- phenixbb - phenix-online.org

Newest phenix version for Unix cluster
by Xiao Lei 20 Jul '15

20 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 15 Jul '15

15 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 14 Jul '15

14 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 14 Jul '15

14 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 11 Jul '15

11 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 11 Jul '15

11 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 11 Jul '15

11 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 10 Jul '15

10 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 09 Jul '15

09 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 09 Jul '15

09 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 06 Jul '15

06 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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