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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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