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[求助]
求一张关于RMSD和回旋半径数据分析图的画法 已有1人参与
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图片如附件所示，图 1 从文献里看来的，原文如下： We focused on a fast-folding mutant of the λ-repressor, λ-HG, with a folding time of 15 microseconds in temperature-jump experiments. By means of a recently developed tempering method (see Zhang and Ma, J. Chem. Phys. 132:244101 (2010)), we observed reversible folding and unfolding of λ-repressor in a 10-microsecond trajectory (see movie at right). The folded state is ranked as the most populated cluster without any prior knowledge of the crystal structure in the subsequent cluster analysis. Moreover, the pathway that leads to complete folding of the protein can be followed based on this cluster analysis. Due to the enhanced sampling method used in the current study, the folding pathways observed may not be the most probable ones. Nevertheless, they represent one of the many physical pathways on the folding landscape. In addition to accelerating the search in conformational space, the enhanced sampling method also covers a broad range of temperatures in the simulation, permitting the calculation of the temperature dependence of certain structural characteristics given enough sampling (see figure below). These results highlight the potential of this enhanced sampling method and the accuracy of the underlying physical model (force field) in studying a relatively large helical protein. The simulations also revealed that the folding of λ-repressor is not a simple two-state process as proposed for most fast-folding proteins. 图中横坐标，纵坐标都知道什么意思，就是不知道最右边的颜色的值是什么意思，0-1的值怎么算来的，如图2。 自己画了用excel画了一张， 如图3，不知道怎么画颜色，颜色的值怎么算，求教！！  图1.png  图2.png  图3.png |
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2楼2017-05-01 07:04:06
【答案】应助回帖
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飞云儿: 金币+50, ★有帮助 2017-06-23 14:27:55
飞云儿: 金币+50, ★有帮助 2017-06-23 14:27:55
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可以用WHAM方法来做你要的带颜色的图。 WHAM(Weighted histogram Analysis Method)。网上也有现成的code，你可以找找看。 Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM (1992) The weighted histogram analysis method for free-energy calculations on biomolecules .1. the method. J Comput Chem 13: 1011-1021. |
3楼2017-05-02 19:49:58
