[ccp4bb] Berkeley Server Downtime
Dear Colleagues, the CCI group in Berkeley is moving to a new building this week. As a result several structural biology web services will be offline for a short while. These include: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) The servers will be shutdown at 9am Pacific time on Wednesday 10th. Services should resume by the morning of Friday 12th at the latest. During the downtime bug reports and emails requesting help should be queued and received by us once the servers are back online. We greatly appreciate your understanding, and hope that this doesn’t present too much of an inconvenience. Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] PDBe workshop on programmatic access to macromolecular structure information, 24-25 September 2015
Programmatic Access to Macromolecular Structure Information PDBe Workshop for Programmers, 24-25 September 2015 Deadline for application: Friday 26 June 2015 What? The Protein Data Bank in Europe (PDBe;www.ebi.ac.uk/pdbe/ http://www.ebi.ac.uk/pdbe/) is organising a hands-on, interactive workshop for developers interested in using primary and value-added information about the 3D structures in PDB and EMDB. Programmatic access to macromolecular structure data as well as information about assemblies, structure quality, literature and citations, and up-to-date cross-references to other biomedical resources (UniProt, Pfam, CATH, SCOP, etc.) are a critical requirement for integrative bioinformatics analyses and workflows. PDBe has developed a set of REST APIs (http://www.ebi.ac.uk/pdbe/api/doc) that provide easy access to high-quality information regarding biomacromolecular structures archived in PDB and EMDB. They provide a simple, reliable, light-weight mechanism to query macromolecular structure data, select entries or molecules of interest, and access targeted information about them, including information about the molecules, experimental details, assemblies, motifs, function, taxonomy, structure quality, etc. The API is used by PDBe services and is also integrated in Jmol/JSmol. We will also present Solr/Lucene based query API for macromolecular structure information including PDB, EMDB and value added information on assemblies, structure quality and up-to-date cross-reference information to other biomedical databases based on SIFTS (http://pdbe.org/sifts) . Is it for me? Do you (plan to) develop software or online resources that use or need access to information about structures in PDB or EMDB? Would you rather not maintain your private infrastructure for retrieving, parsing, storing and updating such information? If so, then this workshop is for you. We will explain what information is available through the API and how you can access it from your own software or resource. There will be plenty of time for hands-on work where experienced PDBe developers will help you to use the API for your specific needs. When and where? The workshop will take place on 24 25 September 2015 (starting at 12.00 on 24 September, and finishing at 16.00 on 25 September) at EMBL-EBI (www.ebi.ac.uk http://www.ebi.ac.uk) in Hinxton, near Cambridge. How much does it cost? There is no fee for the workshop. However, we expect you to arrange and pay for your own travel to and from EMBL-EBI. Accommodation will be provided if required at the Wellcome Trust Conference Centrewww.wtconference.org.uk http://www.wtconference.org.ukwhich is on the same campus as EMBL-EBI. Refreshments, lunch on both days and a workshop dinner on 24 September will all be provided. How can I apply? To apply for the workshop, email Jose Dana at d...@ebi.ac.ukno later than Friday 26 Junewith the following details: · a brief description of the software you have developed or are developing - i.e. what it does, in which field, how many users, relevant publications, etc. · programming language(s) you are specifically interested in (Python examples and tutorials will be provided) · how you would benefit from this workshop · any specific topics or questions you would like to see addressed in the workshop If the workshop is oversubscribed, we will select participants based on the information provided. You will be informed by the end of June if you have been selected for the workshop or not. Prerequisites? Basic programming experience in use of REST API’s. Bring your own laptop with git and iPython notebook pre-installed if you want to follow the Python tutorial and examples. If you need to make plots, make sure that matplotlib is also installed. = Questions? Jose Dana (d...@ebi.ac.uk) at PDBe will be happy to answer any queries you have about the workshop.
Re: [ccp4bb] Refmac fatal error with newly added ligand
Hi Sze Yi, There is already a compound named LIG in the Refmac dictionary. So either you have to choose a new name or you overrule the dictionary by supplying a restraint file in your Refmac run. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Lau Sze Yi (SIgN) Sent: Monday, June 08, 2015 12:00 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refmac fatal error with newly added ligand Hello, I generated my new ligand using smiles string in Phenix with elbow to generate my ligand cif and pdb file. I then open these in Coot along with my protein model and mtz and fitted this new ligand into my density. However Refmac failed with the following details in my log file: PDB_code:4F80 PDB_name:IMMUNE SYSTEM PDB_date:16-MAY-12 ERROR : atom :C01 LIG 1 EE is absent in the library ERROR : atom :C02 LIG 1 EE is absent in the library ERROR : atom :C03 LIG 1 EE is absent in the library ERROR : atom :C04 LIG 1 EE is absent in the library ERROR : atom :C05 LIG 1 EE is absent in the library ERROR : atom :O06 LIG 1 EE is absent in the library ERROR : atom :P07 LIG 1 EE is absent in the library ERROR : atom :O08 LIG 1 EE is absent in the library ERROR : atom :O09 LIG 1 EE is absent in the library ERROR : atom :O10 LIG 1 EE is absent in the library ATTENTION: atom:C28 LIG 1 EE is missing in the structure ATTENTION: atom:C26 LIG 1 EE is missing in the structure ATTENTION: atom:C24 LIG 1 EE is missing in the structure ATTENTION: atom:C22 LIG 1 EE is missing in the structure ATTENTION: atom:C21 LIG 1 EE is missing in the structure ATTENTION: atom:C4 LIG 1 EE is missing in the structure ATTENTION: atom:N3 LIG 1 EE is missing in the structure ATTENTION: atom:C20 LIG 1 EE is missing in the structure ATTENTION: atom:C17 LIG 1 EE is missing in the structure ATTENTION: atom:C5 LIG 1 EE is missing in the structure ATTENTION: atom:C6 LIG 1 EE is missing in the structure ATTENTION: atom:N1 LIG 1 EE is missing in the structure ATTENTION: atom:C7 LIG 1 EE is missing in the structure ATTENTION: atom:C15 LIG 1 EE is missing in the structure ATTENTION: atom:C13 LIG 1 EE is missing in the structure ATTENTION: atom:N12 LIG 1 EE is missing in the structure ATTENTION: atom:C10 LIG 1 EE is missing in the structure ATTENTION: atom:C8 LIG 1 EE is missing in the structure Number of chains : 5 Total number of monomers : 217 Number of atoms :2162 Number of missing atoms : 18 Number of rebuilt atoms : 908 Number of unknown atoms : 10 Number of deleted atoms : 0 IERR =1 There is an error. See above === Error: Fatal error. Cannot continue BFONT COLOR=#FF!-- SUMMARY_BEGIN-- Refmac_5.8.0123: Fatal error. Cannot continue Times: User: 2.1s System:0.1s Elapsed: 0:04 /pre /html What went wrong? Am I missing any steps in my ligand fitting? Appreciate your feedback. Regards, Sze Yi
[ccp4bb] Refmac fatal error with newly added ligand
Hello, I generated my new ligand using smiles string in Phenix with elbow to generate my ligand cif and pdb file. I then open these in Coot along with my protein model and mtz and fitted this new ligand into my density. However Refmac failed with the following details in my log file: PDB_code:4F80 PDB_name:IMMUNE SYSTEM PDB_date:16-MAY-12 ERROR : atom :C01 LIG 1 EE is absent in the library ERROR : atom :C02 LIG 1 EE is absent in the library ERROR : atom :C03 LIG 1 EE is absent in the library ERROR : atom :C04 LIG 1 EE is absent in the library ERROR : atom :C05 LIG 1 EE is absent in the library ERROR : atom :O06 LIG 1 EE is absent in the library ERROR : atom :P07 LIG 1 EE is absent in the library ERROR : atom :O08 LIG 1 EE is absent in the library ERROR : atom :O09 LIG 1 EE is absent in the library ERROR : atom :O10 LIG 1 EE is absent in the library ATTENTION: atom:C28 LIG 1 EE is missing in the structure ATTENTION: atom:C26 LIG 1 EE is missing in the structure ATTENTION: atom:C24 LIG 1 EE is missing in the structure ATTENTION: atom:C22 LIG 1 EE is missing in the structure ATTENTION: atom:C21 LIG 1 EE is missing in the structure ATTENTION: atom:C4 LIG 1 EE is missing in the structure ATTENTION: atom:N3 LIG 1 EE is missing in the structure ATTENTION: atom:C20 LIG 1 EE is missing in the structure ATTENTION: atom:C17 LIG 1 EE is missing in the structure ATTENTION: atom:C5 LIG 1 EE is missing in the structure ATTENTION: atom:C6 LIG 1 EE is missing in the structure ATTENTION: atom:N1 LIG 1 EE is missing in the structure ATTENTION: atom:C7 LIG 1 EE is missing in the structure ATTENTION: atom:C15 LIG 1 EE is missing in the structure ATTENTION: atom:C13 LIG 1 EE is missing in the structure ATTENTION: atom:N12 LIG 1 EE is missing in the structure ATTENTION: atom:C10 LIG 1 EE is missing in the structure ATTENTION: atom:C8 LIG 1 EE is missing in the structure Number of chains : 5 Total number of monomers : 217 Number of atoms :2162 Number of missing atoms : 18 Number of rebuilt atoms : 908 Number of unknown atoms : 10 Number of deleted atoms : 0 IERR =1 There is an error. See above === Error: Fatal error. Cannot continue BFONT COLOR=#FF!--SUMMARY_BEGIN-- Refmac_5.8.0123: Fatal error. Cannot continue Times: User: 2.1s System:0.1s Elapsed: 0:04 /pre /html What went wrong? Am I missing any steps in my ligand fitting? Appreciate your feedback. Regards, Sze Yi
[ccp4bb] ITC workshop [Off-topic]
Dear All, In the spirit of complementary methods (e.g. see Acta Cryst.D Vol 71), I would like to bring to your attention an upcoming bootcamp on“Isothermal Titration Calorimetry Analysis”, to be held 10-11 September, 2015at the NIH in Bethesda, MD, USA. Topics will include basic principlesand advanced topics like multi-site binding models, experimental design,multi-method global analysis, and use of cutting-edge analytical softwareincluding NITPIC, ITCsy, and GUSSI. The bootcamp is organized by theFoundation for Advanced Education in the Sciences. You can sign up andget more information at http://www.faestraining.org/index.php/conferences-bootcamps Sincerely, Chad
