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ganchao1776

至尊木虫 (职业作家)

MolEPI: 12
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注册: 2007-03-24
性别: GG
专业: 生物大分子结构与功能

[交流] 介绍一个查看蛋白质三维结构的好软件

软件的名称是pymol，在百渡上搜一下就能找到下载的地方，我当初就是这么下载一下来，有10多M大小，传不上来，实在不好意思！！

该软件是用来观看pdb格式的不错软件，可以提供多种模式观看蛋白质三维结构，有幸趣的可以下下来试一下，对搞蛋白分子改造研究的非常有用，如果你要写蛋白分子改造方面的论文，它会使你的文章增光不少！！

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1楼 2007-04-01 14:53:56

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yalefield

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老汉一枚

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专业: 高等教育学
管辖: 计算模拟

PyMOL是用Python语言开发的FOSS (Free and Open Source Software)。

作者Warren L. DeLano曾经跟老汉抱怨说：
用PyMOL制作的、漂亮的、印刷质量的分子结构图，
频繁地出现在Nature、Science等科技期刊上，
但是，却从来没有人把PyMOL作为参考文献引用。
如果有这个引用的话，PyMOL将是几十年来引用率最高的“文献”(之一)！
这也是科研软件开发者的悲哀。

作者Warren L. DeLano创立了DeLano Scientific公司
联系地址：
P.O. Box 1118
Palo Alto, CA 94302-1118
U.S.A.

除了PyMOL之外，FreeMOL是DeLano Scientific公司的一个宏伟的作品：
http://www.bioinformatics.org/freemol/

FreeMOL Home Page
Introduction
Many computational tools exist for biomedical research from both commercial, academic, and free sources. However, we lack a set of standard assumptions necessary for creating software systems that effectively combine diverse components.

The FreeMOL Project is an attempt to meet this need through specification of a minimal set of common assumptions that will enable construction of systems which reliably combine multiple components from a variety of sources.

What are the FreeMOL Assumptions?
The FREEMOL environment variable contains the root directory for FreeMOL.
A csh-based command shell is present in /bin/csh.
A minimal set of tools from the Free Software Foundation are in the path.
Compilers for building packages are in the path.
Notes
The $FREEMOL directory is designed to be a user-space equivalent of /usr/local. Users should not need to be root in order to install and utilize FreeMOL packages.
Most packages require some kind of environment variable or path configuration. FreeMOL provides a standard and robust mechanism for establishing such prerequisites.
FreeMOL requires GNU-make and a few other common tools.
Each packages may have its own compiler dependencies. A C compiler is essential, C++ and Fortran compilers will be needed in many cases.
What is the FreeMOL Distribution?
The FreeMOL distribution ("freemol" CVS tree) consists of a FreeMOL directory skeleton and associated Makefile and scripts capable of building FreeMOL packages on multiple platforms from pristine source distributions (gzipped tarballs of specific versions).

In addition to the "freemol" distribution, there is a "freemol-src" CVS tree which contains compressed copies of all the pristine source files for FreeMOL packages which can be legally redistributed.

How Will This Help?
Because FreeMOL packages are autoconfigured in a consistent manner, naive users will be able to install a collection of interoperable software in a matter of minutes from source code without any manual reconfiguration.

Once installed, programs and scripts will be able to call one another in a reliable manner to conduct complex tasks involving multiple components.

What Platforms Will Be Supported?
FreeMOL holds that cross-platform compatability is athe responsibility of the package, not the distribution. For now, x86 Linux will be the primary target platform, but the package Makefiles are constructed in such a way as to enable divergent building procedures on different platforms.