- phenixbb - phenix-online.org

Phenix GUI big reporting
by Nigel Moriarty 24 Jul '15

24 Jul '15

Folks One of the features of the Phenix GUI is the bug reporting which allows a user to send a program traceback. This allows the developers to zero in on the line that causes the problem but it is much easier if we have the inputs. This is why we ask that you include you email se we can work with you to resolve the problem ASAP. One of the weaknesses of the current system is that it relies on the user typing their email address correctly. If it is incorrect, we are sending replies that bounce. This happens occasionally and it's almost impossible to track the user down. We can also only assume, given that this misstyped user is sending in more reports, that he is getting frustrated. To that end, I'm naming names. If you typed in jwaning(a)umich.edu please contact us or fix the email in your preferences. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, 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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Announcing the 2015 EMDataBank Map Challenge
by Cathy Lawson 24 Jul '15

24 Jul '15

Dear PhenixBB List Members, EMDataBank/Unified Data Resource for 3DEM is pleased to announce the 2015 Map Challenge. All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors. Seven benchmark raw image datasets have been selected for the challenge. Six are selected from recently described single 3D electron microscopy single particle structure determinations with image data collected as multi-frame movies; one is based on simulated (in silico) images. Challengers are sought to create single particle reconstructions from the targets, and then to upload their results with associated details. Assessors are sought to participate in evaluating submitted reconstructions. Registration is now open for all interested participants. Challengers may submit maps between August and December. Before submissions open, all are encouraged to provide feedback on submission requirements. An open assessment period will commence in early 2016. To learn more about this challenge and to register, please visit http://challenges.emdatabank.org and click on "MAP CHALLENGE" in the menu bar. The map challenge is the first of two community-wide challenges being sponsored by EMDataBank this year to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model. The second challenge, focused on creating coordinate models from 3DEM maps, will be announced later this year. Sincerely, Cathy Lawson on behalf of the EMDataBank Team and the Map Challenge Committee emdatabank.org www.facebook.com/emdatabank3dem

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Short contact with symmetry mate
by Ashok Nayak 23 Jul '15

23 Jul '15

Dear Phenix BB, I am refining a helical bundle structure where I have been obtaining an invariant short contact (close to 2A) at a Glu residue with Lys of symmetry related molecule of one helix of the bundle. I had been using Rigid body, TLS, occupancy and Indv ADP for the refinement (which gave the best Rfree values). If I include coordinate refinement the short contact seems to be gone rather with higher Rfree values. I ll appreciate some suggestions regarding this. Thank you in advance. Ashok Nayak CSIR-CDRI Lucknow, India

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NIH Request for Information about Technology Development
by Paul Adams 23 Jul '15

23 Jul '15

Dear Colleagues, my apologies for the slightly off-topic and US-centric posting, but I felt this was of sufficient interest to the structural biology community at large. The NIH, specifically the National Institute of General Medical Sciences, is in the process of considering how best to support the development of biomedical technologies, and access to those technologies. They have issued a request for information: http://grants.nih.gov/grants/guide/notice-files/NOT-GM-15-118.html This covers a very broad range of biomedical activities, including the development of new hardware and software for techniques such as NMR, crystallography, SAXS, and cryo-EM. It also includes the provision of technologies through facilities such as synchrotrons and other national research centers. For those of us in the US this provides an excellent, and rare, opportunity for researchers to voice their thoughts about how important technology development and national facilities are to the success of structural biology research. Please note that the deadline for response is August 7th. 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 33, Room 347 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 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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histidine flip in refinement
by Joel Tyndall 23 Jul '15

23 Jul '15

Hi all, We are trying to optimise a histidine interaction where NE2 would ideally make a hydrogen bond with an adjacent tyrosine hydroxyl. The starting point contains the hydrogen bond. However upon refinement the ring flips (chi2 x 180 degrees) to place the CE1 adjacent to the tyrosine hydroxyl. Is it possible to stop this as I see no reason why phenix.refine would want to do this Regards Joel _________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293

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Newest phenix version for Unix cluster
by Xiao Lei 21 Jul '15

21 Jul '15

Hi All, I'd like to download the newest phenix version ( 1.10pre-2104 July13th2015 nightly build) and install it on HPC cluster (Unix system). Is CentOS 5 ok for my purpose? It seems for a 64bit linux this is the only download option: 64-bit Linux (Intel/AMD) Kernel 2.6 (64-bit; CentOS 5) [ download command-line installer ] Thanks ahead. Xiao

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Re: [phenixbb] pdb LINK record lost after phenix refine in GUI
by Pavel Afonine 17 Jul '15

17 Jul '15

Hi Lu, could it be that you define a conflicting restraint? On one hand you want that O-C bond to be 1.44A (that's what I see on your picture), on the other hand you want that H to be reasonable distance apart from O (and not 1.14A). I would guess if you want to define that bond you nee to delete H first. Could this explain what you observe? Pavel On 7/16/15 18:38, luzuok wrote: > Dear Pavel, > Thank you for your explanation. > After adding the bond restrain and refinement, the position of the > hydrogen from the bonded atom of the ligand seems not reasonable. This > hydrogen is too close to the other bonded atom. I can even see this H > atom links to two atom. > It seems that the riding H of C23 cannot see the OG neighbouring > to it. > > Best wishes! > Lu > > > -- > 卢作焜 > 南开大学新生物站A202 > > Lu Zuokun, Ph.D. Candidate > College of Life Science, Nankai University > > At 2015-07-16 23:07:49, "Pavel Afonine" <pafonine(a)lbl.gov > <mailto:[email protected]>> wrote: > > Hi Lu, > > seeing the link in graphics and actually having bond defined in > refinement are two different things. Refinement uses standard > restraints and those you define on top of that. Visualization > tools use standard bonding patterns to show you the bonds (and > sometimes also use distance based connectivity, such as Pymol). > Visualization tools are unlikely to guess anything on top of that. > > So if you want to have specific bond in refinement, then tell > refinement program to add it (and checking .geo file is not a bad > idea to verify that it was actually added). Seeing that bond on > graphics is a different story and it is outside the scope of > Phenix refinement. Check documentation of visualization program > you use to learn what's required to see what you want to see. > > Pavel > > On 7/16/15 00:54, luzuok wrote: >> >> Dear Pavel and Nigel, >> >> I can see: >> >> bond pdb=" OG SER A 265 " >> pdb=" C23 AIX A 700 " >> ideal model delta sigma weight residual >> 1.330 1.339 -0.009 2.00e-01 2.50e+01 2.16e-03 >> >> I think this bond is what I want. >> >> If I want to _see_ this bond in graphical tool, like coot or >> pymol, Do I have to add a link record in PDB? >> >> You are right Nigel, I made a mistake of python and Phenix version. >> >> Best withes! >> Lu >> >> -- >> >> Lu Zuokun, Ph.D. Candidate >> College of Life Science, Nankai University >> >> 在 2015-07-16 14:21:24，"Pavel Afonine" <pafonine(a)lbl.gov> 写道： >> >> All connectivity information is in .geo file: check it to see >> if the bind in question is present there. >> phenix.refine does not read/write LINK records given that all >> info is in .geo file, and input (custom) linking is specified >> via custom bonds using atom selection syntax (or clicking in >> the GUI). >> >> Pavel >> >> On 7/15/15 18:04, luzuok wrote: >>> Dear all, >>> Although Custom geometry restrains was added (see log). >>> After phenix refine, the link record was lost and there seem >>> no bond between this two atoms (1.44 angstrom). >>> Do you think this is a real bond? How to maintain this record? >>> Any comment is appreciated! >>> Best regards! >>> >>> Data resolution: 2.4 >>> Phenix version:v2.7 >>> >>> phenix refine log: >>> ======================== Summary of geometry restraints >>> ======================= >>> >>> Number of disulfides: simple=1, symmetry=0 >>> Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS >>> A 484 " distance=2.04 >>> Custom bonds: >>> bond: >>> atom 1: "ATOM 1205 OG SER A 265 .*. O " >>> atom 2: "HETATM 3413 C23 AIX A 700 .*. C " >>> symmetry operation: x,y,z >>> distance_model: 1.339 >>> distance_ideal: 1.330 >>> ideal - model: -0.009 >>> slack: 0.000 >>> delta_slack: -0.009 >>> sigma: 0.2000 >>> Total number of custom bonds: 1 >>> Time building geometry restraints manager: 0.20 seconds >>> >>> pdb file LINK record: >>> LINK OG SER A 265 C23 AIX A 700 >>> 1555 1555 >>> >>> >>> -- >>> >>> Lu Zuokun, Ph.D. Candidate >>> College of Life Science, Nankai University >>> >>> >>> >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> Unsubscribe:[email protected] >> >> >> > > >

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Map alignment
by Mullins, Elwood A. 17 Jul '15

17 Jul '15

All, Is it possible to align two structures and two maps without moving both to a P1 box? This seems to be the default, if not the only, option in Structure Comparison and Superpose Maps. Thank you, Elwood Elwood A. Mullins, Ph.D. <> elwood.mullins(a)vanderbilt.edu<mailto:[email protected]> <> tel 615.936.5234 <> fax 615.343.6707

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pdb LINK record lost after phenix refine in GUI
by luzuok 16 Jul '15

16 Jul '15

Dear all, Although Custom geometry restrains was added (see log). After phenix refine, the link record was lost and there seem no bond between this two atoms (1.44 angstrom). Do you think this is a real bond? How to maintain this record? Any comment is appreciated! Best regards! Data resolution: 2.4 Phenix version:v2.7 phenix refine log: ======================== Summary of geometry restraints ======================= Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 484 " distance=2.04 Custom bonds: bond: atom 1: "ATOM 1205 OG SER A 265 .*. O " atom 2: "HETATM 3413 C23 AIX A 700 .*. C " symmetry operation: x,y,z distance_model: 1.339 distance_ideal: 1.330 ideal - model: -0.009 slack: 0.000 delta_slack: -0.009 sigma: 0.2000 Total number of custom bonds: 1 Time building geometry restraints manager: 0.20 seconds pdb file LINK record: LINK OG SER A 265 C23 AIX A 700 1555 1555 -- Lu Zuokun, Ph.D. Candidate College of Life Science, Nankai University

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phenix.superpose_ligands
by cedric bauvois 16 Jul '15

16 Jul '15

Dear all, I would like to superimpose a small organic compound (file format sdf) on a small peptide (file format pdb). Is there a way to use phenix.superpose_ligands to this ? thank you for your help Cédric -- .................................................................. Dr. Cedric Bauvois Cristallographie des protéines Institut de Recherches Microbiologiques J.-M. Wiame -IRMW Campus CERIA - Av. E. Gryson, 1 B-1070 Bruxelles, BELGIUM e-mail: Cedric.Bauvois(a)ulb.ac.be tél: +32 (0)2 5273634 fax: +32 (0)2 5267273 ..................................................................

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simulated annealing composite omit map or iterative build composite omit map at 2.7A resolution
by Xiao Lei 16 Jul '15

16 Jul '15

Dear Phenixbb members, I am thinking of generating a composite omit map for my whole structure model (the model is solved by phaser MR in CCP4 and refined by phenix.refine program, results of phenix.refine shows Rfree/Rwork is 27% / 20%. The resolution of data is 2.7A). From previous phenix posts and information from internet, I know there are four composite omit map types in Phenix: "simple"; "refine"; "simulated annealing" and "iterative build" composite omit map. Because I want to get rid of model bias as much as possible, I am thinking of choosing either "simulated annealing" or "iterative build" method, though I know it needs much longer time to run. I know "iterative build" composite map option is more powerful to get rid of model bias as I found in phenix manual that "A more powerful approach is to generate an "iterative-build" omit map (Terwilliger et al. 2008), which rebuilds the structure instead of annealing." But at the "autobuild-iterative guild omit map" manual it also said "The AutoBuild Wizard produces a refined model that can be nearly complete if the data are strong and the resolution is about 2.5 A or better. At lower resolutions (2.5 - 3 A) the model may be less complete and at resolutions > 3A the model may be quite incomplete and not well refined." My questions are: 1. As the resolution of my data is 2.7A, does this mean Simulated annealing composite map option is better for me in this case? 2. Inside phenix panel, there are two map tools for generating composite omit map, one is "Composite omit map" tool and the other is "Autobuild-iterative build omit map" tool. I tried the "composite omit map" tool with simulated annealing option with my refined model and original x-ray data, in the output file I only get 2mFo-DFc map (I know this is by default) but no pdb output, I am guessing this is because in this "composite omit map" tool my model is not modified (or refined) by the program, just the composite omit map is generated, am I right? If I am right, does this mean the following step is to open the output map in coot with my model, and do manual adjustment of the model in the regions which does not fit the map? 3. In the "autobuild-iterative build omit map" tool, there is also an option of "simulated annealing" composite omit map, is this option the same as the "simulated annealing" option in the "composite omit map" tool and will give the same output (just the 2mFo-DFc map by default, not modifying my model) ? 4. If I use iterative-build composite map with this 2.7A resolution, I'm guessing I will get a modified or refined pdb model output and a composite 2mFo-DFc map, but my model may not be complete because of the resolution, does this mean I have to manually add the missing part of model in the following step? 5. Is there an option to generate composite omit mFo-DFc map along with composite 2mFo-Fc map at the same time? Thanks ahead. Xiao

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The difference of using data label "Imean and SigImean" or "F and SigF" in Phenix
by Xiao Lei 15 Jul '15

15 Jul '15

Dear All, I am using Phenix1.9-1962 version on Mac OS X 10.10.3. I notice in Phenix refinement or composite omit map GUI panel, there is an option for me to select data labels. I have two options of data labels: one is "Imean and SigImean"; the other is "F and SigF". My experimental data is from a single crystal diffraction set, after convert scale file (.sca) to mtz file using scalepack2mtz in ccp4, I have a mtz file output. I checked the mtz file using viewhkl program, it shows I have both Imean, SigImean, and F, SigF columns. Is there any difference between the data label choices in these phenix programs? Xiao

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message after refinement
by Almudena Ponce Salvatierra 15 Jul '15

15 Jul '15

Dear all, after refinement of my nucleic acid structure with phenix.refine I get: "warning: rms deviation from ideal geometry (bonds and/or angles) is suspisciously high. You may need to optimize X-ray stereochemistry weighting" However when I move to the molprobity tab I see no outliers no anything... looking weird. I even more wonder where this comes from because the fact is that I had one refinement with no warnings or anything and today I repeated the same, exactly the same, except for the fact that I renumbered one of the chains. Now all out of a sudden (I know it doesn't sound scientific at all), I get this warning regarding the rmsd when I was actually considering that the refinement stage was over. Does anybody have a theory regarding where the problem might be here? Thanks a lot in advance. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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Refinement with new mtz.file
by Aleksandar Bijelic 15 Jul '15

15 Jul '15

Dear CCP4 user and experts, I refined (with PHENIX) a 3.0 A dataset obtaining Rfree of about 0.24 (with good geometry according to Ramachandran, Beta Outliers, etc.) .... Everything seems to be ok (especially in relation to the resolution) .... because the mtz.file I used was quite old and I cannot find my xscale.hkl file, I processed the data set again (this time with optimizng and polishing) and received a "better" file according to almost everything (resolution limit, I/sigma, CC(1/2), Rmeas), thus I used this new mtz.file and put it in my last refinement step (the refinement which led to the above mentioned Rfree = 0.24). Suprisingly, the refinement starts at Rwork = 0.18 and Rfree = 0.19 but ending up with 0.20 and 0.22, respectively. So I wanted to know if this is usual? I was expecting my data to become slightlly better but what is irritating me is the starting R-values of the refinement and that it get worse during refinement. Maybe I did something wrong? Is it reasonable to replace the mtz.file with a new one in the last refinement step or should I start the refinement from the scratch? In the sake of completeness, I deleted the header of the used pdb.file because of the R-flag error which occurs, since Phenix reconizes that the pdb.file was already used with other Rflags. Sorry, but I am still a beginner in this field, so I would be very grateful if somebody could explain me this situation and my mistake and if I need to start refinement from the beginning. Thank you in advance! Best Regards. Aleksandar -- ------------------------------------------- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 A-1090 Wien Tel: +43 1 4277 52536 e-Mail: aleksandar.bijelic(a)univie.ac.at --------------------------------------------

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Set up Simulated Annealing starting tempreture
by Xiao Lei 14 Jul '15

14 Jul '15

Dear Phenixbb members, I'm learning phenix this days. I use phenix refinement and found there is a simulated annealing option (SA Cartesian or SA torsion option). However, I found the SA cartesian starts at 5000K and SA torsion starts at 2500K by default, and I'd like to change the starting temperature by myself. I search phenix manual and found: To change starting SA temperature: % phenix.refine data.hkl model.pdb simulated_annealing=true \ strategy=individual_sites simulated_annealing.start_temperature=10000 I do not understand this, does this mean I have to type the above command in somewhere in phenix? is there a place I can simply put SA start temperature numbers in? Xiao

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NCS and R-Values Hung up at 0.42/0.46 for 2.1Å resolution
by John Bruning 12 Jul '15

12 Jul '15

I collected two datasets of the same ligand bound structure at 2.4 and 2.1 Å resolution. The apo structure has already been solved to 2.2Å resolution in P31 (and P3121 for SeMet). After processing each dataset as both P31 and P3121 in MOSFLM, I proceeded with MR with Phaser using sequential partial search models to place either 3 copies in the ASU for P3121, or 6 copies for P31. (The previously solved apo structure had 6 copies of the same protein in the ASU). *** in summary two datasets, processed as both P31 or P3121 After running xtriage for either .mtz, I get this warning about NCS: Distance to origin : 56.728 Height relative to origin : 26.388 % Translational pseudo-symmetry is very likely present in these data. Be aware that this will change the intensity statistics and may impact subsequent analyses, and in practice may lead to higher R-factors in refinement. Regardless, I can proceed with the MR using sequential partial search models to place either 3 copies (P3121) or 6 copies (P31) with decent solutions (i.e. packing looks good upon inspection, scoring looks appropriate -> SOLU SET RFZ=2.8 TFZ=8.3 PAK=13*LLG*=-37 *LLG*=2199 as an example). However, I did get the following somewhat expected warnings: Number of known components (1) not divisible by 2: Translational *NCS* correction not applied Large non-origin Patterson peak indicates that translational *NCS* is present Upon any attempt at initial refinement (with a number of different strategies), the R-factors are hung up > 0.42 (for example in the P3121, 2.1Å case): Start R-work = 0.4966, R-free = 0.5133; Final R-work = 0.4231, R-free = 0.4477 My concern is that there is some pathology that is not being recognized (merohedral twinning) or that the NCS/pseudosymmetry is not being addressed appropriately. -- Cheers, John

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Re: [phenixbb] Fwd: [ccp4bb] Phenix; converting a map to structure factors
by Pavel Afonine 12 Jul '15

12 Jul '15

Hi Mark, Tom copied me your email. > As I'm sure you are aware there is tremendous interest in building > into and refining against low resolution (by X-ray standards) EM maps. > Could you comment to the phenix BB about whether its appropriate to > convert maps to reciprocal space and use ML refinement? While it is a possible way of doing this (and this is how it's been done in the past) I don't think it is a good route to follow. In case of cryo-EM your data is map, so why not just refine against the map? Why take a detour through reciprocal-space by converting map into structure factors (=manipulating your original data) and doing reciprocal space using refinement programs that were designed for crystallography? With this in mind we have developed a new refinement tool in Phenix (it is still in active development!) called phenix.real_space_refine that is designed to refine atomic models directly into maps (any map: X-ray, neutron, cryo-EM, low or high resolution), for quick summary see http://phenix-online.org/presentations/real_space_refine.pdf as well as documentation page (at the bottom): http://phenix-online.org/documentation/ and newsletter article (page 43): http://phenix-online.org/newsletter/CCN_2013_07.pdf Let me know if you have any questions or comments! Pavel

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atom vdW dictionary for Python
by David Shin 12 Jul '15

12 Jul '15

Hi - I'm writing a Python script to measure the volume of pockets within protein structures - plus extra bells and whistles... thus a custom job. I was wondering just for speed, if someone could point me to values for van der Waals radii that are somewhat agreed upon for protein atoms, or if there is some dictionary already made that someone could point to that resides in phenix or some other structural biology package that would be ok for me to copy/use. Thanks, Dave

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Re: [phenixbb] [ccp4bb] Phenix; converting a map to structure factors
by Terwilliger, Thomas Charles 11 Jul '15

11 Jul '15

Hi Reza, Just use: phenix.map_to_structure_factors map.ccp4 d_min=2.5 or something like that, All the best, Tom T On Jul 10, 2015, at 11:27 AM, Reza Khayat wrote: Hi, Is it possible to convert a map to structure factors using Phenix? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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NCS and R-Values Hung up at ~0.42/0.46
by John Bruning 11 Jul '15

11 Jul '15

Hi Everyone, I collected two datasets of the same ligand bound structure at 2.4 and 2.1 Å resolution. The apo structure has already been solved to 2.2Å resolution in P31 (and P3121 for SeMet). After processing each dataset as both P31 and P3121 in MOSFLM, I proceeded with MR with Phaser using sequential partial search models to place either 3 copies in the ASU for P3121, or 6 copies for P31. (The previously solved apo structure had 6 copies of the same protein in the ASU). *** in summary two datasets, processed as both P31 or P3121 After running xtraige for either .mtz, I get this warning about NCS: Largest Patterson peak with length larger than 15 Angstrom: Frac. coord. : 0.333 -0.333 -0.153 Distance to origin : 56.728 Height relative to origin : 26.388 % p_value(height) : 2.659e-03symmetry. Translational pseudo-symmetry is very likely present in these data. Be aware that this will change the intensity statistics and may impact subsequent analyses, and in practice may lead to higher R-factors in refinement. Regardless, I can proceed with the MR using sequential partial search models to place either 3 copies (P3121) or 6 copies (P31) with decent solutions (i.e. packing looks good upon inspection, scoring looks appropriate -> SOLU SET RFZ=2.8 TFZ=8.3 PAK=13*LLG*=-37 *LLG*=2199 as an example). However, I did get the following somewhat expected warnings: Number of known components (1) not divisible by 2: Translational *NCS* correction not applied Large non-origin Patterson peak indicates that translational *NCS* is present Upon any attempt at initial refinement (with a number of different strategies), the R-factors are hung up > 0.42 (for example in the P3121, 2.1Å case): Start R-work = 0.4966, R-free = 0.5133 Final R-work = 0.4231, R-free = 0.4477 *** best R-factors from ~ 15 different strategies My concern is that there is some pathology that is not being recognized (merohedral twinning) or that the NCS/pseudosymmetry is not being addressed appropriately. Any suggestions in troubleshooting this would be much appreciated, as I have pretty much exhausted everything I could think of. -- Cheers, John

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(no subject)
by Ashok Nayak 10 Jul '15

10 Jul '15

Dear Phenixites, I have a helical bundle structure, where in I wish to understand by what rotation and about which axis the dimers are inter-related. What I get from the superposition with Superpose is the transformation matrix and not the axis, and the angles are also elusive. Ashok Nayak CSIR-CDRI Lucknow, India --

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Axis of Rotation
by Ashok Nayak 10 Jul '15

10 Jul '15

Dear Phenixites, I have a helical bundle structure, where in I wish to understand by what rotation and about which axis the dimers are inter-related. What I get from the superposition with Superpose is the transformation matrix and not the axis, and the angles are also elusive. Thanks in advance -- Ashok Senior Research Fellow - Dr JV Pratap, Lab No-LSN 008 Molecular and Structural Biology Division Central Drug Research Institute, Janakipuram Extension Lucknow-226031 India

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rosetta.build_phenix_interface problem
by Appu kumar 10 Jul '15

10 Jul '15

Dear All, I have installed Rosetta on Linux machine. When i am issuing the command " rosetta.build_phenix_interface" it is giving me following error scons: Building targets ... scons: *** [build/src/release/linux/2.6/64/x86/gcc/4.4/python/libObjexxFCL.so] Implicit dependency `/usr/local/lib/libdl.so' not found, needed by target `build/src/release/linux/2.6/64/x86/gcc/4.4/python/libObjexxFCL.so'. scons: building terminated because of errors. Would you please give me your valuable suggestions to successfully carry out the Rosetta refinement. Thank you Appu

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Rosetta Refinement problem
by Appu kumar 10 Jul '15

10 Jul '15

Dear All, I have installed Rosetta successfully on Linux machine and after installation it say building done. While refining a structure with "phenix.rosetta_refine" it is giving following problem End of input processing Sorry: The RosettaScripts executable could not be located. Please add the appropriate directory to your PATH environment variable, or set the variable ROSETTA_BIN to point to it. In my .cshrc file i have setup the path as follow setenv PHENIX_ROSETTA_PATH /home/appu/2014_09_29_NSLS_X29/rosetta_bin_linux_2015.25.57927_bundle setenv ROSETTA_BIN /home/appu/2014_09_29_NSLS_X29/rosetta_bin_linux_2015.25.57927_bundle/main/source/bin setenv phenix /home/appu/software/phenix/phenix-1.9-1692 setenv ROSETTA3_DB /home/appu/2014_09_29_NSLS_X29/rosetta_bin_linux_2015.25.57927_bundle/main/database I would appreciate any help and suggestions in executing the Rosetta refinement Thank you Appu

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Problem with python while running Autobuild
by Tam＠em.uni-frankfurt.de 09 Jul '15

09 Jul '15

Dear all, I am currently facing a problem of python while running the Autobuild in Phenix. phenix.autobuild data=data1.mtz model=model.pdb seq_file=protein.dat rebuild_in_place=False \ composite_omit_type=iterative_build_omit then it stopped with error Error in `/home/mauricetam/software/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/bin/python2.7': free(): invalid next size (normal): 0x0000000003e100a0 *** I wonder what's wrong with it. Regards Heng-Keat

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problems with rosetta
by Benny Belviso 09 Jul '15

09 Jul '15

Dear all, I am trying to use rosetta with the Phenix Gui (Phenix is installed on Debian). I have downloaded the tar.gz file named "rosetta_bin_linux_2015.25.57927_bundle" that contains source and binary files. Becouse the tar.gz contains pre-compiled files, I have not compiled rosetta again (however, I have the same problems also in the case of tar.gz containing source after the compilation). According to the instructions showed on http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix#Installa… I have setup my environmental variables in .bashrc as: export PHENIX_ROSETTA_PATH=/home/bbdanilo/program/rosetta_bin_linux_2015.25.57927_bundle export ROSETTA3_DB=$PHENIX_ROSETTA_PATH/main/database However, by opening MR-Rosetta on Phenix GUI, I get a first warning message that says me that rosetta directory seems to be not correct. By running rosetta, the program says that it is not able to find PHENIX_ROSETTA_PATH. I have tried to change the path also in the "Directory setup" by typing /home/bbdanilo/program/rosetta_bin_linux_2015.25.57927_bundle as directory for rosetta path /main/source/bin as Rosetta binary directory name mr_protocols.linuxgccrelease as binary of rosetta In this case, the program says that does not find the binary for rosetta (it requires mr_rosetta.default, instead I should use mr_protocols.linuxgccrelease). What am I doing wrong? Any help is welcome. Thanks. Danilo This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Re: [phenixbb] on determination whether a protein is a monomer or complex by phenix
by Valerie Pye 07 Jul '15

07 Jul '15

Hi Smith, Your solvent content is most likely the 66% one (if you have diffraction to about 1A there's a chance it could be 33%.....in which case try to solve it with Balbes (ccp4)). You can not tell what the crystal packing is like until you solve the structure! Even if you know how many molecules you have in your a.s.u. you can not tell if the contacts are formed because of crystal packing or oligo formation! Its much better to look at your protein in solution for this (as i said before!) Cheers, val On 7 July 2015 at 03:17, Smith Liu <smith_liu123(a)163.com> wrote: > Dear Valerie and all, > > My space group is I422 (attached image for I422). There are 2 solutions > for Mathews coefficient, one is solvent content 66.76%, the other is > 33.52%. Based on this message and the attached images, how can we know > whether my protein is a monomer (for example, monomer protein only exist in > the "+" position), a tetramer (or crystal packing as a "tetramer", each > chain exist in the "+" position, and each chain so close to each other so > that they contact each other and a tetramer forms), a 8-subunit protein > complex (or crystal packing as a " 8-subunit protein complex ", each 2 > chains exist in the "+" position, and each 2 chians so close to each other > so that they contact each other and a 8-subunit protein complex form)? > > I am looking forward to getting a reply from you. > > Best regards. > > Smith > > > > > > At 2015-07-07 00:34:32, "Valerie Pye" <valpye(a)googlemail.com> wrote: > > Hi Smith, > > I'm fairly sure you can not tell the oligomeric state of your protein from > an mtz and your sequence. > What you can do is calculate the Matthews co-efficient with your given > unit cell parameters and size of monomer to see how many copies of your > monomer you may have in the a.s.u. > The difficulty lies in the fact that if say you have 4 copies of your > protein in the a.s.u - this doesn't necessarily mean you have a tetramer - > they could be 4 monomers related by n.c.s - or 2 dimers.... > Is it possible to solve your structure? Then you confirm your space group > and number of molecules in the a.s.u. - then look at the area of contact > between monomers to see if they are likely to be because of multimerisation > or crystal packing. > > Totally agree with Tim that a better way (which you'd probably want to do > to back-up a multimeric crystal structure) is by SEC or native PAGE. You > could also try SAXS, SEC-MALS, EM, or DLS depending on the size of protein > you're looking at. You'd also want to know that you have a clean oligomer > and not an aggregate ;) > > Good luck, > > val > > On 6 July 2015 at 12:21, Smith Liu <smith_liu123(a)163.com> wrote: > >> Dear Tim, >> >> I mean based on the mtz file, can I know whether I will get a PDB file of >> a monomer or dimer, or trimer, or tetramer or oligomer? >> >> Best regards. >> >> Smith >> >> >> >> >> >> At 2015-07-06 18:14:03, "Tim Gruene" <tg(a)shelx.uni-ac.gwdg.de> wrote: >> >Dear Smith, >> > >> >I would say that size exclusion chromatography or native PAGE are better >> >experimental techniques than crystallography for this type of question. >> > >> >Best regards, >> >Tim >> > >> >On 07/06/2015 11:20 AM, Smith Liu wrote: >> >> Dear All, >> >> >> >> >> >> Suppose I have got a mtz file, and I know the aa sequence of the protein from which I got the crystal and the corresponding mtz file, will you please tell me which phenix function (program) can tell me whether my protein crystal was formed by protein monomer or by protein complex, and if formed by protein complex, how many subunits existing in the complex? >> >> >> >> >> >> Best regards. >> >> >> >> >> >> Smith >> >> >> >> >> >> >> >> _______________________________________________ >> >> phenixbb mailing list >> >> phenixbb(a)phenix-online.org >> >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> >> >> > >> >-- >> >-- >> >Dr Tim Gruene >> >Institut fuer anorganische Chemie >> >Tammannstr. 4 >> >D-37077 Goettingen >> >phone: +49 (0)551 39 22149 >> > >> >GPG Key ID = A46BEE1A >> > >> > >> >> >> >> >> _______________________________________________ >> 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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Weird problem of Coot fetch PDB&Map using PDB_redo
by Xiao Lei 07 Jul '15

07 Jul '15

Hi All, Today I found one weird problem of coot. I have coot installed in different platforms, I have coot 0.8.1 version in Ubuntu 15.04 and coot 0.8.1 version in Mac OS X 10.10.3, and I also have wincoot 0.8.1 in Windows 8.1. When I tried to fetch pdb&map using EDS, coot in all three platforms works very well. However, when I tried to fetch pdb&map using PDB_redo, only the windows wincoot works, which shows "successfully read coordinates...". The coot in mac and Ubuntu failed to fetch and shows "failed to read coordinates file...". I do not think the problem comes from PDB_redo as I tried to fetch the same pdb to compare coot in three platforms, only wincoot works well. I do not know if anyone else has this problem and how to fix it. Thanks ahead. Xiao

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on determination whether a protein is a monomer or complex by phenix
by Smith Liu 07 Jul '15

07 Jul '15

Dear All, Suppose I have got a mtz file, and I know the aa sequence of the protein from which I got the crystal and the corresponding mtz file, will you please tell me which phenix function (program) can tell me whether my protein crystal was formed by protein monomer or by protein complex, and if formed by protein complex, how many subunits existing in the complex? Best regards. Smith

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Re: [phenixbb] phenix rosetta refine
by kaiser 07 Jul '15

07 Jul '15

Thanks, Nigel! <div>-------- Original message --------</div><div>From: Nigel Moriarty <nwmoriarty(a)lbl.gov> </div><div>Date:2015/07/06 14:11 (GMT-08:00) </div><div>To: Jens Kaiser <kaiser(a)caltech.edu> </div><div>Cc: phenixbb(a)phenix-online.org </div><div>Subject: Re: [phenixbb] phenix rosetta refine </div><div> </div>Jens I believe that is all true and correct. 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 On Mon, Jul 6, 2015 at 1:55 PM, Jens Kaiser <kaiser(a)caltech.edu> wrote: Nigel, Sorry for the late reply, I was away from the office last week. Yes, I did follow these instructions. At the moment I'm using rosetta_bin_linux_2015.22.57859_bundle and phenix-1.10pre-2084. I requested 20 models (which I get) but there are rosetta_##.sh files created that are empty and subdirectories _ros_temp?????? that contain files with _adp_refine in their names. I'm just wondering if it is really running as intended. Cheers, Jens On Mon, 2015-06-29 at 10:25 -0700, Nigel Moriarty wrote: > Jens > > > Have you followed the instructions? > > > http://www.phenix-online.org/documentation/reference/rosetta_refine.html > > > 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 > > On Sat, Jun 27, 2015 at 2:38 AM, Jens Kaiser <kaiser(a)caltech.edu> > wrote: > Hey there, > who would be the person to talk about setting up > phenix.rosetta_refine? I tried our SBgrid installation with > overrides to > "nightly" for phenix and rosetta; I tried a clean install of > rosetta and > phenix - production version and nightly's in all combinations > - and all > combinations of compiling (rosetta first, then > rosetta.build_phenix_interface, phenix first, then > rosetta.build_phenix_interface). The problem is that > "phenix.rosetta_refine" seems to run, and produce a log file > that looks > reasonable, but geometry params are worse than with an > ordinary refine. > I think I tracked it down to the fact that the "rosetta_XX.sh" > files are > empty, and rosetta actually does not run. > > Any help is welcome - and any support will be extended. > > Cheers, > > Jens > > _______________________________________________ > 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 rosetta refine
by Jens Kaiser 07 Jul '15

07 Jul '15

Hey there, who would be the person to talk about setting up phenix.rosetta_refine? I tried our SBgrid installation with overrides to "nightly" for phenix and rosetta; I tried a clean install of rosetta and phenix - production version and nightly's in all combinations - and all combinations of compiling (rosetta first, then rosetta.build_phenix_interface, phenix first, then rosetta.build_phenix_interface). The problem is that "phenix.rosetta_refine" seems to run, and produce a log file that looks reasonable, but geometry params are worse than with an ordinary refine. I think I tracked it down to the fact that the "rosetta_XX.sh" files are empty, and rosetta actually does not run. Any help is welcome - and any support will be extended. Cheers, Jens

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Re: [phenixbb] Optimal settings for finding NCS from density
by Terwilliger, Thomas Charles 06 Jul '15

06 Jul '15

Hi William, For find_ncs_from_density the shape of the molecule itself is not so important. What matters is if there is some local part of the molecule that is recognizable in both copies. So I would try default parameters first. I assume you did that and it didn't give you a useful answer...so then I would do these things: 1. try many locations : n_center_use=20 This is the best option...it will try 20 times using density at 20 different locations to search. If you have an older version of phenix you may need to download a nightly build to do this. 2. Try varying the resolution 3. Try varying the angular spacing of the search (delta_phi) All the best, Tom T ________________________________ From: CCP4 bulletin board [CCP4BB(a)JISCMAIL.AC.UK] on behalf of William Chao [William.Chao(a)CRICK.AC.UK] Sent: Friday, July 03, 2015 10:24 AM To: CCP4BB(a)JISCMAIL.AC.UK Subject: [ccp4bb] Optimal settings for finding NCS from density Dear all, What would be the best settings to look for NCS using phenix.find_ncs_from_density on an elongated (~150A) molecule? No coordinate is available unfortunately and there should be 2 copies in a P21 space group. Many thanks in advance! William --- The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE.

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labelit access in Phenix?
by Keller, Jacob 03 Jul '15

03 Jul '15

Dear Phenix list, Does anyone know how to access labelit through Phenix to determine whether the highest possible symmetry has been found? I exclusively use the GUI, and it's on win7. In the labelit documentation/homepage it mentions the command: labelit.check_pdb_symmetry [pdb coordinate file] [data=mtz file] But I did not find any executables called labelit, nor can I figure out how to run Phenix from command line in Win7, short of installing Cygwin or something. JPK

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metal refinement: adps and restraints
by Alexandra Marques 03 Jul '15

03 Jul '15

Hi, I am refining a protein with a Mo in the active site and which is bound to a cofactor and to a water molecule. After each refinement step there is always a lot of positive and negative density around the Mo and the cofactor molecules, although their occupancy refined to 1. I read this message http://www.phenix-online.org/pipermail/phenixbb/2015-May/022031.html, but I still have doubts about how to choose the refinement parameters. I know I have to select the Mo atoms to be refined anisotropically. And the other atoms, do I have to specifically select them to be refined isotropically?. For instance: Isotropic atoms: not element Mo Anisotropic atoms: element Mo I am asking that because I have been using TLS for the protein atoms during refinement, so I am not sure if it is correct to select the other atoms as isotropic or if I leave it in blank… My other problem is with the metal restraints. I am not sure about the ideal distance between the Mo and O atom but based on homologous protein structures I choose the following: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MO and chain A and resname 4MO and resseq 1 atom_selection_2 = name O and chain A and resname O and resseq 2 distance_ideal = 1.900000 sigma = 0.050 } } However after the refinement this ideal distance interval (1.95-1.85) is not respected; I have 4 active sites and in some of them the Mo-O distance refines to 0.83 A although there is a lot of density for the water molecule to be at 1.9 A. How to make the restrainst work? Am I missing something? Thank you very much, Alexandra

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accept MR solution even if the number of clashes is above the threshold
by Almudena Ponce Salvatierra 02 Jul '15

02 Jul '15

Hi everyone, I am running Phaser (from Phenix) and while checking the .log file (it is still running) I realize that it found some solutions with a TFZ score over 7, but it won't take them I guess because the number of clashes is higher than allowed (>12, I guess they're not so many either). My models are poor and for so I would like to check these solutions that for now Phaser will reject. However in the input I don't want to increase the allowed number of clashes because this will then affect all the other solutions and this will take forever... So my question is: can I tell phaser somehow to write down/save the solutions for which the TFZ score will be higher than 7? Even though the clashes Thanks a lot in advance All the best, Almu -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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C-beta RMSD
by Kaushik Hatti 02 Jul '15

02 Jul '15

Hi, Is there a tool which can calculate C-beta RMSD for equivalent amino acids of homologous structures, post C-alpha superposition? Sorry if its off topic, Thanks, Kaushik -- Stupidity is everyone’s birthright. However, only the learned exercise it! --Kaushik (28Oct2014)

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Simulated annealing refinement for just one domain
by Appu kumar 01 Jul '15

01 Jul '15

Hello All, I was wondering if there is a simulated annealing refinement for the just one domain and keeping the other domain fix. I have a structure where the electron density is poorly defined which could be because of the some conformation of domain is different. Although the resolution of the data is 4A but channel has well defined density in the TM domain. Thanks in advance for your advice and suggestions. Appu

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while doing tar xvzf of nightly build 1.10pre-2089
by Murpholino Peligro 30 Jun '15

30 Jun '15

I get an error >>>> gzip: stdin: unexpected end of file phenix-installer-1.10pre-2089-intel-linux-2.6-x86_64-centos5/modules/phenix_regression/wizards/command_line_rosetta_tests/test_mr_rosetta_ncs.tgz tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now <<<< Should I try another version?

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Re: [phenixbb] labelit access in Phenix?
by R.D. Oeffner 29 Jun '15

29 Jun '15

This should have been forward to the mailing list. Rob -------- Original Message -------- Subject: Re: [phenixbb] labelit access in Phenix? Date: 2015-06-26 21:46 From: "R.D. Oeffner" <rdo20(a)cam.ac.uk> To: "Keller, Jacob" <kellerj(a)janelia.hhmi.org> Copy: Aaron Brewster <asbrewster(a)lbl.gov>, Nigel W Moriarty <NWMoriarty(a)lbl.gov> Hi Jacob, Labelit is not present on Windows in the last official release of Phenix from May last year, version 1.9-1692. But it is present in recent pre-releases of Phenix as command line tools. When you install Phenix on Windows a startup group is created that includes a command line prompt which recognises Phenix commands. From there you can execute all labelit command line tools. I think Nigel is about to put the recent Windows pre-release online on the Phenix website. Feel free to get in touch with further questions. Regards, Rob On 2015-06-26 18:44, Aaron Brewster wrote: > Hi Jacob, replying off of the list for now. There is no labelit gui > support in the phenix gui. There may be a batch script you have to > run to get the phenix command line binaries in the path for the cmd > program in win7, but I don't know it. If you can run phenix.refine on > the command line but not labelit, that would be instructive. > > cc'ing Rob who has been working on the phenix windows build. > > -Aaron > > On Thu, Jun 25, 2015 at 7:58 PM, Keller, Jacob > <kellerj(a)janelia.hhmi.org> wrote: > >> Dear Phenix list, >> >> Does anyone know how to access labelit through Phenix to determine >> whether the highest possible symmetry has been found? I exclusively >> use the GUI, and it's on win7. >> >> In the labelit documentation/homepage it mentions the command: >> >> labelit.check_pdb_symmetry [pdb coordinate file] [data=mtz file] >> >> But I did not find any executables called labelit, nor can I figure >> out how to run Phenix from command line in Win7, short of installing >> Cygwin or something. >> >> JPK >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb [1] >> Unsubscribe: phenixbb-leave(a)phenix-online.org > > > > Links: > ------ > [1] http://phenix-online.org/mailman/listinfo/phenixbb

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phenix-1.9-1692 pymol problem
by ChenWeiFei 27 Jun '15

27 Jun '15

Dear all, I just install phenix and I found phenix-1.9-1692/pymol/install and it says: INSTALLATION of the PyMOL Executable Build for Unix 1) Extract the appropriate archive. tar -zxvf pymol-0_99-bin-linux-x86-glibc23.tgz 2) Change directory into the root level of the archive. cd pymol 3) Run "./setup.sh" which will create "./pymol" with a record of the current working directory. ./setup.sh 4) Link or copy ./pymol into a directory that is in your path. ln -s `pwd`/pymol /usr/local/bin/pymol (or perhaps) cp pymol /usr/local/bin/pymol 5) Now try it! ./pymol I follow it and when I type pymol there comes an error: $ pymol /usr/local/bin/pymol: /usr/local/phenix-1.9-1692/pymol/pymol.exe: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory Is any one konw how to deal with it? Best, Weifei

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phenix.composite_omit_map
by Dyda 27 Jun '15

27 Jun '15

Dear Phenix list, I have generated an mtz file with phenix.composite_omit_map. It has labels assigned as 2mFo-DFC for F and PH2mFo-DFC for P. Now, I would like to generate a map file. I was trying to convince phenix.maps to use this mtz file to do that, however it didn't seem to like the labels. I tried both the GUI interface of phenix.maps and also tried to force feed it through the command line with a maps.param file. Neither of these worked, so I'm obviously missing something. Btw., Coot can open the mtz file and display the map, and it does look reasonable. This is phenix-1.9-1692 running under RHEL6. Thank you for your help. Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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Re: [phenixbb] [ccp4bb] phenix installtion problem
by Hattne, Johan 26 Jun '15

26 Jun '15

> On Jun 26, 2015, at 09:05, ChenWeiFei <weifei_c(a)OUTLOOK.COM> wrote: > > Dear all, > Sorry to disturb you. > I have install Phenix to my computer Centos 7.0. > When I want to use it I need to > cd /usr/local/phenix-1.9-1692/ > and > . /usr/local/phenix-1.9-1692/phenix_env.sh > then type phenix in the command line every time. > I wish to use phenix in every terminate window and just type phenix. > Some told me use export PATH to do it but I don't know how to do it. > I am new to linux(centos) > Thank you so much! > Best, > Weifei You could edit ~/.bashrc and add a line . /usr/local/phenix-1.9-1692/phenix_env.sh This will not necessarily have an affect on newly spawned login shells. To address that, you could make sure that your ~/.bash_profile contains a line like test -r "${HOME}/.bashrc" && . "${HOME}/.bashrc" near the top. // Johan Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

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Re: [phenixbb] [ccp4bb] phenix installtion problem
by Alexandre OURJOUMTSEV 26 Jun '15

26 Jun '15

Dear Weifei, I am neither in the Phenix nor in the CCP4 teams so I let me remark that it does not look reasonable, just a few minutes after Tom Terwilliger's mail : "I'll answer you on the Phenix BB as you've asked specific questions about Phenix tools." sending your mail (see below) asking explicitly phenix questions again through the CCP4bb. I do not think that you "disturb", you should not sorry for this, the BB are for this, but we need to follow the rules. I ask everybody to respect both ccp4 and phenix teams, who assures a lot of service and help for our community, and send your requests properly (for your own benefit), through the BB concerned. My another request (luckily not applicable to the Weifei mail) is that people always sign properly their mails and give their name when asking their questions : ccp4, phenix teams and other experts answer you openly and this looks quite weird seeing anonymous requests. Again, this is for your own benefit, for your better integration into the research community. With best regards, Sacha Urzhumtsev ________________________________ De : CCP4 bulletin board <CCP4BB(a)JISCMAIL.AC.UK> de la part de ChenWeiFei <weifei_c(a)OUTLOOK.COM> Envoyé : vendredi 26 juin 2015 15:05 À : CCP4BB(a)JISCMAIL.AC.UK Objet : [ccp4bb] phenix installtion problem Dear all, Sorry to disturb you. I have install Phenix to my computer Centos 7.0. When I want to use it I need to cd /usr/local/phenix-1.9-1692/ and . /usr/local/phenix-1.9-1692/phenix_env.sh then type phenix in the command line every time. I wish to use phenix in every terminate window and just type phenix. Some told me use export PATH to do it but I don't know how to do it. I am new to linux(centos) Thank you so much! Best, Weifei

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anomalous phasing with HySS - phaser - Autobuild
by Almudena Ponce Salvatierra 26 Jun '15

26 Jun '15

Hi all, I have SeMet data for which HySs locates 127 Selenium atoms with a CC of 0.31, which I think is decent. Then I run Phaser to generate the first maps, and it gives a score of 25 and LLG of 190 or so... The next step would be running Autobuild, however, the first models I realize it is building have R work and R free between 50 and 55%. So I guess it is just some random stuff there. If the result from HySS and Phaser looks more or less good, why does AutoBuild show these numbers?? Any idea of what I could do to improve so? Any ideas are welcome. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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Optimal Linux configuration for Phenix.refine
by Colin Levy 25 Jun '15

25 Jun '15

Apologies for the slightly off topic question. I am configuring a Linux workstation and would like your thoughts on an optimal setup for running Phenix. A lot of my computing time is spent in refinement and I am keen to put something together that will see a considerable increase in speed from my creaking Mac Pro (2 2.4GHz Quad core Intel Xeon with 24Gb RAM). Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk<mailto:[email protected]>

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Fw:Re: Autobuild Density
by Smith Liu 19 Jun '15

19 Jun '15

Dear All, Is any method to make the density modified map (from AutoBuild) comparable to the 2mFo-DFc map (from phenix.refine)? Smith -------- Forwarding messages -------- From: "Pavel Afonine" <pafonine(a)lbl.gov> Date: 2015-06-19 00:16:45 To: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Autobuild Density Hi Appu, a guess: perhaps you are comparing density modified map (from AutoBuild) with 2mFo-DFc map (from phenix.refine). If that's the case the maps are going to look differently indeed, so it's not too unexpected. Pavel On 6/18/15 08:47, Appu kumar wrote: > Dear All, > I have query about the density map from autobuild. The density map > from the autobuild look exceptionally good at 3.8A resolution. But > when i refined the autobuild pdb against the original mtz file, the > density become worse. Is it i am doing something wrong or i have to > use some parameterization? Structure is solved with the MR. > Appu _______________________________________________ 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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Autobuild Density
by Appu kumar 19 Jun '15

19 Jun '15

Dear All, I have query about the density map from autobuild. The density map from the autobuild look exceptionally good at 3.8A resolution. But when i refined the autobuild pdb against the original mtz file, the density become worse. Is it i am doing something wrong or i have to use some parameterization? Structure is solved with the MR. Appu

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Get R values without refining in phenix.refine
by Murpholino Peligro 18 Jun '15

18 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 18 Jun '15

18 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 18 Jun '15

18 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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