- phenixbb - phenix-online.org

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

2 3

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.

2 2

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

3 2

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

3 2

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

3 2

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)

3 2

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

2 1

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?

1 0

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

1 0

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

27 Jun '15

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

1 0

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

2 1

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

1 0

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

1 0

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

2 1

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]>

5 5

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

19 Jun '15

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

2 1

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

2 1

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?

3 4

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 > > >

3 3

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

4 4

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 ******************************************************

3 3

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

1 0

phenix refine of my EM data
by Smith Liu 17 Jun '15

17 Jun '15

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

1 0

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

2 1

on real_space_refine
by Smith Liu 12 Jun '15

12 Jun '15

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

2 1