- phenixbb - phenix-online.org

wxu scale in phenix.refine
by Jan Abendroth 18 Sep '07

18 Sep '07

Hi all, in the final stages of refining a structure, I would like to optimize the restraint weights for geometry and B factors. It seems to work fine for geometry by defining " refinement.target_weights.wxc_scale=1.0". However, when the respective definition for B-factors does not seem to have an impact at all. I tried both: "refinement.target_weights.wxu_scale=2.0" in the parameter file or "wxu_scale=2.0" in the command line. The main reason why I try to fiddle around with the B-weights is that coot gives me a whole bunch of red bars in the Temperature factor variance analysis... I am using phenix 1.3d (downloaded past Sunday), mac-intel-osx, osx-10.4.10 Any ideas? Cheers Jan

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Re: [phenixbb] Problem in Autosol
by Eric Tee 16 Sep '07

16 Sep '07

Hi Tom, Many thanks for your reply. I was running phenix in my d_drive (a vfat partition) and got the error message. However, when I moved the mtz file to a directory under home directory (home/user/phenix-local), The program work without any problem. Let me explain how this work: I'm running phenix on fedora7 (a dual boot machine with Windows). I installed phenix under home/user/program/phenix (not /usr/local). I have a vfat partition (as d_drive) where I keep all my data and basically process everything there. I got the error message if I run phenix in the vfat partition but the program can be run successfully under the home directory /home/user/phenix-local). Following is what I got if I run phenix in the vfat partition (d_drive): WORKDIR: /mnt/d_drive/ccp4_data/SAD/phenix-localmachine Checking for KnownWizards: ['AutoSol', 'AutoBuild', 'ImportRawData'] application method: Null Getting inputs on first pass... SETTING UP INPUTS AutoSol Wizard Screen 1 of 4 AutoSol: Choose data files for dataset #1 A "dataset" is a group of data with a single set of heavy-atom sites You will be able to combine the results of all datasets later Note: Data files can be any format. If they are not all Scalepack premerged or all Scalepack unmerged then all will be converted to Scalepack premerged SUMMARY Input files dataset #1 Se_pk.mtz Creating new Data Storage /mnt/d_drive/ccp4_data/SAD/phenix-localmachine/PDS/AutoSol.1 sh: TEMP0/temporary.com: Permission denied Could be something related to permission problem but I have set permission to read/write/execute in vfat partition by adding the following line to /etc/fstab: /dev/sda6 /mnt/d_drive vfat users,uid=eric,gid=users,umask=0002,utf8=true 0 0 Any suggestion to enable running phenix in the vfat partition? Eric On 9/16/07, Tom Terwilliger <terwilliger(a)lanl.gov> wrote: > > Hi Eric, > > Can you possibly check to see that you have a recent version of phenix: > > phenix.version will do this. > > > Then if that is ok, I'm not sure what is causing the problem. This > message means that solve could not run with the data it got, but > usually an error message should come up earlier if there is a > problem. Have a look at LAST.LOG in your AutoSol directory and see > if it has any hints. Also look at AutoSol_run_1_.output and see the > end of this log file. > > If none of those work, if you can send me your input data file I can > see if there is a problem with it (all I would need is the first 100 > lines or so). > -Tom T > >

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Problem in Autosol
by Eric Tee 15 Sep '07

15 Sep '07

Hi All, I was trying to run SAD phasing with phenix GUI for the first time. After conversion of mtz to sca file, at the step of autosol_scale_and_analyze_mad, I got the following message: failed to carry out Autosol_scale_and_analyze_mad None of the solve versions worked I'm pretty sure I choose the right package. Should I do something to configure solve? Eric

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elbow.builder to generate charges on individual atoms?
by Francis E Reyes 13 Sep '07

13 Sep '07

Ok, this is probably an unsupported feature(TM),but is there anyway to hack elbow.builder to output an electronic charge (presumably from the AM1 calculation) for each atom of a ligand? (by say substituting in for the Bfactor)) Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Position for PSI Knowledgebase development
by Paul Adams 12 Sep '07

12 Sep '07

======================================================================= Lawrence Berkeley National Laboratory Software Developer II ======================================================================= Software Developer II Job ID: 20930 Division: Physical Biosciences Date Opened: 8/7/2007 Summary This position will be part of the Computational Crystallography Initiative at Lawrence Berkeley Lab and will be responsible for developing a web site to disseminate information about the Technologies developed by the NIH Protein Structure Initiative (PSI). This program funds the majority of structural genomics efforts within the US and is responsible for the development of many new technologies that are useful to macromolecular crystallographers. This technology resource is part of the larger PSI Knowledge Base that will provide an information portal for the scientific community. Duties Essential: Under general direction of the Principal Investigator: Develop and maintain web site documenting PSI developed technologies. Interact with PSI researchers to collect information about new technologies. Create a relational database to store crystallographic data. Install and maintain SVN repositories for the PSI community. Marginal: Perform routine analysis of crystallographic data. Maintain web site computing hardware and software. Other duties as assigned. Qualifications Essential: Experience with writing and maintaining HTML web pages. Knowledge of standard programming methods, and Python in a UNIX environment. Strong analytical and organizational skills. Ability to handle multiple tasks in parallel. Excellent interpersonal skills for working in a diverse team environment, ability to interact effectively with other scientists, and to address their needs in an effective and timely manner. Marginal: B.S. Degree or higher in biophysics, computer science, chemistry, electrical engineering, physics or related field preferred or equivalent experience, with demonstrated programming experience. Experience maintaining computing hardware and software. Experience with analysis of crystallographic data. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about the CCI visit: http://cci.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 20930. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Senior Scientist, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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pseudo-merohedral twinning in P212121
by Schneider Sabine 12 Sep '07

12 Sep '07

Hi everyone, I have a data set to 2.8A, with most likely 2 molecules in the asu and a molecular replacement model with 40% sequence identity. (Cell 71.3 71.3 227.9 90 90 90) Initially the data appeared to be either P4322 or P43212 (Rsym = 7.4%; Cell 71.3 71.3 227.9 90 90 90), but the molecular replacement solutions had major clashes with the symmetry related molecules and a lower LLG for the solution of the second molecule. No twinning was detected by Xtriage. Processing the data in P212121 (Rsym 5.6%, cell 71.3 71.4 228.2 90 90 90) gave me a better molecular replacement solution (LLG 121/373), but I had 5 clashes with the second molecule in the asu. (I tested all alternative spacegroups) I also have a MAD dataset (very low quality!) and I combined the phases with the one obtained from molecular replacement in Sharp. After NCS averaging the maps had improved (still not great). I tried to improve things in the model and run Phaser again and the solution had better statistics (LLG 338/1223) and the clashes were reduced to 2. Xtriage detected pseudo-merohedral twinning with a twin fraction of 43% with twin operator -k, -h, -l. So I tried refining the model with phenix telling it the twinning operator and fraction, but R/Rfree are stuck around 45%. I also tried simulated annealing but that gave even higher R/Rfree. Is there anything I can do, or is it a hopeless case? Thanks for your help in advance! Sabine 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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phenix.refine error
by Jianghai Zhu 11 Sep '07

11 Sep '07

Hi, I was trying the twinning refinement by phenix.refine and I got the following error messages during TLS refinement. Traceback (most recent call last): File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/ refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ command_line.py", line 81, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ driver.py", line 1244, in run log = log) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ strategies.py", line 866, in refinement_machine h_params = h_params) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ adp_refinement.py", line 175, in __init__ macro_cycle = macro_cycle) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/tls/tools.py", line 600, in __init__ fmodel.info().show_targets(text = prefix+" start model", out = out) AttributeError: 'info' object has no attribute 'show_targets' Could somebody help me? Thanks. Jianghai PS. the version is 2007_08_18_1856. +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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What does mmtbx.twin_map_utils output?
by Francis E Reyes 11 Sep '07

11 Sep '07

Specifically I'm asking about the obs_and_calc.mtz file it produces. Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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So I think I have a twinning problem... ?
by Francis E Reyes 10 Sep '07

10 Sep '07

Hi all The short of the long is that phenix.xtriage on a C2 data set shows twinning with 3 twinning operators (-h,-k-l -k-h-l and k,h,-l). Pushing it through twin_utils, the soution k,h,-l gives an r/rfree of 0.30 and 0.3014 when the twin fraction is 0.352 . The question is where to go from here? I try to phenix.refine the same model in phenix.xtriage (except the mtz file is from the latest round of refinement of that model) and the R/Rfree on macro cycle =2 is 30 and 34 . Unfortunately, it doesn't seem to finish the refinement, I get a seg fault. In the def file for the refinement I set twinning = True and twin_law = k,h,-l . I tried to subject the same model and the .ref file to an autobuild passing in a .eff file for refinement specifying the twin_law, and again I get a segfault / crash when refining the input model. Please advise! --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Twinning in phenix.autobuild?
by Francis E Reyes 10 Sep '07

10 Sep '07

Hello all So I discovered from xtriage that my crystal is twinned. I have a pretty decent model that xtriage says has an r/rfree of 30/30 to a resolution of 2.6. I wanted to try a phenix.autobuild at 2.8A. I couldn't find a parameter flag for autobuild that turns on twinning. I already autobuilt this model once, and the xtriage log did find that the crystal was twinned, but twinning in refinement of the model during rebuilding wasn't turned on. Is there a way to tell autobuild to rebuild using twinning? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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crash during refinement with twinned data
by Scott White 10 Sep '07

10 Sep '07

Dear PhenixBB, I'm trying to refine a structure against potentially twinned data. I got the twin law from xtriage. phenix.refine starts, and at some point crashes with the messages below. Refinement proceeds to the end if I don't include twinning. Any suggestions? Thanks, Scott Traceback (most recent call last): File "/software/phenix-1.3b/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/software/phenix-1.3b/phenix/phenix/refinement/command_line.py", line 81, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/software/phenix-1.3b/phenix/phenix/refinement/driver.py", line 1325, in run log = log) File "/software/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 559, in refinement_machine log = log) File "/software/phenix-1.3b/mmtbx/mmtbx/refinement/rigid_body.py", line 347, in __init__ fmodel_copy = fmodel.resolution_filter(d_min = res) File "/software/phenix-1.3b/mmtbx/mmtbx/twinning/twin_f_model.py", line 1042, in resolution_filter sf_and_grads_accuracy_params = dc.sfg_params File "/software/phenix-1.3b/mmtbx/mmtbx/twinning/twin_f_model.py", line 890, in __init__ u_part=self.scaling_parameters.u_part ) RuntimeError: cctbx Internal Error: /net/anaconda/scratch1/phenix/phenix-1.3b/cctbx/include/cctbx/xray/f_model.h(91): CCTBX_ASSERT((f_mask.size() == 0) || (hkl.size() == f_mask.size())) failure. -- _______________________________________ Dr Scott A. White Protein Crystallography Group School of Biosciences University of Birmingham B15 2TT E: s.a.white(a)bham.ac.uk T: +44-(0)121-414-7534 F: +44-(0)121-414-5925 W: http://www.bip.bham.ac.uk/cryst ______________________________________

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Re: [phenixbb] Unknown atoms revisitied
by Ralf W. Grosse-Kunstleve 06 Sep '07

06 Sep '07

> Does the atom type have to be a known element or can it something like > element X as seen in some pdb files? > > An example from 1aqn: > HETATM 1951 UNK UNX 277 -4.541 50.540 38.754 0.25 13.93 X > HETATM 1952 UNK UNX 278 -4.443 49.701 37.169 1.00 15.64 X Pavel is correct, but I'll add a some more details. If you want to use these atoms in refinement, you have to decide what scattering type to use. That has to be one of the symbols published in the International Tables for Crystallography, Volume C (see cctbx/eltbx/xray_scattering/it1992.cpp under $PHENIX or cci_app_sources). Regarding the .cif file: data_comp_SIN loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge SIN N N N 0.000 | | | | | this must be a valid "energy type" (see below) | this must be a valid scattering type symbol (Int. Tab.) this can be anything you want mon_lib/ener_lib.cif defines energy types (phenix.where_mon_lib_list_cif shows the path to mon_lib). You can define other energy types in additional .cif files you give to phenix.refine, using the same syntax as in the central ener_lib.cif. Regarding the .pdb file: HETATM 1952 UNK UNX 278 -4.443 49.701 37.169 1.00 15.64 X | | | | this must match the data_comp_UNX | | this must match _chem_comp_atom.type_symbol this must match _chem_comp_atom.atom_id You cannot use X in columns 77-78 because it must match _chem_comp_atom.type_symbol, and that in turn must be a valid scattering type symbol. However, you can leave the column blank. I think I'll change phenix.refine to treat the X like a blank, then you don't have to remove it. But in the current release you have no choice. Ralf

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Re: [phenixbb] Unknown atoms revisitied
by Ralf W. Grosse-Kunstleve 06 Sep '07

06 Sep '07

Hi Jeff, > I was wondering if there were any way to have a single unknown atom > recognized by phenix for refinement. Make up any residue name you like, e.g. SIN (for single N). Create a .cif file like this: data_comp_SIN loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge SIN N N N 0.000 In your PDB file add: ATOM 68 N SIN 15 20.000 20.000 20.000 1.00 20.00 N Add the name of the .cif file to the phenix.refine command line. You can have more than one data_comp_ in the same cif file, if you want to use different element types. Ralf

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Unknown atoms in refinement
by Jeff Habel 06 Sep '07

06 Sep '07

What's the best way of dealing with unknown atoms (UNK) in phenix.refine? I have a long disordered loop that runs basically the length of the protein on the back side and there is a single "amino acid" in the middle that I'm trying to model as UNK. I can run a round of refmac and auto generate a lib file with my ligand and the unk atoms but phenix.refine balks at that with respect to the Van der Waals radii. Thanks for the help, -Jeff

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wxu_scale during TLS + INDIVIDUAL_ADP refinement
by Jose M de Pereda 06 Sep '07

06 Sep '07

Dear colleagues, I am refining a structure with phenix.refine (cci_apps 2007_08_18_1856). The strategy includes refinement of tls, individual_adp, and individual_sites (during the same run.) In order to test different restraints for ADP´s refinement, I have changed the value of the wxu_scale from the default. Yet, the value of the wxu_scale parameter is always automatically reset to the same value as indicated in the log file under the section "Automatic adjustment due to TLS refinement". That is, phenix.refine uses in all cases the same wxu_scale independently of the value I set in the definitions file. Of course, when TLS refinement is not done, the wxu_scale value remains as specified. I would appreciate if someone could indicate me how to modify the ADPs restraints when doing TLS refinement. Cheers Jose -- -------------------------------------------------- Jose M de Pereda, PhD Centro de Investigación del Cáncer Spanish National Research Council - U. Salamanca Campus Unamuno s/n E-37007 Salamanca, Spain Phone: +34-923-294819 Fax: +34-923-294795 http://xtal.cicancer.org/ -------------------------------------------------

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statistics for highest shell in phenix.refine
by michael hothorn 05 Sep '07

05 Sep '07

Dear all, For the crystallographic table in my manuscript, can I define a highest shell in phenix.refine and have it output the refinement statistics for this range? If not, how can I calculate the highest shell statistics using the same parameters as used for the overall refinment? Thanks Michael

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Re: [phenixbb] selective nonbonded restraint removal
by Cathy Lawson 05 Sep '07

05 Sep '07

Thanks to all who replied. And thank you Ralf for your suggestion (quoted below), this worked very nicely! Somehow I missed this possibility in the online documentation. To reply to Pavel's question regarding how I figured out that tris is present at 1/2 occupancy: (1) density was first modelled with waters but they were too close together, and there was a fairly clear tetrahedral shape. (2) phosphate didn't refine well -- lead to huge negative difference peak at the P atom. (3) only other tetrahedral shape molecule in the soup was tris (TAM), and after refining just the tetrahedral core it was possible to see where the three arms extended. (4) b-factors for the tris were high relative surrounding protein atoms, and extraneous density suggested two alternate conformations for the nearby arg side-chain, one of which is too close to realistically exist next to the tris ligand. the other clue was that trial occupancy refinement of all atoms put most tris atoms in the 0.4-0.6 occupancy range. (5) tris with 0.5 occupancy, arg with two alt confs, plus a few waters at 0.5 occupancy is so far the best model with no significant different densities for this region. (6) the modelling will need to be confirmed with an SA omit ... > Hi Cathy, > > > The density suggests that when tris is not there, > > a side chain moves very close to that position > > You could model this with alternative conformations. If you assign > "altloc" A and B to two conformers of your protein, and just, say, B > to your TAM, then the ligand would only "see" your B protein. If you > don't define the B conformer (no atoms) then TAM wouldn't see that > part of the protein at all. > Actually, this approach seems better to me than working with > atom selections. > > Ralf

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Re: [phenixbb] selective nonbonded restraint removal
by Cathy Lawson 05 Sep '07

05 Sep '07

Hi Ralf, That is disappointing. Lovely maps produced after a few phenix.refine runs for a 1.6 A structure revealed an unexpected tris ligand (TAM) with occupancy ~0.5. The density suggests that when tris is not there, a side chain moves very close to that position, thus my question. In other regards phenix seems a great step forward in automating refinement, and I look forward to new developments. best wishes, Cathy > Hi Cathy, > > > Is it possible to turn off nonbonded restraints for particular > > residues/monomers, or for atoms with occupancy less than 1.0? > > Nope, sorry. It is on the (long) to-do list. > BTW: each time someone asks the priority goes up. > > Ralf

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selective nonbonded restraint removal
by Cathy Lawson 04 Sep '07

04 Sep '07

Hi Phenix bber's, I have been trying out phenix.refine and like it very much so far. Is it possible to turn off nonbonded restraints for particular residues/monomers, or for atoms with occupancy less than 1.0? Thanks, Cathy Lawson /////////////////////////////////////////////////////// http://rutchem.rutgers.edu/~lawson

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SAD related query
by tara kashav 04 Sep '07

04 Sep '07

Dear all, I am a novice user of phenix. I am trying to obtain phases for SAD dataset collected at 2.5 angs from autosol.But when i give the phases to autobuild, the R-factor is not decreasing below 49%. Also, in warp, it is unable to built with a message "encounterd an unknown element". Can someone suggest me what could be the problem. Thanks for any suggestion in advance. Tara Kashav On 9/3/07, phenixbb-request(a)phenix-online.org < phenixbb-request(a)phenix-online.org> wrote: > > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. command-line Patterson maps (Bryan W. Lepore) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 2 Sep 2007 00:07:51 -0500 (CDT) > From: "Bryan W. Lepore" <bryanlepore(a)mail.utexas.edu> > Subject: [phenixbb] command-line Patterson maps > To: phenixbb(a)phenix-online.org > Message-ID: > < > Pine.LNX.4.64.0709020001190.16588(a)cpe-70-116-17-26.austin.res.rr.com> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > will phenix calculate Pattersons from trial sites or a reflection file on > the command line? i.e. something besides hacking what is already there. > > e.g. cns has predict_patterson.inp. i can't seem to find a way to do it > from the command line - such as `phenix.patterson --sg=94 > reflections.mtz`. i saw phenix.maps but that looks like electron density > only. > > -bryan > > > ------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > End of phenixbb Digest, Vol 22, Issue 1 > *************************************** > -- Tara Kashav, Dr. S. Gourinath's Lab, Lab No 430, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067

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command-line Patterson maps
by Bryan W. Lepore 03 Sep '07

03 Sep '07

will phenix calculate Pattersons from trial sites or a reflection file on the command line? i.e. something besides hacking what is already there. e.g. cns has predict_patterson.inp. i can't seem to find a way to do it from the command line - such as `phenix.patterson --sg=94 reflections.mtz`. i saw phenix.maps but that looks like electron density only. -bryan

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ligand restraints
by Jeff Habel 30 Aug '07

30 Aug '07

I have a ligand with two phenyl rings where 2Fo and difference density clearly shows some torsion angle between the two rings. However, no matter how many times I tilt one ring refinement always makes them coplanar. Is there an option that I can use in phenix.refine to prevent the co-planarity or how do people typically handle this situation? Thanks for the help. All the best, -Jeff **************************************** Jeff Habel PhD Scripps Florida Drug Discovery 5353 Parkside Dr, RF-1 Rm 102 Jupiter, FL 33458 Phone: 561-799-8849 Fax: 561-799-8957 Email: jhabel(a)scripps.edu *****************************************

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Turing off Auto-Modify initial isotropic ADP
by James Fraser 30 Aug '07

30 Aug '07

I'm trying to do an Fcalc with "main.number_of_macro_cycles=0 main.bulk_solvent_and_scale=false export_final_f_model=mtz ", but the b-factors get randomized before the 0th cycle of refinement (see excerpt from log below). Is there anyway to turn this off? Thanks, jf <<LOG FILE>> ----------Auto-Modify initial isotropic ADP---------- Randomizing |-ADP statistics (Wilson B = -4.823)------------------------------------------| .... -- James Fraser jamesfraser(a)berkeley.edu Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

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occupancy refinement question
by John Bruning 27 Aug '07

27 Aug '07

Hi, I have a ligand with dual conformations. I want to do group occupancy refinement on the conformers (each conformer is one group). I keep having trouble. The ligand is one chain named chain E and conformer 1 has residue name ADRG and conformer 2 has residue name BDRG. This is what I suppose my .def file should have in it: occupancies { individual = None group = "chain E and resname ADRG" group = "chain E and resname BDRG" one_occupancy_group_per_residue = True } When I run this it tells me I have an ambiguous selection. Any ideas why this isn't working and how I can change my .def file to make it work?

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Re: [phenixbb] occupancy refinement question
by Paul Adams 27 Aug '07

27 Aug '07

Hi is it possible that the A and B in the residue name are the alternate conformation ids? If so your selection should use the DRG resname and the altloc to select the appropriate residues. Paul Adams Lawrence Berkeley Laboratory -----Original Message----- From: John Bruning <jbruning(a)gmail.com> Date: Monday, Aug 27, 2007 1:38 pm Subject: [phenixbb] occupancy refinement question To: phenixbb(a)phenix-online.orgReply-to: PHENIX user mailing list <phenixbb(a)phenix-online.org> Hi, > >I have a ligand with dual conformations. I want to do group occupancy refinement on the conformers (each conformer is one group). I keep >having trouble. The ligand is one chain named chain E and conformer 1 has residue name ADRG and conformer 2 has residue name BDRG. This is what I suppose my .def file should have in it: > >occupancies { > individual = None > group = "chain E and resname ADRG" > group = "chain E and resname BDRG" > one_occupancy_group_per_residue = True > } > >When I run this it tells me I have an ambiguous selection. > >Any ideas why this isn't working and how I can change my .def file to make it work? >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb >

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