Re: [ccp4bb] PDB format survey?

Does it matter what the PDB use? They will export PDB and mmCIF for us to use, so what they use internally doesn't matter. (IIUC the EBI uses SQL). From my perspective as a developer I am not bothered in the slightest whether we use PDB or mmCIF, because I read everything through MMDB which ha

[ccp4bb] imgCIF workshops at BSR 2007

Dear Colleagues, The agenda for the imgCIF workshops in conjunction with BSR 2007 in Manchester and at Diamond has been posted at: http://www.medsbio.org/meetings/BSR_2007_imgCIF_Workshop.html We hope you can join us. The BSR 2007 meeting organizers have asked me to urge anyone who is

Re: [ccp4bb] PDB format survey?

My frustration comes from what I deem to be an obvious action to disregard the opinion of the user community. From Bernhard's comments below, it sounds like a better plan of action is in the works. Bernhard Rupp wrote: ... > > Anyhow, if I understand correctly, your suggestion of polling the user

Re: [ccp4bb] PDB format survey?

> > Single letter chain IDs cause me a bit of pain in buccaneer. > > Kevin > In general I think that the 'improvements' in the new PDB format are sensible, especially the tidying up of the DNA and RNA names. However the new way of naming hydrogen atoms will break many vintage programs such as m

[ccp4bb] Postdoctoral Position for PHENIX development

=== Lawrence Berkeley National Laboratory Computational Postdoctoral Fellow === Computational Postdoctoral Fellow Job ID: 2

[ccp4bb] stacking interaction!

Hi All! I have found stacking interaction between aromatic residues of a structure of an enzyme. does anybody knows any server which can quantify the stacking interaction between side chains of aminoacids. Thanking very much in advance! Sreeram Mahesh Research Student Prof S Ramakumar's

[ccp4bb] Postdoctoral Position in USC Los Angeles

University of Southern California Molecular and Computational Biology, Department of Chemistry, Norris Cancer Center Postdoctoral/Research Associate positions are available for studying the structure and function of receptor-ligand, protein-protein, and protein-DNA complexes involved in immune,

[ccp4bb] Molrep question

Hi all, I'm using molrep with an MTZ file as input, so according to the manual I should end up with a formatted CIFF file with the F_observed, but I only get a pdb file for the coordinates. Any idea of what I'm doing wrong? Thanks in advance, Cynthia

Re: [ccp4bb] stacking interaction!

Hi Sreeram, Ironically IISc Bangalore, your host institute has the server that exactly does what you want and more! The paper has just been published in the Nucleic Acid Research. Tina KG, Bhadra R, Srinivasan N. PIC: Protein Interactions Calculator. Nucleic Acids Res. 2007 Jul 1;35(Web Serv

[ccp4bb] Biophysicist (SAXS, crystallography) position at LBNL, SF Bay Area

*BIOPHYSICIST* Job # 20882 The Physical Biosciences Division of LBNL is accepting applications for a biophysicist be a part of an interdisciplinary team to help operate, maintain, and improve the small angle X-ray scattering (SAXS) station in the SIBYLS (12.3.1) beamline at the Advanced Light

[ccp4bb] density histogram

Dear All - before I code ahead - is there a simple program/script available where I can read in a map and it gives me a basic 1d density histogram (or the tabular data at least) in return? Thx, br - Bernhard Rupp http://www.ruppwe

Re: [ccp4bb] density histogram

Hi Bernard, it this is relatively easy. Copy this text: #phil __ON__ xmanip { input { xray_data { file_name = porin.mtz labels = FOFCWT name = map_coef write_out =False } } parameters { action = *manipulate_miller manipulate_miller { task = *custom cu