Recent Changes

Monday, June 6

Monday, May 16

  1. page proteins edited ... New proteins Parsing PDB files for the protein rezzer based on Troy's scripts. This has only …
    ...
    New proteins
    Parsing PDB files for the protein rezzer based on Troy's scripts. This has only been tested with small, monomeric structures, e.g. 1t0c, 1rex. You will also need the Protein Rezzing Toolkit (see under Toolkits).
    Data entry
    RSS feed for new deployments and new models

    Toolkits
    Peter Miller [SL: Graham Mills]
    (view changes)
  2. page proteins edited ... in this topic. topic although activity has recently migrated somewhat to OpenSim grids (Q1,…
    ...
    in this topic.topic although activity has recently migrated somewhat to OpenSim grids (Q1, 2011).
    Existing proteins (needs updating; dabbledb service ended 18th May 2011)
    Proteins deployed in SL
    (view changes)
  3. page proteins edited Structural biologists, biochemists, molecular biologists and others may be interested to know that …
    Structural biologists, biochemists, molecular biologists and others may be interested to know that a number of 3D protein structures have been rezzed in SL. Many were built using scripts developed by Troy McLuhan. Data on these pages comes from the SiSL database (Structures in Second Life). The SL Molecular Structure Group provides a forum for those interested in this topic.
    ...
    proteins (needs updating)updating; dabbledb service ended 18th May 2011)
    Proteins deployed in SL
    Proteins potentially available for deployment in SL
    ...
    Andrew Lang [SL: Hiro Sheridan]
    Web application for conversion of pdb file to sculpted prim
    Region module for OpenSim: contact Olish Newman (New World Grid)
    Media
    Peter Miller [SL: Graham Mills]
    (view changes)

Wednesday, May 11

  1. page PRT instructions edited ... Rez your copy of the prim by dragging it from inventory to the ground before you. Open it and …
    ...
    Rez your copy of the prim by dragging it from inventory to the ground before you. Open it and take its contents into inventory. Note that it contains: a notecard with this text, a protein rezzer prim (black), a BB packaging base prim (white), a BB positioner script.
    You need to choose a pdb file, e.g. from http://www.rcsb.org/ You can use the search field at the top of the page. Go for a small monomeric protein, e.g. 1rez or the even smaller 1t0c (NB 0 is the number zero). The script we use is not smart enough to parse anywhere near the entire pdb file. The proteins in this case comprise just the backbone (N, CA, C atoms) of the polypeptide chain. At the moment the script handles just the ATOM, HELIX and SHEET data and generates its own CONECT data on the assumption that it is a linear molecule. If you have multiple subunits, these can typically be identified by the abnormally long bond (which, of course, you delete) or a shouted error.
    Go to http://biolsci.webfactional.com:8080/sisl/sisl1.ks/selectPdb/ .http://biolsci.webfactional.com/sisl/sisl1.ks/selectPdb/ . Select option
    Go to a sim where there is a sandbox with a good prim allocation. Move to a location at least 10 m away from any other avatar rezzing proteins. Rez a copy of the protein rezzer prim. Right-click the prim and choose edit. You should see .sn1 and .sn2 files. Double-click the .sn1 file, and replace the contents with the augmented ATOM data from the previous step. Save. Likewise, replace the contents of the .sn2 file with the augmented CONECT data. Again, save.
    Type '/42 rezatoms'. You should see the atoms of the molecule rez above the rezzer. The completion of this step will be reported in chat. Then type '/42 rezbonds' and allow the bonds to be rezzed to completion. Don't attempt to do both at the same time.
    (view changes)

Friday, January 21

  1. page proteins edited Structural biologists, biochemists, molecular biologists and others may be interested to know that …
    Structural biologists, biochemists, molecular biologists and others may be interested to know that a number of 3D protein structures have been rezzed in SL. Many were built using scripts developed by Troy McLuhan. Data on these pages comes from the SiSL database (Structures in Second Life). The SL Molecular Structure Group provides a forum for those interested in this topic.
    Existing proteins (needs updating)
    Proteins deployed in SL
    Proteins potentially available for deployment in SL
    ...
    Toolkits
    Peter Miller [SL: Graham Mills]
    ...
    (PRT instructions; available from Daxos Centre[SLURL])IM Graham Mills for availability)
    Multi-sculpted proteins (blog posts: basic concept, stragegy for adding back atoms)
    Mesh proteins (currently in beta release)
    Andrew Lang [SL: Hiro Sheridan]
    Web application for conversion of pdb file to sculpted prim
    (view changes)
    2:41 am

Monday, April 26

  1. page proteins edited ... Toolkits Peter Miller [SL: Graham Mills] ... (PRT instructions; availability) available …
    ...
    Toolkits
    Peter Miller [SL: Graham Mills]
    ...
    (PRT instructions; availability)available from Daxos Centre[SLURL])
    Multi-sculpted proteins (blog posts: basic concept, stragegy for adding back atoms)

    Andrew Lang [SL: Hiro Sheridan]
    Web application for conversion of pdb file to sculpted prim
    (view changes)

Sunday, September 6

Thursday, August 13

  1. page proteins edited ... Proteins potentially available for deployment in SL New proteins ... under Toolkits). SER…
    ...
    Proteins potentially available for deployment in SL
    New proteins
    ...
    under Toolkits). SERVER CURRENTLY DOWN AND UNDER INVESTIGATION (August 12th; 06:04 PST)
    Data entry
    RSS feed for new deployments and new models
    (view changes)

More