- phenixbb - phenix-online.org

Select atoms by B-factors?
by Oliver Clarke 25 Feb '09

25 Feb '09

Hi, I'm currently refining a structure at 1.6A. Substantial portions of the structure are very well ordered, with B-factors < 15. I'd like to refine these well ordered regions using anisotropic thermal parameters, while keeping everything else isotropic. However, in doing so, the atom selections tend to become quite convoluted. Is there any way to select all atoms which initially have an isotropic B less than a certain cuttoff value? That way one could (after isotropic B-factor refinement) select the most ordered regions of the structure for anisotropic refinement. Cheers, Oliver Clarke

2 1

links and REMARK 3 record in the final PDB
by Pascal Egea 24 Feb '09

24 Feb '09

Dear All, I apologize if this question has already been answered. I am refining a structure of a glycosylated-enzyme and I understood the way to define all the links (N-glycosylation to the ASN and beta-glycosidic bonds between the NAG units) and refinement is complete and everything is good. All the links I included in my cif_link definition file where taken into account and dealt with by Phenix (the .def and .geo files are fine). Is it normal however that in the resulting refined PDB file, no such links are written by PHENIX under the REMARK 3 record ? Same thing for the 5 disulfide bonds present in the protein. Thanks in advance for the clarification. Pascal Egea University of California San Francisco Department of Biochemistry and Biophysics Laboratory of Robert Stroud

3 2

Please help with neutron composite SA-omit
by Anna Gardberg 24 Feb '09

24 Feb '09

Hello. I am attempting to create an SA-omit composite map with neutron scatterers. Unfortunately, phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb" composite_omit_type=sa_omit scattering_table=neutron results in an error: "Sorry, unknown file or keyword: scattering_table=neutron Possibilities... (use 'phenix.autobuild --help all' to get full help): general.resolve_pattern_command_list=neutron density_modification.use_resolve_pattern=neutron decision_making.semi_acceptable_r=neutron decision_making.acceptable_r=neutron multiple_models.multiple_models_starting_resolution=neutron " Can someone here help, please? (For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled binaries) works on my computer, CNS 1.1 version seems to compile, it will not run. When I apply the nCNS patch to CNS 1.1, again it seems to compile, but will not run. ) Regards, Anna Gardberg

2 1

Re: [phenixbb] Please help with neutron composite SA-omit
by Thomas C. Terwilliger 23 Feb '09

23 Feb '09

Hi again Anna, Can you possibly try this syntax for the "refine.eff" file: refinement{ main {scattering_table=neutron} } and then say phenix.autobuild <your usual parameters> refine_eff_file=refine.eff That should do it! All the best, -Tom T > Hello. > > I am attempting to create an SA-omit composite map with neutron > scatterers. > > Unfortunately, > > phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb" > composite_omit_type=sa_omit scattering_table=neutron > > results in an error: > > "Sorry, unknown file or keyword: scattering_table=neutron > Possibilities... (use 'phenix.autobuild --help all' to get full help): > general.resolve_pattern_command_list=neutron > density_modification.use_resolve_pattern=neutron > decision_making.semi_acceptable_r=neutron > decision_making.acceptable_r=neutron > multiple_models.multiple_models_starting_resolution=neutron > " > > Can someone here help, please? > > (For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled binaries) works on my computer, CNS 1.1 version seems to compile, it will not run. When I apply the nCNS patch to CNS 1.1, again it seems to compile, but will not run. ) > > Regards, > Anna Gardberg > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

1 0

Re: [phenixbb] Please help with neutron composite SA-omit
by Thomas C. Terwilliger 23 Feb '09

23 Feb '09

Hi Anna, Try putting your cmmand "scattering_table=neutron" in a "refine.eff" file and then run phenix.autobuild including the keyword refine_eff_file=refine.eff (note that you may need to specify the scope of scattering_table just as if you were using the command directly for phenix.refine) That is the way you can put any phenix.refine parameters into autobuild. Let me know if that doesn't do it! -Tom T > Hello. > > I am attempting to create an SA-omit composite map with neutron > scatterers. > > Unfortunately, > > phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb" > composite_omit_type=sa_omit scattering_table=neutron > > results in an error: > > "Sorry, unknown file or keyword: scattering_table=neutron > Possibilities... (use 'phenix.autobuild --help all' to get full help): > general.resolve_pattern_command_list=neutron > density_modification.use_resolve_pattern=neutron > decision_making.semi_acceptable_r=neutron > decision_making.acceptable_r=neutron > multiple_models.multiple_models_starting_resolution=neutron > " > > Can someone here help, please? > > (For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled > binaries) works on my computer, CNS 1.1 version seems to compile, it > will not run. When I apply the nCNS patch to CNS 1.1, again it seems > to compile, but will not run. ) > > Regards, > Anna Gardberg > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

2 1

DTT at special position
by Nikos Pinotsis 23 Feb '09

23 Feb '09

Dear all, even though I checked the documentation and previous threads I didn't find something relative to my problem: I have an elongated e-density that looks like DTT and appears to be located on a special position (there is actually an axis betwenn C2 and C3 atoms of DTT). Refining with phenix.refine using either 0.5 or 1.0 occupancy, I am getting the DTT molecule outside the density (and the symmetry related DTT from the other side and still in the middle the strong difference density. thanks in advance for any suggestions-solutions Nikos -- --------------------------------- Dr. Nikos Pinotsis Section of Structural Biology Institute of Cancer Research Chester Beatty Laboratories 237 Fulham Road London SW3 6JB, UK Tel: +44 20 7153 5453 / 5447 --------------------------------- The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

2 1

ADP refinement
by Katya Heldwein 20 Feb '09

20 Feb '09

Hi, I would like to use TLS refinement for protein (I have selected TLS groups) and individual isotropic refinement for water. How can I specify this in phenix.refine? Thanks, Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

2 1

Strange negative density when refining at low resolution
by Andrew Purkiss-Trew 20 Feb '09

20 Feb '09

Dear Phenixers I've been helping a colleague with a dataset at ~3.8 Angstroms (phases and map from AutoSharp using SAD phasing). At the moment he has an incomplete polyALA model consisting of two chains related by NCS and a few extra sections. Refinement seems to proceed OK using phenix.refine version 1.4-3, but the resultant maps have blobs of negative density in the core of the protein. I am assuming that these are a side-effect of the bulk-solvent correction part of the refinement which is confusing the region where the protein sidechains would be as solvent. There are no corresponding negative peaks on the surface of protein, but some positive peaks where larger sidechains may be. Is this interpretation likely to be correct and if so, which parameter should be altered in the Bulk Solvent section of the input to allow for a bigger mask around the protein. I see that it isn't recommended to change the parameters, but the refinement.mask.solvent_radius=1.0 looks like an obvious candidate. If necessary, I can get an image made showing the maps. Thanks Andrew Purkiss-Trew This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.

2 1

2 Wonderings: adding H atoms and overcoming overfitting problem
by Young-Jin Cho 19 Feb '09

19 Feb '09

Hi, my current wonderings are as below: First, how can I add H atoms into nucleotide ligands in pdb file? I did 'phenix.reduce model.pdb > model_h.pdb', but as I see it didn't add H's of sugar (1', 2', 3' 4' and 5'). Once I had this kind of problem before, I was suggested to use phenix.ready_set command but seemingly this does not work any longer with last version that I am using now. Also, is it possible to add H into phosphate group? The second very general question is about getting over overfitting problem. My phenix runs gave me too much difference between R and Rfree about .7 w/o adding H atoms. I assume it came from water molecules because it(huge gap) just starts to happen after 1_bss stage. If anybody can suggest a good way to get over this problem, you will save my tremendous times and useless efforts. Big thanks in advance, Young-Jin

3 4

optimizing target weights in phenix
by Yusuf Akhter 19 Feb '09

19 Feb '09

*Hi Everybody, I am using phenix-1.3b. When i tried to use "Optimizing target weights" utility by typing following command line * *phenix.refine data.hkl model.pdb optimize_wxc=true optimize_wxu=true I got following error. * Traceback (most recent call last): File "/public/xtal/phenix/phenix-1.3b/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 "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/command_line.py", line 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/driver.py", line 1308, in run log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 642, in refinement_machine log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 327, in __init__ self.wxc_optimization() File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 450, in wxc_optimization rw, rf, b, a, a_xc = self.wx_opt_helper(w = wxc_scale_0 * wxc, sites=True) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 387, in wx_opt_helper verbose = 0) TypeError: __init__() takes at least 5 non-keyword arguments (3 given) *May anybody tell me please how can i fix these errors?? Thanks in advance. yusuf *

3 3