Oct '10

07 Oct '10

Hello all, I've been running phenix.refine over ssh on a remote computer, on command line. I always run it in the background (adding & to the command line). If I disconnect the ssh (or it gets disconnected) the job hangs. Any way of leaving it running even after the ssh disconnects? Thank you. Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

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phenix.refine : mask
by Lepore, Bryan 07 Oct '10

07 Oct '10

i gather that the only way to define an "a priori" mask of the molecular envelope in phenix.refine is to generate Fmask and combine those in refinement - is that right? i.e. there isn't a more intuitive way using a mama mask or somesuch to keep the bulk solvent from flattening out parts you think are model, besides the model that is being refined in the first place? -bryan

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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 01 Oct '10

01 Oct '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 30 Sep '10

30 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 29 Sep '10

29 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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mlhl refinement
by Florian Schmitzberger 28 Sep '10

28 Sep '10

Dear All, I am running Phenix version 1.6.4.-486 on imac. I just wanted to refine (phenix.refine) a model with MLHL target and experimental phase information. Strange thing is when I load the mtz file, as written out from Phenix Autosol (overall_best_denmod_map_coeffs.mtz) into the GUI, the Phenix refine GUI does not seem to any phase information. Only picks up FP and SIGFP labels; but not the Hendrickson-Lattman coefficients, which are present. The following message comes up when I try to chose mlhl refinement: " You have selected 'mlhl' as the refinement target, but no experimental phases were supplied. If you wish to use phase restraints in refinement, please add or select experimental phases, or choose another target function". I guess it is not such a major problem as I can save the .eff file and manually edit it to include the HL coefficients and then run Phenix (as long as Phenix then recognizes them from the mtz file). I would also like to refine f' and f'', as the data are from a selenomethionine derivatized protein. From what I can see the default in Phenix.Autosol seems to be not to keep the F+/- and Dano labels for the output mtz file? So I suppose I do need to provide the initial mtz file or is there a way to change the output options for the coefficients in Phenix Autosol? Cheers, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

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Does Phenix have the library or program to maintain bond angle and bond length to create an extended chain?
by Rojan Shrestha 28 Sep '10

28 Sep '10

Hello: I am wondering whether Phenix has the library or program to maintain the ideal bond length and bond angle. The torsion angles of residue and xyz of each atoms are already known. I want to juxtapose residue or residues to create an extended chain. Thanks Regards, Rojan

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CCP4 Study Weekend 2011: "Model Building and Refinement and Validation"
by ronan.keegan＠stfc.ac.uk 24 Sep '10

24 Sep '10

Dear All, We're pleased to announce that registration for this coming January's CCP4 Study Weekend meeting is now open. The meeting will take place from January 5th to 7th, 2011 at University of Warwick in the UK. The topic of the meeting will be "Model building and Refinement and Validation". This year's organisers, Roberto Steiner and Bernhard Rupp, have arranged the usual mix of interesting and stimulating lectures from some of the foremost speakers in the field along with the opportunity to see demonstrations of the latest software developments from CCP4 during the lunch-time bytes sessions. For more information on the program and registration details please go to the Study Weekend website: http://www.cse.scitech.ac.uk/events/CCP4_2011/ We look forward to seeing you in Warwick. Best wishes, The CCP4 team -- Scanned by iCritical.

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