- phenixbb - phenix-online.org

Get R values without refining in phenix.refine
by Murpholino Peligro 17 Jun '15

17 Jun '15

How can I get R values without refining anything? Just to check if my newest model is better than the old one?

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Re: [phenixbb] anomalous difference map calculation
by Alexandra Marques 17 Jun '15

17 Jun '15

Thank you very much for your replies. Here is what I did: 1)I rerun xdsconv again with Friedls law=false in order to get the mtz file with the F(+) and F(-) columns (new.mtz). 2) I used my pdb file from the last refinement together with the new.mtz file as input for “Calculate maps” in Phenix and selected the option for anomalous map. Now I obtained the ANOM PHANOM map. I hope this is correct… In the anomalous map the largest density is in the Mo and Fe atoms. There is no density in the S of SO3 or SO4 groups, so, this will not help me to decide whether there are SO3 groups in the structure (because for the SO4 I have no doubt). However, while searching the mailling list I foud this post http://www.phenix-online.org/pipermail/phenixbb/2009-September/013799.html which worried me. Should I have used from the beginning this “new” mtz file with F+/F- in order to obtain anomalous differences map at each refinement step? Do you think that I should go back, transfer the R-free flags to my new mtz file and repeat all the refinements? Best regards, Alexandra 2015-06-17 16:59 GMT+01:00 Pavel Afonine <pafonine(a)lbl.gov>: > Hi Alexandra, > > to get anomalous difference map you do not need to do anything special: > phenix.refine calculates this map by default as long as your input data are > Fobs(+) and Fobs(-) or Iobs(+) and Iobs(-). > > Refining occupancy of Mo may not be a bad idea given it is likely to be > partially occupied. > > Pavel > > > On 6/17/15 06:04, Alexandra Marques wrote: > > Hi, > > > I am in the last refinement steps of a MR model and I want to calculate > an anomalous difference map essentially to confirm the presence of a > sulfite molecule and to locate vanadium (present in soaking solution). I > read that it is necessary to have a mtz file with anomalous data (i.e. > F+,F- or I+,I-). However, my data was collected at “normal” wavelenght > (0.97) and it was processed with XDS considering Friedls law= true and my > mtz file contain the following columns: H K L FP SIGFP. So, can I still > calculate a anomalous difference map based on my data? > > > Since I also have a Mo atom in the active site can I try to refine its > occupancy by using the option “anomalous groups” in the refinement > strategy? > > > Thank you very much, > Alexandra > > > _______________________________________________ > phenixbb mailing [email protected]://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > >

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anomalous difference map calculation
by Alexandra Marques 17 Jun '15

17 Jun '15

Hi, I am in the last refinement steps of a MR model and I want to calculate an anomalous difference map essentially to confirm the presence of a sulfite molecule and to locate vanadium (present in soaking solution). I read that it is necessary to have a mtz file with anomalous data (i.e. F+,F- or I+,I-). However, my data was collected at “normal” wavelenght (0.97) and it was processed with XDS considering Friedls law= true and my mtz file contain the following columns: H K L FP SIGFP. So, can I still calculate a anomalous difference map based on my data? Since I also have a Mo atom in the active site can I try to refine its occupancy by using the option “anomalous groups” in the refinement strategy? Thank you very much, Alexandra

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keep torsion restraint on ligand
by CPMAS Chen 17 Jun '15

17 Jun '15

Hi, All Phenix Users, I am fitting 2-bromoethanol to the density map. I want to keep its gauche conformation, so I edited the cif for this ligand to restrain the torsion angle, loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period BRJ Var_01 BR1 CB CB1 OB1 -60.00 0.0 3 But, after refinement, this angle can be close to 90 or even 120. Even worse is that the fitting at such angles are not better than at -60/60 angle. How could I fix/restrain the angle during refinement? Thanks! Charles *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Re: [phenixbb] anomalous difference map calculation
by Ashok Nayak 17 Jun '15

17 Jun '15

Hello Alexandra, I believe you have to reprocess the data keeping friedel pairs (f+ and f- ) separate to make use of the little most anomalous signal (if any) at your collected wavelength. The best thing would be to collect a high redundant set of peak data (if not all the three data sets including mad remote and inflection data) If you have access to a tunable source and xtals left. Once you process differently, you can do all sorts of substructure search and later refine anomalous scatterers using wavelength, atom type and f ' and f“ values. Sulphur sad is also a good possibility if you have a decent nmbr of sulphurs in your protein. Hope this suffices your query. Regards Ashok Nayak CSIR CDRI, Lucknow, India Alexandra Marques <at.marques(a)fct.unl.pt> wrote: >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb >Unsubscribe: phenixbb-leave(a)phenix-online.org

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phenix refine of my EM data
by Smith Liu 17 Jun '15

17 Jun '15

Dear All, By phenix.real_space_refine, I have fitted the a PDB file to an EM map, with Ramachandran favored around 90% and acceptable level of Ramachandran outlier (1.5%) and rotamer outlier (1.2%). Besides visual checking indicating the fitting of the main chain and sid chains to the dnsity map is acceptable. I hope the refine results can be improved by phenix reciprocal space refine. By phenix.map_to_structure_factors I convert my mrc file to mtz file, with the above mentioned phenix.real_space_refine refined pdb amd mtz files as the input files for the graphical phenix refine, in which I never select real space refine, and I always check xyz coordinates and Group B-factors (sometimes I check xyz coordinates and individual B-factors ). Fot this kind of phenix reciprocal space refine, I find the molprobity anslysis results have improved a little, but I find both the contouring level of 2FOFCWT map and the FOFCWT map is more than thousands of thousands high (and it seems the contouring level of FOFCWT is much higher), and visual checking indicated both the main chain and side chains hardly fit with the density map. But I really find there were publications which did phenix.real_space_refine first, and then process the reciprocal space refine, which get good results as introduced in the publications. Will you please tell me why my phenix reciprocal refine after phenix.real_space_refine did not work? Best regards. Smith

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on phenix.map_to_structure_factors
by Smith Liu 13 Jun '15

13 Jun '15

Dear All For phenix.map_to_structure_factors, it needs to input the resolution d_min. But for an EM map, usually the resolution is the general resolution of the whole map (or to some extent the average resolution of the whole map). Is d_min for phenix.map_to_structure_factors the general EM map resolution, or the best resolution of the whole EM map, which is only for part of the EM map with the best quality? Smith

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on real_space_refine
by Smith Liu 12 Jun '15

12 Jun '15

Dear All, After fitting a PDB into a 3.5-5 A resolution EM map by phenix.real_space_refine, should I still need to do a reciprocal space refine? For crystallography, the reciprocal space is in fact not purely imaginary, it corresponds to the diffaction spot. But for the EM data refinement, what is the reciprocal space refine? And what reciporce spce refine works on for the data refinement? Smith

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refinement of ligands and waters
by Alexandra Marques 10 Jun '15

10 Jun '15

Hi, I still have little experience in the refinement of protein structures. So, I have some (basic) doubts that I would like you to help me please. 1) I have a metal coordinated to a cofactor in the active center of my protein structure. The initial solution provided by phaser/autobuilding already contained the metal+cofactor modelled in the density but with zero occupancy. Then I created all the necessary restraints and cif files with phenix_ready_set and did two cycles of model building/phenix refinement. The refined structures always contained zero occupancy for those atoms. My question is: should I manually change the occupancy for the metal+cofactor to 1? I thought this would be made automatically by phenix because I selected the option “occupancies” and “individual B-factors” in the refinement strategy… 2) When manually placing waters in the density with coot, what is the maximum value of B-factor that is acceptable for a water? I am asking that because I have some water molecules with weak density and consequently B-factors between 45 and 55 but that are involved in interactions with other molecules. Is it better to keep those waters or remove them? Best regards, Alexandra

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does the lastest Phenix only support windows 7
by Xiao Lei 09 Jun '15

09 Jun '15

Hi All, I am a beginner of crystallography and I'd like to install Phenix. I tried to download phenix for my Windows 8.1 system (64bit) but in the download page it says "64-bit (Windows 7 only) ". I do not know if I really have to use Windows 7. Does anyone have experience of installation Phenix on Windows 8.1? Thanks ahead. Xiao

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Berkeley Server Downtime
by Paul Adams 08 Jun '15

08 Jun '15

Dear Colleagues, the CCI group in Berkeley is moving to a new building this week. As a result several structural biology web services will be offline for a short while. These include: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) The servers will be shutdown at 9am Pacific time on Wednesday 10th. Services should resume by the morning of Friday 12th at the latest. During the downtime bug reports and emails requesting help should be queued and received by us once the servers are back online. We greatly appreciate your understanding, and hope that this doesn’t present too much of an inconvenience. Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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no merge original index
by Tarek DawoD 07 Jun '15

07 Jun '15

obtaining unmerged data from HKL2000 when i use "no merge original index" it either does nothing or gives this error ((could not read file /,,,/,,,,//,,///,,,,/.sca header: format is not supported by HKL-2000, File could be corrupted or it may be a result of a "no merge" command)) How could this be fixed?? did somebody else managed to get the unmerged data from HKL2000 or it is problematic? Thank you for your explanation and providing solutionTKDawoD

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problem with B-factor plot within the Structure Comparison tool
by Emilia C. Arturo (Emily) 06 Jun '15

06 Jun '15

Hello All. I am trying to zoom in on a section of the B-factors v. residue plot that is generated using the Structure Comparison tool of the phenix GUI. I zoom in by selecting a narrow residue range. When I do so, the plot does not show all parts of each trace; they are broken up and/or residues are missing that are certainly in the pdb files that I supplied, and that showed up when I displayed a wider residue range. I am using phenix version 1.9-1692 on a Mac (OS X Yosemite). I'd input 21 pdb files. I've done some typical refresher-type things like closed and reopened the project, and restarted phenix (with no rationale, really), but the display problem persists. Does anyone else recognize this problem? Regards, Emily.

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Model bias in MR-SAD
by mohamed noor 05 Jun '15

05 Jun '15

Dear all In the case of MR-SAD, how bad can model bias be? Does it also depend on the data resolution and resolution at which there is still enough anomalous signal? Or can the anomalous signal help in overcoming the bias inherent in the MR model? Thanks.

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R free assignment in thin shells
by mohamed noor 04 Jun '15

04 Jun '15

Dear all I found a not-so-old thread about this topic: http://phenix-online.org/pipermail/phenixbb/2012-January/018259.html. Maybe there has been significant changes in phenix.refine since then. However, I couldn't find a conclusion. In my case, my data extends to 1.4 A with the R/R free being around 23/26 %. There is also pseudo symmetry, so there are 16 NCS copies in a lower symmetry group than what Xtriage suggested. The map looks fine with density for some H atoms even being visible. On what basis should I decide whether to use (or not) thin shell assignment? And what is the cut-off for number of NCS copies? Thanks.

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Problems running phenix.rosetta_refine
by Klose, Thomas 04 Jun '15

04 Jun '15

Dear all, I was trying to set up phenix.rosetta_refine to test it for the refinement of a 4.5Å structure. I installed the latest phenix release and compiled the latest rosetta version (2015.19) using rosetta.build_phenix_interface. However, when I try to run phenix.rosetta_refine I get the following error message: …. Generating 5 models on 4 processors... DEBUG dumping error message ERROR: Rosetta exited with status 1 stderr output: Sorry: Wrong map type requested: %%map_type%% Allowed format is: [p][m]Fo+[q][D]Fc[kick][filled] where [p] and [q] are any numbers (optional), [m] and [D] indicate if the requested map is sigmaa (optional), Fo and Fc are Fobs and Fcalc, [kick] is for Average Kick Map (optional), [filled] is for missing Fobs filled map. Examples: 2mFo-DFc, 3.2Fo-2.3Fc, mFobs-DFcalc_kick, 2mFobs-DFcalc_filled, Fc, 2mFobs-DFcalc_kick_fill, anom, anom_diff, anomalous_difference, Fo ERROR: PhenixInterface::calculateDensityMap() : error writing map ERROR:: Exit from: src/core/scoring/cryst/PhenixInterface.cc line: 1122 This happens with our actual data as well as test data that I downloaded (PDB: 1yip). Any help in solving this problem would be greatly appreciated. Thanks, Thomas

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Help with using FFT map coefficients tool
by Emilia C. Arturo (Emily) 04 Jun '15

04 Jun '15

Hello. I'd like to generate a map appropriate for viewing in PyMOL, using a model and structure factors downloaded from the PDB. But I'm unable to do so, and perhaps you can help me figure out what I might be doing wrong: To generate the map, I did the following using the phenix GUI (version 1.9-1692): 1. I used Reflection tools > Import CIF structure factors to convert the .cif format structure factors for PDB id 1J8U to an mtz file. 2. Then, to configure the job to generate the CCP4 map, I loaded this mtz file, but when I did that I got the following error: "This reflections file does not appear to contain any suitable map coefficients" I went through the same steps again for two other PDB ids, this time generating the mtz file by either letting phenix do it from a PDB id, or by supplying the tool with both a .cif file with structure factors and a pdb model file. I get the same error. Has anyone any advice? Regards, Emily.

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Re: [phenixbb] Changing an amino acid to an unusual amino acid
by Schubert, Carsten [JRDUS] 03 Jun '15

03 Jun '15

Hi Nat, bonds in COOT do not mean much, as they do not translate into bonded interactions in the refinement programs. Phenix for instance tries to figure out the bonding by itself through some distance based heuristics. However in your case it looks as if the CRO residue may not be defined as a polymer, i.e. part of a protein chain in the monomer library you are using. In Windows the monomer library is located in C:\WinCoot\share\coot\lib\data\monomers. Look at the difference in the headers for CYS.cif and CRO.cif or PTR.cif (phosphotyrosine). The aminoacids or modified aminoacids considered part of the peptide chain have all 'peptide' in the header, CRO does not. That is probably the reason why coot does not make any bonds. This would probably cause problems later on with Phenix as well. You could pull out the CRO.cif into your directory, modify it to make it a peptide and read it into coot and phenix during refinement. I would also run it through REEL to make sure the definitions are kosher. HTH Carsten From: Natalia Ketaren [mailto:[email protected]] Sent: Tuesday, June 02, 2015 5:42 PM To: Schubert, Carsten [JRDUS] Subject: Re: Changing an amino acid to an unusual amino acid Hi Carsten, Th residue is a part of the correct chain. It just doesn't make an bonds with the residues on either side of it. Is this common for unusual amino acids when adding to the main chain? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Postdoctoral Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/ On Jun 2, 2015, at 5:26 PM, Schubert, Carsten [JRDUS] <CSCHUBER(a)its.jnj.com<mailto:[email protected]>> wrote: Hi Natalia, if the missing/wrong chain IDs are really the problem you can change them in COOT under Calculate -> Change Chain IDs. The dialog is a bit tricky, since you probably have to use the correct residue range to change an individual residue into an existing chain. In your case I would write out the PDB file and use a text editor to change the chain ID and move the residue into its correct place in the file. HTH Carsten From: phenixbb-bounces(a)phenix-online.org<mailto:[email protected]> [mailto:[email protected]] On Behalf Of Natalia Ketaren Sent: Tuesday, June 02, 2015 5:17 PM To: phenixbb(a)phenix-online.org<mailto:[email protected]> Subject: [phenixbb] Changing an amino acid to an unusual amino acid Hello All, I'm working on a GFP structure and I'm trying to incorporate the CRO (chromophore) residue into the structure using coot. My process is to use Extension->Modelling->Replace residues, where it's suppose to replace a Tyr residue. I type the 3 letter code, CRO, the residue appears, I'm able to real space refine it, but it does not incorporate CRO into the desired chain. Would someone be able to help me figure out what I'm doing wrong? And possibly walk me through a solution? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Postdoctoral Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

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Negative density
by mohamed noor 03 Jun '15

03 Jun '15

Dear all After refinement, there is a single negative peak in my map where nothing is modeled. What does it mean? Thanks.

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Changing an amino acid to an unusual amino acid
by Natalia Ketaren 02 Jun '15

02 Jun '15

Hello All, I’m working on a GFP structure and I’m trying to incorporate the CRO (chromophore) residue into the structure using coot. My process is to use Extension->Modelling—>Replace residues, where it’s suppose to replace a Tyr residue. I type the 3 letter code, CRO, the residue appears, I’m able to real space refine it, but it does not incorporate CRO into the desired chain. Would someone be able to help me figure out what I’m doing wrong? And possibly walk me through a solution? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Postdoctoral Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

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Merging reflections
by mohamed noor 02 Jun '15

02 Jun '15

Dear all I have a few native datasets, one anomalous dataset with signal up to 10 A and two other datasets (also collected at the phasing wavelength but no anomalous signal seems to be present) and a sulfur SAD dataset with signal to about 7 A. All the datasets have a resolution of about 2-3 A and processed with xia2/XDS. I couldn't do fluorescence scan as the detector couldn't detect at such a high energy (20 keV). A few questions: 1. Why is there at least some signal from one dataset but not others? The signal should come from a covalently bound ligand, molybdopterin to be precise. 2. Since I(+) should not be equal to I(-) when there is anomalous signal, should I just merge the native dataset together with those collected at phasing wavelength that have no anomalous signal? Or do I merge everything together? 3. Will the anomalous signal to 10 A be useful to do MR-SAD? I could solve the structure with MR but I wanted to be sure my ligand is there. Thanks.

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Allignment of multiple structures
by jens j birktoft 01 Jun '15

01 Jun '15

I apologize if this question this question has been asked before but I still need help finding an answer to the following. I am looking for a program/web-server that will calculate the superposition of multiple structures (non-protein!) Thanks -- +++++++++++++++++++++++++++++++++++++++++++++++++++ Jens J. Birktoft Structural DNA Nanotechnology Department of Chemistry New York University e-mail: jens.knold(a)gmail.com; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++++++++++++++++++++++++++++++++++++++++++++++++++

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a question on phenix.real_space_refine
by Smith Liu 01 Jun '15

01 Jun '15

Dear Pavel, By phenix.real_space_refine, I fit a PDB with a 4.0 map. Most of the fitting were nice, but for the Ala residues, it indicates the o of the C=O occupies the density position which should be occupied by the CH3 side chain of the Ala, which also means the CH3 side chain of Ala cannot occupy the density position which clearly should be occupied by the CH3 side chain of Ala. Is any method or restraint to have the CH3 of Ala to ccupy its density position? Smith

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alternate side chains conjugated with water molecules
by Jorge Iulek 31 May '15

31 May '15

Dear all, I have a 1.70 A resolution dataset in which I observe, with certain confidence, that some (few) side chains are alternated with waters. Though managing to tie occupancies of each alternate side chain with a water molecule to give an overall occupancy of 1.00, phenix refine still pushes them (water from side chain) apart as if there were bumping restraints (but their occupancies sum up to no more than 1.00). The closest to this I could find is: http://www.phenix-online.org/pipermail/phenixbb/2009-May/013354.html But I could not find how to turn off specific bumping restraints. I would be thankful if someone could point me to the recipe to do this. Jorge

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Low resolution refinement - rotamers and Ramachandran
by mohamed noor 29 May '15

29 May '15

Dear developers I am refining a low resolution structure (3.8 A). After I fix most of the outliers (red bars) in Coot, phenix.refine is causing my structure to be worse than the start with 13 % Ramachandran outlier and 13 % rotamer outlier. Secondly, when I used phase_and_build to build my model, my R/Rfree is around 30/35 with atoms from some residues missing. When I fill them in with Coot, fix the outliers above and re-refine, R/Rfree jumps to 36/42 and the rmsd angles are too high (2.9). I have already used weight optimization and NCS. Am I doing something wrong? Thanks.

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reference model restraints by segid
by jp d 28 May '15

28 May '15

Hi,I am having trouble getting phenix to used segid's in reference model restraints when my reference and target pdbs both don't use chain ID's.phenix quits with this message: *** Adding Reference Model Restraints *** Sorry: chain ' ' in /home/path/removed/agnref2.pdb contains one or more errant TER cards. Please remove and try again. my definition file looks like this:refinement { main { reference_model_restraints = True } reference_model { file = two.pdb } } refinement.reference_model.reference_group { reference = segid A16S selection = segid A16S } (above about 50 more times) this was on versions 1.9-1692 , dev-2016 and dev-2056 any suggestions ?thanksjpd

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riding hydrogen model
by Filip Qbukarski 27 May '15

27 May '15

Dear phenix community I am currently refining a 1.75A structure and wanted to usethe riding hydrogen model in pehnix.refine. From what I found in the manual andprevious discussions on the mailing list and if I understand well, using ridingHs is advised for every resolution and the way of doing this in phenix.refine is notRefmac-like but instead I should 1) put Hs using ReadySet, 2) select the‘riding’ option for Hs and 3) use the PDB containing the H coordinates fordeposition, even though they were not individually refined. In this case theircontribution to scattering is also taken into account (which makes sense),which is a different way of treating riding Hs compared to Refmac, if Iunderstand well. Would it be possible to comment on this and in case I got thingswrong, correct?In fact for my structure, after adding the Hs prior to refinement using ReadySet and using theriding option, I actually got Rfree dropping by 1% (from 19.5 to 18.5) and better clash score (~0.5 according to Molprobity). Thanks in advancebestFilip

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Re: [phenixbb] Refinement
by Pavel Afonine 26 May '15

26 May '15

Hi Mohamed, > How do tell phenix.refine to not move my HEM ligand around? yes, you can exclude selected atoms from refinement of coordinates in Phenix refinement GUI: Refinement settings -> Modify selection for: XYZ coordinates -> Edit -> type atom selection in "Edit selected" field (under XYZ refinement) like "chain A and resseq 1" or "chain A and resname ATP" However, I would rather find why correct geometry is not preserved. > I have a cif file describing the ligand but in my case, I can see > clear density of it not following the ideal geometry. If you send me files (off mailing list of course!) I will see if I can explain it.. You can copy to Nigel too as chances are that if you choose to send files I will be talking to him anyway. > As an example, I have attached a screenshot from Coot. It's hard to infer what's going on from a static image.. > In fact, the C atom is covalently linked to the nearest Cys, so the > HEM side chain should be 'moved' into the density and the green blob > shouldn't be there. Is this link defined anywhere in restraints used in refinement? Pavel

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Fw: on the convergence of phenix refine
by Smith Liu 26 May '15

26 May '15

Dear All, For the meaning of non-convergence here, I mean in the whole 30 macro-cycles, both the Rwork and Rfree curves were in zigzag format, which I never met before. I am looking forward to getting an explanation from you. Smith -------- Forwarding messages -------- From: "Smith Liu" <smith_liu123(a)163.com> Date: 2015-05-26 09:26:23 To: phenixbb(a)phenix-online.org Subject: [phenixbb] on the convergence of phenix refine Dear All, Recently I have done a phenix refine, I find even I have 30 macro-cycles, the refine did not converge well. For example, for the last 5 cycles refine, the Rwork can still fluctuate between o.21 and 0.22, although both the final Rwork and Rfree decreased in comparison with the start Rwork and Rfree. What is wrong for my map and refine strategy? Smith

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on the convergence of phenix refine
by Smith Liu 26 May '15

26 May '15

Dear All, Recently I have done a phenix refine, I find even I have 30 macro-cycles, the refine did not converge well. For example, for the last 5 cycles refine, the Rwork can still fluctuate between o.21 and 0.22, although both the final Rwork and Rfree decreased in comparison with the start Rwork and Rfree. What is wrong for my map and refine strategy? Smith

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on B-factor refine of the phenix.real_space_refine
by Smith Liu 23 May '15

23 May '15

Dear Pavel, For the input, the last line of PDB is as followng, ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116 1.00100.56 H For the run=ADP of the phenix.real_space_refine, the last line of the first model of all states pdb is, ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116 1.00194.44 H and the last line of the second model of all states pdb is ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116 1.00164.47 H. Clearly in each PDB of each model of the all states pdb produced, the b-factor is different, and they are different with the b-factors of the input pdb. Thus will you please explain why there are 2 states pdbs which seems both are refined pdbs? In addition, is it normal that the single state refined pdb cannot be opended? Next, will you please explain based on what of the mrc file, the phenix.real_space_refine run=ADP function got the b-factors? Further, I have noticed that the phenix.real_space_refine run=ADP gave a resolution which is different from the mrc general resolution given by relion or some other software. Will you please explain base on what the phenix.real_space_refine run=adp gives the resolution? Best regards. Smith -------- Forwarding messages -------- From: "Pavel Afonine" <pafonine(a)lbl.gov> Date: 2015-05-23 00:48:00 To: "Smith Liu" <smith_liu123(a)163.com>,"phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: Re: Fw:Re: [phenixbb] on B-factor refine of the phenix.real_space_refine For the all states PDB, it contains the input pdb for the phenix.real_space_refine and the real spaced refined PDB Yes I think so.. Is it not? Pavel

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Fw:Re: on B-factor refine of the phenix.real_space_refine
by Smith Liu 22 May '15

22 May '15

Dear Pavel, It looks work. But for the refined PDB, it seems it was in read-only format, which I cannot copy. For the all states PDB, it contains the input pdb for the phenix.real_space_refine and the real spaced refined PDB, am I right? Smith -------- Forwarding messages -------- From: "Pavel Afonine" <pafonine(a)lbl.gov> Date: 2015-05-21 14:44:30 To: "Smith Liu" <smith_liu123(a)163.com>,phenixbb(a)phenix-online.org Subject: Re: [phenixbb] on B-factor refine of the phenix.real_space_refine I have a EM map (.mrc), with fitting and based on a crystal structure I got the fitted PDB file. I convert the mrc map to the CCP4 map， no need to convert .mrc into .ccp4 (isn't it the same thing?). Anyways, phenix.real_space_refine can use both. and I run phenix.real_space_refine model.pdb map.mtz run=adp, with phenix-dev-2034, in order to get my own b-factors for my fitted PDB based on my EM map. However after the above phenix.real_space_refine, I checked the refined PDB, and I find phenix.real_space_refine neither change the coordinates, nor change the b-factors for each atom. I need to see the files to be able to comment. If you share the files (off list and not sending directly via email but using things like Dropbox instead) then I will be happy to have a look. Thus will you please introduce to me how can I get my own b-factors for my fitted PDB in order to deposit my map and fitte pdb to the EM database? phenix.real_space_refine model.pdb map.mtz run=adp should just do what you want. If it didn't - see above (I need to see the files). Pavel

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metal-ligand distances, and Optimize X-ray/stereochemistry weights
by Emilia C. Arturo (Emily) 21 May '15

21 May '15

I'm refining a model at 2.9 A, where four chains are in the ASU, and each active site has an iron with a few ligands; the configuration of this active site is the topic here. Currently the iron-ligand distances are not ideal (according to CheckMyMetal and the ideal distances generated by phenix.metal_coordination), but they are within a range observed previously for structures of truncated versions of this enzyme; furthermore, the more the metal-ligand distances change towards ideal distances, the more positive and negative density I observe in the Fo-Fc, so it appears that this deviation from the 'ideal' is supported by the data. However, when I use the 'Optimize X-ray/stereochemistry weights' option during refinement, the metal-ligand distances change (the metal appears to do most of the moving), getting closer to ideal, and this generates more positive and negative density in the Fo-Fc map). However, clearly it's nice that optimizing the X-ray/stereochemistry weights reduces R-free (and keeps the R-f/R-work ratio fine as well). So what is the most appropriate approach here, in order to keep the metal-ligand distances that best support the data, but still reap the benefits of the optimized stereochemistry weights? Some details of the structure and refinement are these: The iron in each of the four chains in the ASU is coordinated with atoms from two histidines, a glutamate, and a water (so four ligands per Fe) and there remains un-modeled density in the iterative build comp OMIT map used for modeling (because resolution is 2.9A and adding more water (which is my best guess, given what truncated structures at higher resolution show coordinating the Fe) does nothing to the Rf). I am working with an .edits file generated by phenix.metal_coordination. After some experimentation, I've left the sigma values (for Fe-O and Fe-N) at default values, and added a restraint for Fe-O (water), using an ideal distance of 2.3 and a sigma value of 0.1. Emily.

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Your abstract can still be considered for an oral presentation at the American Crystallographic Assn Annual meeting
by Terwilliger, Thomas Charles 21 May '15

21 May '15

Hi Phenix users, A message from the American Crystallographic Association! YES! We are still accepting abstracts. No late fee. ACA Annual Meeting • Philadelphia, PA • July 25 - 29, 2015 Submit now to be considered for an oral presentation. Once all the lectures are scheduled, abstracts will continue to be accepted for poster presentations. see: http://www.AmerCrystalAssn.org All the best, Tom T Vice-President, ACA

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on B-factor refine of the phenix.real_space_refine
by Smith Liu 21 May '15

21 May '15

Dear All, I have a EM map (.mrc), with fitting and based on a crystal structure I got the fitted PDB file. I convert the mrc map to the CCP4 map， and I run phenix.real_space_refine model.pdb map.mtz run=adp, with phenix-dev-2034, in order to get my own b-factors for my fitted PDB based on my EM map. However after the above phenix.real_space_refine, I checked the refined PDB, and I find phenix.real_space_refine neither change the coordinates, nor change the b-factors for each atom. Thus will you please introduce to me how can I get my own b-factors for my fitted PDB in order to deposit my map and fitte pdb to the EM database? Smith

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Map quality
by mohamed noor 19 May '15

19 May '15

Dear all Is there a single (or a few) metrics that can be used to quantitatively assess map quality instead of looking at each one in Coot? For example, I want to compare the effect of having low completeness in the low resolution shells. Thanks.

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Several postdoc opportunities, Shanghai University
by Pavel Afonine 18 May '15

18 May '15

Posted on behalf of Prof. Ren Wei and Jeffrey Reimers. **************************** *Post-Doctoral Fellowships in Quantum Refinement of Protein X-ray Crystallographic Structures and related work in Biophysics, Biochemistry, Biomaterials, Chemistry, and Soft Condensed Matter*** Shanghai University (http://www.shu.edu.cn) isseeking multiple outstanding postdoctoral researchers to be part of the newly created International Centre for Quantum and Molecular Structure (ICQMS). Parallel Adjoint Appointments at The University of Technology, Sydney (UTS) (http://www.uts.edu.au/about/faculty-science/physics-and-advanced-materials), Department of Mathematical and Physical Sciences, will also be available. Most available positions relate to the core project of ICQMS: the development of codes for automatic quantum refinement of protein crystallographic structures. For these positions, previous experience at the PhD or post-doctoral level in the simulation of protein structure is essential. This could involve mastering of quantum-chemical software, molecular dynamics methods, statistical mechanics theories, or protein structure refinement. Positions are available for both software users and methods developers. ICQMS also has a wider view, considering the determination of protein function and spectroscopy, especially for photosynthetic proteins, understanding the effects of solvation and environment on molecular properties, quantum dynamics and coherence in proteins, understanding order/disorder transitions, the fundamental role played by entropy in controlling protein structure, the properties of biomaterials such as cement, general self-assembly processes such as organic self-assembled monolayer formation and properties, and the properties of bulk materials. A position is also available concerning the development and application for GPUs of Hartree-Fock theory or Density-Functional Theory or molecular dynamics. All positions require a PhD in Chemical Physics, Quantum Chemistry, Computational Biochemistry, Crystallography, or related disciplines. Excellent verbal and written communication skills in English are essential. Proven independence is also essential. Candidates that have contributed to scientific-community activities and/or teaching innovation will be considered favourably, as will those that have contributed independently to multidisciplinary team projects. Shanghai University is a well funded, internationally connected, rapidly raising University with a strong profile in Material Science, and indeed under the direction of University President Prof. H. J. Luo is a central player in the extensive Chinese Materials Genome Initiative (MGI) Project. ICQMS extends this vision into mainstream chemical and biochemical research. Adjunct Appointments at the University of Technology Sydney will allow each Postdoctoral Fellow to spend 6 months doing joint research in Sydney with UTS staff. Shanghai University and The University of Technology Sydney have a 20-year history of close collaboration, including the joint Smart Cities Institute and the Sydney Institute of Language and Commerce. This collaboration also includes the dual PhD degree program between the two universities. The negotiable anticipated start date is 2015 between August and December. The positions are available for two years and renewable subject to a performance review. Shanghai University is an Equal Opportunity Employer and all persons are encouraged to apply. Applicants should send their curriculum vitae including lists of publications, summaries of their research interests, lists of prizes and awards, summaries of any teaching, community service or administrative experience, and have three reference letters sent directly to yarulove2006(a)shu.edu.cn <mailto:[email protected]>. Further information can be obtained from: ICQMS Director: Jeffrey Reimers reimers(a)shu.edu.cn <mailto:[email protected]> or ICQMS Deputy Director: Wei REN renwei(a)shu.edu.cn <mailto:[email protected]> Closing Date: 2015 December 31^st , or until all positions are filled.

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Submissions for Comput. Cryst. Newsletter
by Nigel Moriarty 14 May '15

14 May '15

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the July 2015 issue is 15 June 2015. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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how to generate an isomorphous difference map
by crystallogrphy 13 May '15

13 May '15

Hi, I am trying to generate an isomorphous difference map with phenix GUI. I input reflection 1 and 2 with mtz format and a PDB model, I got an MTZ format map file. Because I want to load it to coot or pymol with negative and positive density, I need to transform this mtz map to ccp4 map. However, FFT map cannot work. Does any know how can I get a ccp4 format maps with positive or negative density? Thanks!

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Scientist-I (Structural Biology) - Frederick National Lab for Cancer Research
by Dhirendra K Simanshu 13 May '15

13 May '15

Dear colleagues, We have an opening for a Scientist-I (Structural Biology) position here in Frederick, MD. If not interested, please forward this email to those who might be. To apply for this position and for further details, including a job description and qualifications, please click on the link below: http://jobs.leidos.com/ShowJob/Id/475028/Scientist-I-615658-%28NCI%29/ Thank you Dhirendra *------* *JOB DESCRIPTION * The Scientist I will work in support of the FNL/NCI RAS Initiative. One of the major objectives of the RAS initiative at the Frederick National Lab for Cancer Research (FNLCR) is to conduct structural analysis of KRAS mutants and biologically relevant KRAS activator/effector complexes in support of drug discovery efforts. The Scientist I will be responsible for: 1) carrying out structural studies on KRAS-effector complexes through the entire protein crystallographic process, including construct design, protein purification, biochemical and biophysical characterization, crystallization, X-ray data collection, structure determination and analysis, 2) working closely with an integrated team of protein scientists in the Protein Expression Laboratory (PEL) at the FNLCR, 3) participating in experimental design and to independently conduct experiments in a priority-driven environment, 4) completing projects independently and as part of a team, and providing timely updates of the project progress to their supervisor both informally and by formal report writing, and 5) generating high-quality peer-reviewed publications. Work may involve the use of potentially hazardous chemical, biological, or radiological materials or may be located in areas where such materials are used. May require the use of personal protective equipment and adherence to strict safety protocols. *Qualifications:* *BASIC QUALIFICATIONS* - PhD in structural biology, protein biochemistry, crystallography, or in a related discipline from an accredited college or university appropriate to biomedical research, or eight (8) years’ experience in lieu of degree - Foreign degrees must be evaluated for U.S. Equivalency - In addition to the educational requirements the candidate will need proven ability in all aspects of protein crystallography from construct design through structure determination and interpretation - Extensive experience in crystallization of protein-ligand and protein-protein complexes - Experience collecting data at synchrotron beamline and solving ab initio structures - Expertise in commonly used crystallography software packages - Proficiency in protein biochemical and biophysical characterization - Record of publications in peer-reviewed journals *PREFERRED QUALIFICATIONS* - Relevant postdoctoral experience in a structural biology laboratory. - Experience working with small GTPases, RAS-related activator/effector proteins, or membrane-associated complexes. - Knowledge of molecular dynamics simulations and protein-ligand docking. *To apply*, click here: http://jobs.leidos.com/ShowJob/Id/475028/Scientist-I-615658-%28NCI%29/

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on minimization_global of phenix.real_space_refine
by Smith Liu 13 May '15

13 May '15

Dear All, For minimization_global of phenix.real_space_refine, does it has relationship with the input map, or it is only processed based on the input pdb? Smith

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Re: [phenixbb] how to generate an isomorphous difference map
by Edward A. Berry 12 May '15

12 May '15

OK. Knowing that and rereading the OP's question and your reply, I think that was the right answer. Apologies to CCP4 for accidentally cross-posting. eab On 05/12/2015 01:21 PM, Philip Kiser wrote: > There is a tool within PHENIX that prepares an mtz file for generation of an isomorphous difference map (scales the two datasets together, etc). I assumed that is what the OP was talking about. > > On Tue, May 12, 2015 at 12:54 PM, Edward A. Berry <BerryE(a)upstate.edu <mailto:[email protected]>> wrote: > > OK. I guess I was thinking of subtracting 2fo-Fc maps, which would give essentially (Fo1-Fo2) coefficients. But coming out of phenix it will be at least 2mFo-DFc, with different m's and D's for the two datasets. Makes it rather more complicated. > eab > > On 05/12/2015 11:58 AM, Philip Kiser wrote: > > Good points. But also, the traditional isomorphous difference map is not as susceptible to model bias issues compared to a real space difference map (or a "vector" isomorphous difference map). > > On Tue, May 12, 2015 at 11:37 AM, Edward A. Berry <BerryE(a)upstate.edu <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: > > > > On 05/12/2015 09:46 AM, Philip Kiser wrote: > > crystallogrphy, > > If you did everything correctly, you should be able to directly calculate the difference map in Coot from the MTZ file generated by PHENIX. You would need to open it with "Open MTZ" rather than "Auto open MTZ" and then select the appropriate map coefficients. Note that what Tim described (a real space difference map) is technically different from the traditional isomorphous difference map where the SF amplitudes of the two data sets are subtracted prior to the map calculation. > > Philip > > > Should be the same, due to linear property of the Fourier transform, EXCEPT for possible scaling differences and treatment of missing data. This latter could be significant, since presumably the traditional methods omits reflections unless present in both datasets, whereas in Tim's method each map will be made with all data available in that dataset. As a result, the largest coefficients in Tim's difference map might be the reflections which are absent in one map and present in the other. But if both have good completeness, it may not matter. > > eab > > > > On Tue, May 12, 2015 at 9:24 AM, Tim Gruene <tg(a)shelx.uni-ac.gwdg.de <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>>> wrote: > > Dear crystallogrphy, > > you can open the PDB file with Coot, then use File -> Open MTZ to read one > mtz-file after the other into Coot. Coot will offer to generate the map > coefficients from the previously loaded PDB file. > > Once you have both maps, you can go to Extensions -> Maps -> Make a Difference > Map to create the difference map. > > In order to see both positive and negative density, you choose Extensions -> > Maps -> Set Map is a Difference Map. > > Regards, > Tim > > On Tue, May 12, 2015 at 08:43:45PM +0800, crystallogrphy wrote: > > Hi, > > > > I am trying to generate an isomorphous difference map with phenix GUI. I > > input reflection 1 and 2 with mtz format and a PDB model, I got an MTZ > > format map file. Because I want to load it to coot or pymol with negative > > and positive density, I need to transform this mtz map to ccp4 map. > > However, FFT map cannot work. > > Does any know how can I get a ccp4 format maps with positive or negative > > density? > > > > Thanks! > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > > http://phenix-online.org/mailman/listinfo/phenixbb > > Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > > > -- > -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > phone: +49 (0)551 39 22149 <tel:%2B49%20%280%29551%2039%2022149> <tel:%2B49%20%280%29551%2039%2022149> <tel:%2B49%20%280%29551%2039%2022149> > > GPG Key ID = A46BEE1A > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > >

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Postdoc Position - Berkeley, California
by Paul Adams 10 May '15

10 May '15

Lawrence Berkeley Laboratory Postdoctoral Fellow Job ID: 80929 Division: Physical Biosciences Date Opened: 5/8/2015 Summary: A postdoctoral position is available to work on developing new methods for macromolecular structure determination and refinement with the PHENIX software system. To learn more about Phenix visit: http://www.phenix-online.org Duties: Development and implementation of computational algorithms for structure determination using crystallography. Including methods for the assessment of crystallographic data quality, improved methods for minimization of target functions, algorithms for the automated parameterization of structure refinement, new target functions for the refinement of structures, and enhanced structure deposition tools. Qualifications: Ph.D., or equivalent experience, in computational crystallography, computational biology, bioinformatics, computational chemistry or a related field. Demonstrated experience with computational methods development. Publications in macromolecular crystallography or related field. Familiarity with software development tools such as C++, C and scripting languages such as Python. Good programming and mathematical skills. Solid interpersonal skills and the ability to work in a team environment are important. Ability to communicate with a broad range of researchers. Note that this is a multi-year position that is renewed annually on the basis on performance and continued funding. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years, and 57 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. To apply visit https://lbl.taleo.net/careersection/2/jobsearch.ftl?lang=en and search for the job number 80929 or visit: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=80929 -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Molecular replacement at low resolution
by mohamed noor 09 May '15

09 May '15

Dear developers I have a dataset to about 4 A in point group P 4 2 2 (Pointless suggests P 41 21 2). The protein is about 11 kDa and has an identity of about 50 % to my search model. Phaser calculated the eLLG to be about 5, and maybe not surprisingly, it failed even after using Sculptor to prepare the model. It also says that solutions with Z-scores more than 8 were rejected for failing the packing test. Are there any suggestions on getting a solution? Solvent content calculation from Xtriage suggests about 8 copies in the asu. Would this be of any help in MR? Thanks.

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Raw diffraction images required
by mohamed noor 09 May '15

09 May '15

Dear all I am looking for diffraction images that were collected to a resolution of 3 A or so (by visual inspection), highly redundant and the I/sigma at the outermost resolution should be low (not more than 1). Maybe there is something already in the JCSG database but I don't know exactly which one. I want to show that high redundancy can provide a background average to extract weak but useful spots and that this relationship increases to a certain limit. Thanks.

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How to fix atoms in refinement
by Rajeshwer Sankhala 07 May '15

07 May '15

Hi, I have flexible a flexible loop in my structure and every time i refine it derange ramachandrans. Can anyone suggest how can i fix these flexible residues in phenix refinement so basically i don't wanna refine them. Can i do this in GUI? Thanks Raj The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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feature request: update project
by Sebastiano Pasqualato 07 May '15

07 May '15

Dear Phenix developers, it happened to me recently to go from one Mac to another, working on the same Phenix projects. I have the directory synchronised via Google Drive, with the same absolute path. Importing a project is not a problem, at all. The problem is that, if I modify one project on one computer, the changes are not “seen” by the other computer, and there is no way to “update” the project, forcing it to read the info on the .phenix directory. Would that be difficult to implement? Thanks a lot in advance, best, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit <http://is.gd/IEO_XtalUnit>

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on phenix.real_space_refine
by Smith Liu 06 May '15

06 May '15

Dear All, If I only want to refine resi 30-50 in Chain A by phenix.real_space_refine, and my protein contains A, B, C chains of a identical sequence of 800 aas, will you please let me know how can I specify "residue 30-50 of Chain A" in the phenix.real_space_refine command? Smith

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neutron refinement of protonated Glu and residues with alternate conformation
by crystallogrphy 05 May '15

05 May '15

Hi, I am doing joint X-ray and neutron refinement for my structure. I found a few residues with two alternate conformations. After I generated alternation conformations, I used phenix.readyset to generate hydrogen and deuterium atoms for D/H atoms. However, phenix.readyset only gives H atoms for exchangable H atoms, such as the amide H atoms. The reason is that A and B letters have been assigned for the alternate conformation, not for the D/H atoms for particular conformations. Could anyone know how to solve this problem? The second question is that I found one Glu residue is protonated at OE1 atom of its carboxylate side chain. How could I generate protonated Glu? Do I need a strain file for this? Thanks! Qun

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SA
by Irina PROKHOROVA 01 May '15

01 May '15

Hello, I am trying to run coordinate refinement 5 cycles with first cycle of simulated annealing (torsion) via command line. Here is a part of my params file that I adapted from my colleges: refinement.main { number_of_macro_cycles = 5 target = *ml mlhl ml_sad ls simulated_annealing_torsion = True } simulated_annealing { mode = every_macro_cycle second_and_before_last once *first first_half } refinement.refine { strategy = *individual_sites individual_sites_real_space rigid_body \ individual_adp group_adp tls occupancies group_anomalous sites { individual = segid *A individual = segid *B } As a result I get the Error Unused parameter definitions: simulated_annealing.mode (file "refine.params", line 26) Could you help me with the syntax, please. Should I include sites definition for simulated annealing? Irina

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