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[求助]
求一張關(guān)于RMSD和回旋半徑數(shù)據(jù)分析圖的畫法 已有1人參與
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圖片如附件所示，圖 1 從文獻(xiàn)里看來的，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. 圖中橫坐標(biāo)，縱坐標(biāo)都知道什么意思，就是不知道最右邊的顏色的值是什么意思，0-1的值怎么算來的，如圖2。 自己畫了用excel畫了一張， 如圖3，不知道怎么畫顏色，顏色的值怎么算，求教�。� 圖1.png 圖2.png 圖3.png |
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2樓2017-05-01 07:04:06
Cyantulip
金蟲 (初入文壇)
- 應(yīng)助: 6 (幼兒園)
- 金幣: 940.2
- 帖子: 24
- 在線: 41.4小時
- 蟲號: 3924066
- 注冊: 2015-06-14
- 專業(yè): 生物大分子結(jié)構(gòu)與功能
【答案】應(yīng)助回帖
★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★
飛云兒: 金幣+50, ★有幫助 2017-06-23 14:27:55
飛云兒: 金幣+50, ★有幫助 2017-06-23 14:27:55
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可以用WHAM方法來做你要的帶顏色的圖。 WHAM(Weighted histogram Analysis Method)。網(wǎng)上也有現(xiàn)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樓2017-05-02 19:49:58
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