- phenixbb - phenix-online.org

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 13 Jul '15

13 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 10 Jul '15

10 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 06 Jul '15

06 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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phenix rosetta refine
by Jens Kaiser 06 Jul '15

06 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 05 Jul '15

05 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 02 Jul '15

02 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 30 Jun '15

30 Jun '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 29 Jun '15

29 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 28 Jun '15

28 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 26 Jun '15

26 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 26 Jun '15

26 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 24 Jun '15

24 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 18 Jun '15

18 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 18 Jun '15

18 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 17 Jun '15

17 Jun '15

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

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

17 Jun '15

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

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anomalous difference map calculation
by Alexandra Marques 17 Jun '15

17 Jun '15

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

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

17 Jun '15

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

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

17 Jun '15

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

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phenix refine of my EM data
by Smith Liu 16 Jun '15

16 Jun '15

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

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on phenix.map_to_structure_factors
by Smith Liu 13 Jun '15

13 Jun '15

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

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on real_space_refine
by Smith Liu 11 Jun '15

11 Jun '15

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

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

10 Jun '15

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

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does the lastest Phenix only support windows 7
by Xiao Lei 08 Jun '15

08 Jun '15

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

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Berkeley Server Downtime
by Paul Adams 08 Jun '15

08 Jun '15

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

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no merge original index
by Tarek DawoD 07 Jun '15

07 Jun '15

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

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

06 Jun '15

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

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

05 Jun '15

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

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

04 Jun '15

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

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

04 Jun '15

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

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