- phenixbb - phenix-online.org

constrained occupancy groups in phenix.refine
by Lionel Costenaro 04 Sep '10

04 Sep '10

Hello, A portion of my structure have two conformations at an interface between two (NCS) protein chains -in addition to other alternates conformations elsewhere. In both chains, I defined alt_A as one conformation and alt_B as the second conformation, and also for the waters in this region. I would like to constrained the occupancy of these conformations. I though that the following selections would do the job: occupancies { constrained_group { selection = "(chain A or chain B) and (resseq 105 or resseq 110:112 or resseq 140:143) and altid A" After refinement, all alt_A selected residues do have the same occupancy, but not the same occupancies for alt_B and the sum for one residue (occu alt_A +occu alt_B) is not 1. Adding a second group with the same selection but "altid B", constrains also the alt_B occupancies but the sum is still not 1. How should I defined my group(s)? Is it possible to select several non continuous residues from one chain (that's for the waters) without repeating each time "or resseq" ? Best regards, Lionel

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Re: [phenixbb] Can we untoggle molecular weight mean deviation check on ensembles in autoMR?
by James Thompson 04 Sep '10

04 Sep '10

A postdoc in my lab with many more files inside his Phenix build directory just showed me that the Mwt mean deviation check on input ensembles is hard-coded in Phaser. A seemingly arbitrary value of 20% is set within the file emsembles.cc. So, the answer to my previous question is presently NO. We users cannot untoggle or alter this mean deviation value without some recompile of Phaser. I will play with my Sculpt'ed output from the Mustang server to reduce the Mwt deviations within the ensemble of coordinates that I want to feed to Phaser-MP to get by. James R. Thompson <thompson.james at mayo.edu> > Can folks untoggle the molecular weight mean deviation check in > phenix.autoMR on the ensembles input? > > I want to use an ensemble of coordinates generated by the Mustangs > server from a SSM alignment. Therefore, by design the 10 PDBs input to > phenix.autoMR vary greatly in molecular weight from their mean value, > but the whole is likely an excellent probe for molecular replacement. > However, I am stymied by phenix.autoMR: > > ------------------------------------------------------------------------------------- > FATAL RUNTIME ERROR: Molecular weight of > /home/jrt04/Desktop/GB1STAS/MUSTANGServer_10_1.6_0_sculpt-coot-0.pdb > (6610.56) deviates more than 20% from the mean (3977.08). This pdb file > may contain domains or water not present in the other files. > ------------------------------------------------------------------------------------- > > I understand why this check might be of utility to the unobservant. How > can I disable this test? > > Many thanks, > Jim > > -- > James R. Thompson <thompson.james at mayo.edu>

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can phenix.refine output mtz with structure factors not just coeficients?
by amadrona＠uci.edu 03 Sep '10

03 Sep '10

Hi, I am going to deposit a structurein the pdb but noticed that all of the mtz files from phenix.refine only contain coeficients and not reflection info. Is it as simple as running another refinement with write_maps = true instead of false? Will this right out an mtz with structure factors instead of just coeficients. I am a newbie at crystalagraphy so I appolgize if this obvious. Ideally, I would like to create an mtz with structure factors as well as a map for CNS. Is there a way to do this without runing another refinment maybe using "maps.params". Thank you very much for the help! -Yarrow output { prefix = "CIN4_refine" serial = 12 serial_format = "%03d" title = None write_eff_file = True write_geo_file = True write_final_geo_file = False write_def_file = True export_final_f_model = mtz cns write_maps = false write_map_coefficients = True pickle_fmodel = False

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atom selection in phenix.pdbtools
by Michael Hothorn 02 Sep '10

02 Sep '10

Hi, I want to calculate the mean b-value for all atoms of a specific ligand in my structure. I tried: phenix.pdbtools --show-adp-statistic model.pdb keep="chain A and residue 400" , but it still prints out all b-values including solvent etc. any ideas? thanks Michael

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Re: [phenixbb] question on bad geometry
by Thomas C. Terwilliger 02 Sep '10

02 Sep '10

Hi Fengyun, Just to emphasize what Ed points out here, an essential step in completing a structure is to compare it, one residue, solvent molecule, or ligand at a time, with your electron density map, fixing any inconsistencies between the model and the map. There are many wonderful tools in all the crystallographic graphics programs to help you do this. All the best, Tom T >> On Tue, 2010-08-31 at 20:37 -0500, fn1(a)rice.edu wrote: >>> Does >>> that mean I need to manually adjust the model? >> >> Autobuilder is a fantastic tool which greatly simplifies the model >> building process, but you always must validate your structure by >> inspecting the electron density. I fully understand that (hopefully) it >> is what you plan to do and this is more of a reaction to the alarming >> number of obvious and easily correctable systematic errors one finds in >> structures deposited in the PDB these days. >> >> Thanks to Pavel for providing an excellent example to illustrate the >> point. One only needs to take a look at the model in context of >> electron density maps to confirm that autobuilder will fix some errors >> but also sometimes introduce some that require manual correction. >> >> Cheers, >> >> Ed. >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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question on bad geometry
by fn1＠rice.edu 01 Sep '10

01 Sep '10

Hi everyone, I have a structure at 2.3 A refined in phenix to R/Rfree=0.23/0.28. However, the geometry is not that good, the followings are the output from phenix.model_vs_data, Stereochemistry statistics (mean, max, count): bonds : 0.0080 0.0547 3244 angles : 1.1669 12.1085 4374 dihedrals : 15.7241 85.6280 1202 chirality : 0.0706 0.2831 536 planarity : 0.0036 0.0246 573 non-bonded (min) : 2.1217 Ramachandran plot, number of: outliers : 17 (4.02 %) allowed : 37 (8.75 %) favored : 369 (87.23 %) Rotamer outliers : 30 (8.62 %) goal: < 1% Cbeta deviations >0.25A : 0 All-atom clashscore : 40.51 (steric overlaps >0.4A per 1000 atoms) I tried to use fix_rotamer=True, but it doesn't help at all. As to the rotamer outliers, the value is far higher than the ideal one. Does that mean I need to manually adjust the model? Or will autobuild help improve the geometry? Thanks! Fengyun

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How to do a phenix.fmodel calculation incorporating the exponential scaling model only?
by zhangh1＠umbc.edu 01 Sep '10

01 Sep '10

Hi, I want to use phenix.fmodel to do a calculation incorporating the exponential scaling model only (Not the flat model). I am not sure whether I just need simply specify: mask { use_asu_masks = False } since the output maps are just identical no matter use_asu_masks = True or False. Should I do something else to enable exponential scaling model only? Thanks! Best Regards, Hailiang

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0.00 Refined Isotropic ADPs
by Joseph Noel 01 Sep '10

01 Sep '10

Hi All. Me again! LOL I am sure this has come up and related to how the "B-factor" in the refined PDB's ADP column is calculated including the overall anisotropic B-factor, etc but is it unusual to have isotropic ADPs refine to 0.00? I have several nice structures with 0.00 isotropic ADPs. I am not refining TLS or anisotropic ADPs at all. Just the normal course of refinement. These are regions of a high degree of order and the maps are beautiful but just wandering what the 0.00 ultimately means particularly when I eventually submit to the Protein Data Bank. Joe P.S. Nat's tips on COOT and Phenix are working beautifully now! Thanks Nat! ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Re: [phenixbb] Phenix and COOT Together on a Mac (and Probe too?)
by Joseph Noel 01 Sep '10

01 Sep '10

Nat, One thing that seemed to solve all the problems at once was to completely remove any reference to the COOT path in the Phenix preferences! Is that weird? When I removed it completely only leaving the path to PYMOL then COOT is working just fine in conjunction with Phenix and even the Probe issues have disappeared. Prior to this, I was tried two different paths to COOT. 1. /sw64/bin/coot 2. /Applications/coot.app/Contents/MacOS/coot Neither behaved but if I don't specify anything it works. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Problem with low figure of merit
by sankaranarayanan srinivasan 01 Sep '10

01 Sep '10

Hi all, I am new to structure solving. I have a 2.9A dataset for a Seleno crystal of which i am trying to use Autosol to build an initial map. I used the settings for a thorough solution, instead of quick. All the other parameters were set to default settings. The solution that i got from autosol, gave me the following result Solution # 1 BAYES-CC: 23.7 +/- 30.9 Dataset #1 FOM: 0.27 Residues built: 238 Side-chains built: 139 Chains: 15 Overall model-map correlation: 0.65 R/R-free: 0.38/0.42. Score type: SKEW CORR_RMS Raw scores: 0.02 0.77 100x EST OF CC: 16.86 32.11 The density modification map matches, quite well with many of my side chains fitted. My question here is , IS THERE A WAY I CAN IMPROVE THE Figure Of Merit , BY CHANGING ANY PARAMETERS IN PHENIX-AUTOSOL. I HAVE A HIGH SOLVENT CONTENT IN MY CRYSTAL AND I DID NOT INPUT THAT IN MY INITIAL PARAMETERS. DOES PHENIX AUTOSOL CONSIDER SOLVENT FLATTENING FOR SUCH CRYSTALS? I would appreciate someone's help in this regard Thanks Shankar

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