PyMOL Users Manual. ContentsPreviousNext This section steps through a typical PyMOL session, introducing typed commands and describing how PyMOL responds to them. The details of command syntax are in the section titled "PyMOL Command Language. " The PyMOL language is case-sensitive, but upper case is not used in the current package. So just remember to type all your commands in lower case. Recording Your Work (Optional) While you are learning PyMOL or doing complex projects, you may want to keep a record of all the commands you give in a plain text log-file that you can read and edit. To open a log-file, type the command log_open followed by a file-name: SYNTAX log_open log-file-name EXAMPLE PyMOL> log_open log1.pml All your commands, typed or clicked, will be recorded in the log-file.
To stop recording your commands, type log_close. Loading Data Next you need to input your data from a file, say atomic coordinates in PDB format: SYNTAX load data-file-name EXAMPLE PyMOL> load $PYMOL_PATH/test/dat/pept.pdb png Files. Color Values - PyMOLWiki. Background Naming All listed colours can be specified by name (eg color red, mymolecule)American and English spellings of gray/grey and color/colour can be usedSources Pymol colours are specified as triples of independent Red, Green and Blue contribution in range 0-1.0 in square brackets (e.g. [1.0,1.0,1.0] for white)Colour specs from source files Color.c, menu.py and appearance.py of Pymol 0.99 beta29Colour names can be defined/redefined using set_color command or interactively in Colors item within Setting menu Spectral range colours Spectral ranges are available by name including numerical value (eg grey56, s532) Grays from 'gray00' to 'gray99' (white to black)Spectrum from 's000' to 's999' (violet to red)Original spectrum with extra blue and red at ends from 'o000' to 'o999'Reversed offset spectrum from 'r000' to 'r999'Complementary spectrum from 'c000' to 'c999'Complementary spectrum separated by white from 'w000' to 'w999' Color by Element/Atom See: Color by Atom Simple named colours.
Bonvin Lab. High Ambiguity Driven biomolecular DOCKing based on biochemical and/or biophysical information. Version: 2.2 (March, 2015) (changes) Authors: Alexandre Bonvin and members of the computational structural biology group, Utrecht University Contact: Bijvoet Center for Biomolecular Research Padualaan 8, 3584 CH Utrecht, the Netherlands Email: firstname.lastname@example.org Phone: +31-30-2533859 Fax: +31-30-2537623HADDOCK is one of the flagship software in the EU H2020 BioExcel Center of Excellence for Biomolecular Research HADDOCK online (setup your run): HADDOCK manual: HADDOCK webserver: HADDOCK grid-enabled webserver: Getting the software: license form Questions about HADDOCK or looking for support?
A short introduction: View the BioExcel CoE webinar about HADDOCK Publications: Acknowledgments: J.P. Serial Cloner. CCP4 Molecular Graphics. BLAST: Basic Local Alignment Search Tool. JPred: A Protein Secondary Structure Prediction Server. Input Format Help JPred accepts five types of input (link to format examples) Show/hide more... Batch submission of multiple sequences for individual secondary structure prediction could be done using a file in FASTA format (see link to an example above) and each sequence must be given a unique name (up to 25 characters with no spaces). Additional words or descriptions on the defline will be ignored. Batch jobs cannot be run interactively and results will be provided via e-mail only. A limit of 200 sequences are allowed per batch submission. You may submit several batch jobs, but there is a hard limit of 4,000 sequence predictions in total per user per day.
ExPASy - ProtParam tool. Protein Data Bank - RCSB PDB. A Structural View of Biology This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data. The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond. Use this website to access curated and integrated biological macromolecular information in the context of function, biological processes, evolution, pathways, and disease states. A Molecular View of HIV Therapy January Molecule of the Month Nuclear Pore Complex Deposition Preparation Tools Data Extraction Small Molecules Ligand Expo: Search the Chemical Component Dictionary for the IDs of released ligands Data Format Conversion 3D Structure Viewers.
T-Coffee Multiple Sequence Alignment Program Using Lalign and Dialign | EBI. Psipred : index. The PSIPRED Protein Sequence Analysis Workbench aggregates several UCL structure prediction methods into one location. Users can submit a protein sequence, perform the predictions of their choice and receive the results of the prediction via e-mail or the web.
For a summary of the available methods you can read More... NOTE: users who need to run our methods on a large number of proteins should consider downloading our software using the menu on the left (Server Navigation -> Software Download). The PSIPRED Team Current Contributors David T. Jones, Daniel Buchan, Tim Nugent, Federico Minneci & Kevin Bryson Previous Contributors Anna Lobley, Sean Ward, Liam J. McGuffin For queries regarding PSIPRED: email@example.com. UniProt.