- phenixbb - phenix-online.org

Re: [phenixbb] [ccp4bb] Adding H in refinement
by Schubert, Carsten [PRDUS] 13 Jan '10

13 Jan '10

Hi Pavel, sorry I hijacked the thread a bit... A question about the riding Hydrogens and their B-factors. I noticed that at least with earlier versions of PHENIX the B-factor of the Hydrogens was not fixed to the B-factor of the bonded atoms. If I would generate the Hydrogens in reduce they would inherit the appropriate B-factors, but during the course of the refinement and rebuilding they would start to diverge, sometimes drastically. Are you saying the current implementation restrains the B-factors to the bonded atoms and forces them to be equal or are they just inherited and are allowed to float afterwards? Cheers, Carsten > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Pavel Afonine > Sent: Tuesday, January 12, 2010 12:24 PM > To: CCP4BB(a)JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Adding H in refinement > > Hi Sara, > > - what you observe should not happen since phenix.refine uses riding > model for H atoms. The hydrogen's B-factors are automatically inherited > from the atoms these hydrogens are bonded to. For example, in X-H bond > the B-factor of X should be equal to B-factor of H. > > - make sure you are using the latest version of PHENIX: > http://www.phenix-online.org/download/ > > - if this does not help, please contact me directly, and send the data > and model so I can tell you what exactly is not right (all the files > will be handled confidentially). > > - there is PHENIX bulletin board: > http://www.phenix-online.org/mailman/listinfo/phenixbb > > Pavel. > > > I did refinement with phenix of my 1.9-2.0 Angstroem structures and > included the hydrogens (riding). However, when I checked on the > statistics (refinement close to the end), the average B-factor was > extremely high (in phenix.polygon it was higher than with any other > structure in similar resolution range). It makes sense though that this > happens, if you have a residue which has a high B-factor and carries a > lot of hydrogens the average B-factor will raise quite a lot (since the > B-factor of hydrogens is calculated 1-1.5x of B-factor from the atom > it sits on), right? > > (When I removed the hydrogens again, the average B-factor was > fine...) > > > > My question is now did I do something wrong in my refinement (-> do I > have to change something that this does not happen), or is this > something everybody sees? > > > > If this is common, what would happen (during evaluation) if you want > to publish a structure and the statistics show such a high average B- > factor? Is it better to have hydrogens on, but a bad average B, or no > hydrogens on and a good average B... Obviously, I never published a > structure ;) > >

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Beamtime at the ALS
by Peter Zwart 12 Jan '10

12 Jan '10

Dear All, January 15, 2010 is the deadline for the March/April 2010 Rapid Access Proposal cycle. All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with ADSC Q315/Q315R detectors, automated sample changers and data collection software enabling high-throughput crystal screening and data collection. Remote data collection is available on all BCSB beamlines, providing the user with the full complement of sample visualization, sample manipulation, beamline control, data acquisition and data analysis tools exactly as they would see them if they were stationed at the beamline. This enhanced remote operation capability is coupled with 22hr onsite support by BCSB staff who are able to assist immediately with loading additional samples for remote users or troubleshoot any issues that might arise. Remote users can furthermore be kept up-to-date on changes in ring status via an SMS service (http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Ph…) Specific features are summarized below. Beamlines 8.2.1 and 8.2.2: To facilitate studies on small crystals, a microdiffractometer was installed in the beamline 8.2.1 endstation. The new equipment allows precise sample positioning to within 2 microns, excellent sample viewing of very small crystals, and an off-axis crystal positioning stage. Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer (Actor), allowing remote operations to now be a routine mode of access for these beamlines. Beamlines 5.0.1, 5.0.2, 5.0.3: The Berkeley Automounter sample handling system has a routine capacity of 96 samples (6 pucks). In a typical high-throughput screening mode, the mount-to-mount time is around 2.5 minutes per sample, allowing users to screen a full puck within 45 minutes. The sector 5 beamline user stations are equipped with fully high-adjustable, ergonomically friendly work stations. Data analyses in the BCSB is facilitated by software maintained by sbgrid (http://www.sbgrid.org). A 16 core linux machine is available for our users to process their data and solve/refine their structure. An additional mode of access to the BCSB beamlines is through the Collaborative Crystallography (CC) Program. Users apply for beamtime via the general user program, and collaborate with an expert crystallographer who will conduct the experiments and data reduction on behalf of the researchers. Depending on the users, structure solution, model building and refinement can be carried out as well. Please contact BCSBBeamtime(a)lbl.gov for more information. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/ Scroll down to "Structural Biology beamines (includes protein SAXS)." Click on "New Proposal." If you'd like to apply for May/June 2010 beamtime at the Advanced Light Source, please submit a General User proposal by March 15, 2010. If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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January 15, 2009 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 12 Jan '10

12 Jan '10

Dear Users, The deadline for Mar/April 2010 Collaborative Crystallography proposals will be *January 15, 2009. * ------------------------------------------------------------------------ Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ----------------------------------------------------------------------------------------- How To Apply: To learn more, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for Mar/April 2010 allocation period, proposals must be submitted by *January 15, 2009.* The deadline for CC proposals for the time period May/June 2010 will be March 15, 2010. Regards, Banumathi Sankaran

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reduce and ready_set problem
by Jianghai Zhu 11 Jan '10

11 Jan '10

Hi, I believe I have reported this bug before, but it is not fixed in the phenix.reduce and phenix.ready_set yet. The problem is the hydrogens added by reduce when there is a glycan. Here is the error message. Number of atoms with unknown nonbonded energy type symbols: 12 "ATOM 8332 HD22 ASN B 99 .*. H " "ATOM 11820 HD22 ASN B 320 .*. H " "ATOM 12615 HD22 ASN B 371 .*. H " "ATOM 14058 HO4 NAG B3320 .*. H " "ATOM 14086 HO4 NAG B3321 .*. H " "ATOM 14136 HO4 NAG B3371 .*. H " "ATOM 22458 HD22 ASN D 99 .*. H " "ATOM 25955 HD22 ASN D 320 .*. H " "ATOM 26750 HD22 ASN D 371 .*. H " "ATOM 28256 HO4 NAG D3320 .*. H " ... (remaining 2 not shown) ... Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 12 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). The hydrogen left on the N atom of the ASN is correct, but should be named as HD21 as defined in the ccp4 cif library. And the HO4 for the NAG glycan is just wrong. I have to delete all these hydrogens to get phenix.refine going. -- Jianghai

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Resolve after Phaser SAD module - question
by Peter Grey 10 Jan '10

10 Jan '10

Dear Phenix experts, It is recommended to use FWT/PHWT after Phaser SAD module for initial map calculation. Could you please explain how to tell Resolve to pick these fields for the initial map ? With MR it is clear since you need FWT and PHIC but with SAD you really need FWT and PHWT . I thank you in advance, Peter

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Phenix.refine RuntimeError
by JXQI 09 Jan '10

09 Jan '10

Dear PHENIXBBs, I tried to refine a N-linked glycan using phenix.refine and used the data_link=NAG-ASN for ASN-NAG connection. But I got a RuntimeError of unknown atom_id: HD22. From the mon_lib_list.cif file of Phenix-1.5-2, the atom_id HD22 is already defined. Any suggestions are appreciated. Thanks J.X. QI ********************************************************* Monomer Library directory: "/home/jxqi/152Phenix/phenix-1.5-2/chem_data/mon_lib" Total number of atoms: 11844 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain A and resname ASN and resid 170 residue_selection_2: chain A and resname NAG and resid 1 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain C and resname ASN and resid 170 residue_selection_2: chain C and resname NAG and resid 1 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain E and resname ASN and resid 170 residue_selection_2: chain E and resname NAG and resid 1 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Traceback (most recent call last): File "/home/jxqi/152Phenix/phenix-1.5-2/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/jxqi/152Phenix/phenix-1.5-2/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/home/jxqi/152Phenix/phenix-1.5-2/phenix/phenix/refinement/command_line.py", line 227, in __init__ self.pdb_file_names) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/utils.py", line 907, in process_pdb_files stop_if_duplicate_labels = stop_if_duplicate_labels) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/utils.py", line 940, in _process_pdb_file log = self.log) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2995, in __init__ log=log) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2105, in __init__ log=log) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1575, in __init__ prev_mm=prev_mm) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 543, in __init__ mod_mod_id=self.mon_lib_srv.mod_mod_id_dict[apply_data_mod]) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 819, in apply_mod mod_mon = self.monomer.apply_mod(mod_mod_id) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/cif_types.py", line 359, in apply_mod result.delete_atom_in_place(mod_atom.atom_id) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/cif_types.py", line 264, in delete_atom_in_place raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) RuntimeError: delete_atom_in_place: unknown atom_id: HD22 **********************************************************

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Hello
by Pankaj Chauhan 06 Jan '10

06 Jan '10

Hello, While during NCS based restrained refinement, how can we take two chains as single translation unit as the pdb model is a dimer-dimer. Thanks -- Pankaj Chauhan Senior Research Fellow, PhD Scholar Crystallography Laboratory Division of Protein Science & Engg. IMTECH , Chandigarh, INDIA

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coot - display map
by r n 05 Jan '10

05 Jan '10

Hi I am using Phenix GUI, after refinement , tried to load the coot interface in Phenix, it opens up the coot, but did not load the map or model file. I am using coot0.6 version, Is there any place in phenix enviroment that I could mention the path for coot? Thanks

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refinement
by r n 05 Jan '10

05 Jan '10

Hi I am doing refinement using phenix. I did simulated annealing, Rfree goes up to 10% more than before. (40%) and R stays at 35%. If use previous phenix refinment file for same pdb and data , R and Rfree is 25/27%. I thought even different r-free set after simulated annealing and 7 cycles of refinement in phenix should bring Rfree down, but not ? But same data set and model , in CNS, R/Rfree 26/28%. Any suggestions will be appreciated. I am using phenix-dev249 - linux. thanks ram

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text output for model quality and validation report at phenix
by Ravindra D. Makde 04 Jan '10

04 Jan '10

Hi all, I will greatly appreciate the answers to following query: How can I get the text or excel output of the model quality and validation report of a model after phenix refinement? I am specially interested in real space CC of the various residues. I am using phenix.refine_gui at phenix-1.4-162. I have searched all output files, but couldn't find. Thanks in advance. Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA

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