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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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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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