DeepView使用说明
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【资源】蛋白三维结构分析软件DeepView，并附软件使用说明
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这个帖子发布于5年零157天前，其中的信息可能已发生改变或有所发展。
一款功能较强很大的蛋白三维图形分析工具，曾经叫Swiss-PdbViewer。同时附上软件说明！
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广告宣传推广
政治敏感、违法虚假信息
恶意灌水、重复发帖
违规侵权、站友争执
附件异常、链接失效
微信扫一扫
广告宣传推广
政治敏感、违法虚假信息
恶意灌水、重复发帖
违规侵权、站友争执
附件异常、链接失效
微信扫一扫
广告宣传推广
政治敏感、违法虚假信息
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附件异常、链接失效
关于丁香园Deep View of DeepView
Can Your Molecular Viewer Do This?
(Swiss-PdbViewer)
"Between two evils, I always pick the one I never
tried before."
Klondike Annie (Mae West)
Have you tried DeepView&lately?
FAST, FRIENDLY, MENU DRIVEN
All functions are available in menus and on intuitive pallettes. You need no programming skills, unless you want to write DeepView Scripts for automating repetitive tasks.
ALL OF YOUR MODELING TASKS IN ONE PROGRAM
If you now use a variety of programs for studying macromolecular models&analysis of structure and interactions, comparison of models, finding model errors, examining electron-density maps, computing surfaces and electrostatic potentials, minimizing energy, generating structural alignments, searching for functional sites, homology modeling, producing images for publication&you can now do ALL of these tasks, and more, with one powerful, fast, friendly, and easy-to-learn program: DeepView,
available free (your favorite price) for Macintosh and Windows. In addition, you can automate many of your repetitive tasks with DeepView Scripts.
EXTENSIVE INTEGRATION WITH WEB SERVERS
from PDB, ExPDB, GenBank, UniProt, PubChem, Prosite. Submit and retrieve projects from SwissModel.
EASY-TO-FOLLOW
For all DeepView functions, from the simplest viewing to sending and retrieving homology modeling projects, you will find clear tutorials to get you started, whether you are a true beginner or an experienced user needing more than your current program can do. Many of the tutorials are extensively student-tested.
Are you using several program, tools, or servers when you could do it all with just one?
DeepView 4.0 Features
Easy mouse-driven rotation, translation, zoom, centering
Wireframe, ball-and-stick, dotted surfaces, solid surfaces, ribbons
Color by secondary structure, residue type, accessibility, chain, model, threading or force-field energy, B-factor or NMR-ensemble variation, sequence diversity, custom, many more
View multiple models individually or superimposed, or flip through them
View PDB file, click ATOM lines to jump to desired region in model
Create images for publication (OpenGL or scenes for rendering in POV-Ray or MegaPOV)
Improved and expanded handling of nucleic acids
Analyze and Compare Structure
Superimpose and compare two, or many, models simultaneously
Generate structural alignments
Use interactive
Ramachandran diagram, and save
phi-psi statistics
Search for functional signatures with Prosite
Examine subunit contacts
Find structural elements
Find 3D motifs (Define 3d motif in a known structure, by selecting key residues. Then find and import proteins with identical or similar motifs from PDB.)
Analyze ligand binding
Measure bond lengths, angles, dihedral angles
Build protein models from scratch, starting from a sequence (amino acids or codons)
Build loops, break and ligate backbone, add termini, add hydrogens
Build oligomeric proteins from protomers
Build unit-cell contents by crystallographic symmetry
Search ExPDB and UniProt by BLAST
Search ExPDB via SwissModel for homology-modeling templates
Import and align templates, and generate structural alignments
Thread raw sequence onto templates
Minimize energy (GROMOS)
Submit modeling projects to SwissModel, and retrieve final model, all within DeepView
Switch between
SwissModel Workplace and DeepView at any point in a modeling project
Judge Model Quality
Search for protein problems&clashes, buried sidechains lacking expected H-bonds, out of Rama-allowed zones, residues in unlikely environments
Color by B-factor or RMS deviation within an NMR ensemble
Import and view electron-density maps
Refit models into electron density
Minimize energy in modified areas of models (GROMOS)
Compute, Import, and View Surfaces
van der Waals surface
Molecular and accessible surface (SPDBV, MSMS, GRASP)
Electrostatic potential (potential surface or mapped onto molecular surface: SPDBV, GRASP/DELPHI)
Election density (DN6, CCP4, XPLOR)
View all surfaces dotted, solid, or transparent
Import, Edit, and Convert Model Files
Load PDB, MOL (SDF), and (eventually) mmCIF files
Save all file types as PDB
Import PDB, ExPDB (modeling templates or BLAST results from SwissModel Workspace), modeling results (SwissModel Workspace), motif-search results (Vital-IT), ProSite results and definitions, electron-density maps (EDS), compounds (PubChem), sequences to model (ExPASy or NCBI), and others to come
Add and delete residues and termini
Change residue numbers, ligand names, chain designations, model names
Merge models
to build oligomers or protein-ligand complexes
Fit residues or ligands into electron density and save modified model
Save sequence (FASTA) or alignment (gapped FASTA) as amino acids or codons
Write or import DeepView Scripts to carry out repetitive work on one or many models (useful scripts and examples provided)
LEARN Quickly and Painlessly!
Learn how to use all DeepView tools from extensive tutorials.
for users who are new to
molecular graphics, or even new to proteins.
introduce DeepView's most powerful features.
Can your current modeling program do all this?
Get to know DeepView. Version 4.0
available .
Happy Modeling!
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