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debugger pdb
by Krista Joosten 10 Sep '10

10 Sep '10

Hi all, I'm working with Tom Burnley on the development of time_averaging.py. I would like to use the debugger pdb, but am not sure how to do this and whether it's possible. After some googling, I tried to hack into phenix.time_averaging adding -m pdb when the variable DEBUG==1, but I got the error message 'no module called pdb'. Bye Krista

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Beamtime at the ALS-BCSB beamlines
by Peter Zwart 09 Sep '10

09 Sep '10

Dear All, July 15, 2010 is the deadline for the March/April 2010 Rapid Access Proposal cycle. All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with ADSC Q315/Q315R detectors, automated sample changers and data collection software enabling high-throughput crystal screening and data collection. Remote data collection is available on all BCSB beamlines, providing the user with the full complement of sample visualization, sample manipulation, beamline control, data acquisition and data analysis tools exactly as they would see them if they were stationed at the beamline. The main difference between local operation and remote operation, is the length of the network cable! This enhanced remote operation capability is coupled with 22hr onsite support by BCSB staff who are able to assist immediately with loading additional samples for remote users or troubleshoot any issues that might arise. Remote users can furthermore be kept up-to-date on changes in ring status via an SMS service ( http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Ph…) or via twitter (@AlsRingStatus). Specific features are summarized below. Beamlines 5.0.1, 5.0.2, 5.0.3: -------------------------------------- Beamline 5.0.2 is equipped with a novel variable collimator allowing users to adjust the beamsize continuously and on the fly between 25 and 100 micron, both horizontally and vertically. With a collimator setting of 30x30 micron, typical exposures are around 1 to 2 second. The Berkeley Automounter sample handling system has a routine capacity of 96 samples (6 pucks). In a typical high-throughput screening mode, the mount-to-mount time is around 2.5 minutes per sample, allowing users to screen a full puck within 45 minutes. The sector 5 beamline user stations are equipped with fully high-adjustable, ergonomically friendly work stations. Beamlines 8.2.1 and 8.2.2: ----------------------------------- To facilitate studies on small crystals, a microdiffractometer was installed in the beamline 8.2.1 endstation. The new equipment allows precise sample positioning to within 2 microns, excellent sample viewing of very small crystals, and an off-axis crystal positioningstage. Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer (Actor), allowing remote operations to now be a routine mode of access for these beamlines. Data analyses in the BCSB is facilitated by software maintained by sbgrid ( http://www.sbgrid.org). A 16 core linux machine is available for our users to process their data and solve/refine their structure. An additional mode of access to the BCSB beamlines is through the Collaborative Crystallography (CC) Program. Users apply for beamtime via the general user program, and collaborate with an expert crystallographer who will conduct the experiments and data reduction on behalf of the researchers. Depending on the users, structure solution, model building and refinement can be carried out as well. Please contact BCSBBeamtime(a)lbl.govfor more information. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/ Scroll down to "Structural Biology beamines (includes protein SAXS)." Click on "New Proposal." If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

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Help on multi-start-simulated-annealing sigmaA-weighted 2fofc map
by fn1＠rice.edu 09 Sep '10

09 Sep '10

Hi everyone, 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? Thanks! Fengyun

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Can phenix calculate R factor based on the only given mtz file containing Fo and Fc?
by zhangh1＠umbc.edu 07 Sep '10

07 Sep '10

Hi, I am wondering whether phenix can calculate R factor based on the only given mtz file containing Fo and Fc? Thanks! Hailiang

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will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb?
by zhangh1＠umbc.edu 07 Sep '10

07 Sep '10

Hi, For the pdb file generated by refmac which contains only the residual-B, will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb? Thanks a lot! Best Regards, Hailiang

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constrained occupancy groups in phenix.refine
by Lionel Costenaro 03 Sep '10

03 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 03 Sep '10

03 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 02 Sep '10

02 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 01 Sep '10

01 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 01 Sep '10

01 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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