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1. www.rcsb.orgRCSB PDB: Homepage

   www.rcsb.org

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   RCSB Protein Data Bank (RCSB PDB) enables breakthroughs in science and education by providing access and tools for exploration, visualization, and analysis of: Experimentally-determined 3D structures from the Protein Data Bank (PDB) archive. Computed Structure Models (CSM) from AlphaFold DB and ModelArchive.

   • Visualize

     Mol* 3D Viewer. This version of Mol* can be used to ...

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     Use an existing PDB or Computed Structure Model entry ...

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     Download - RCSB PDB: Homepage

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     About PDB-101 Testing instance Researchers around the ...

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     Whether you are looking for a particular PDB structure, ...

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     Documentation - RCSB PDB: Homepage

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     Why Join Us Contribute globally At RCSB PDB, you can ...

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2. spdbv.unil.chSwiss PDB Viewer - Home

   spdbv.unil.ch

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   Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts.

3. 其他人也問了

   Where can I download a PDB file?

   • PDB files can be automatically downloaded from the RSCB PDB. ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards.

   Molecular Graphics Software - RCSB PDB

   www.rcsb.org/docs/additional-resources/molecular-graphics-software

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   How do I manipulate a PDB file?

   • Manipulating PDB files is often painful. Extracting a particular chain or set of residues, renumbering residues, splitting or merging models and chains, or just ensuring the file is conforming to the PDB specifications are examples of tasks that can be done using any decent parsing library or graphical interface.

   A swiss army knife for editing PDB files. - pdb-tools

   www.bonvinlab.org/pdb-tools/

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   What does PDB_sort do?

   • Splits a PDB file into several, each containing one chain. Splits a PDB file into several, each containing one MODEL. Splits a PDB file into several, each containing one segment. Modifies the file to adhere (as much as possible) to the format specifications. Expects a sorted file - REMARK/ATOM/HETATM/END - so use pdb_sort in case you are not sure.

   A swiss army knife for editing PDB files. - pdb-tools

   www.bonvinlab.org/pdb-tools/

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   What are PDB-tools?

   • pdb-tools are open-source and licensed under the Apache License, version 2.0. For details, see the LICENSE file. Modifies the temperature factor column of a PDB file (default 10.0). Modifies the chain identifier column of a PDB file (default is an empty chain). Renames chain identifiers sequentially, based on TER records.

   A swiss army knife for editing PDB files. - pdb-tools

   www.bonvinlab.org/pdb-tools/

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   What does atoms in a PDB file do?

   • Returns a new PDB file only with atoms in common to all input PDB files. Atoms are judged equal is their name, altloc, res. name, res. num, insertion code and chain fields are the same. Coordinates are taken from the first input file. Keeps matching TER/ANISOU records.

   A swiss army knife for editing PDB files. - pdb-tools

   www.bonvinlab.org/pdb-tools/

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   How do I merge multiple PDB files into one?

   • Merges several PDB files into one. The contents are not sorted and no lines are deleted (e.g. END, TER statements) so we recommend piping the results through `pdb_tidy.py`. Usage: python pdb_merge.py Example: python pdb_merge.py 1ABC.pdb 1XYZ.pdb Merges several PDB files into one multi-model (ensemble) file.

   A swiss army knife for editing PDB files. - pdb-tools

   www.bonvinlab.org/pdb-tools/

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4. www.zhihu.com › question › 479566187pdb文件如何打开？ - 知乎簡

   www.zhihu.com › question › 479566187

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   今天跟大家介绍一下命令行的使用方法，假设原PDB文件为name.pdb。同时包含蛋白链多条（A链、B链），核酸链（以RNA链为例，C链、D链、E链、F链）、水链（S链）。 首先提取蛋白链，新的PDB文件命名为为P.pdb。命令行为：

5. discussions.apple.com › thread › 250108761Viewing pdb files on a mac - Apple Community

   discussions.apple.com › thread › 250108761

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   2019年1月23日 · Viewing pdb files on a mac. What's the most efficient PDB visualiser on OSX? Posted on Jan 23, 2019 8:39 AM. 1 reply. Sort By: Rank. BDAqua. Level 10. 245,105 points. Jan 23, 2019 10:03 AM in response to nsridhar27. Depends, are they MS pdb files or Palm pdb files? For the 1st you'd need Windows in Bootcamp or a VM, for the second type...

6. www.rcsb.org › 3d-viewRCSB PDB - 3D View

   www.rcsb.org › 3d-view

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   Mol* 3D Viewer. This version of Mol* can be used to upload single or multiple data files and align structures. WebGL does not seem to be available. This can be caused by an outdated browser, graphics card driver issue, or bad weather. Sometimes, just restarting the browser helps.

7. www.rcsb.org › docs › additional-resourcesMolecular Graphics Software - RCSB PDB

   www.rcsb.org › docs › additional-resources

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   2024年2月26日 · A molecular visualization tool that supports PDB, MOL, MOL2/SYBYL and XYZ file formats. The rendering engine can output high quality molecular graphics. Zeus provides a sequence search that can highlight within the molecular structure. Ramachandran plots of internal dihedral angles can be generated and exported.

8. www.bonvinlab.org › pdb-toolspdb-tools | A swiss army knife for editing PDB files.

   www.bonvinlab.org › pdb-tools

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   Installation Instructions. pdb-tools are available on PyPi and can be installed though pip. This is the recommended way as it makes updating/uninstalling rather simple: pip install pdb-tools.