Wednesday, June 17, 2015

mirrorliwei 几个微米的晶体就可以拍出X光照片 1 000 納米（nm）= 1微米;药物-受体靶位之间的亲和力达到fm水平的都是司空惯见

9]yuelushan1  2013-2-17 23:51
刘士勇 
https://www.linkedin.com/in/liwei4nlp/zh-cn
镜子大概不是搞晶体X射线衍射的。

布鲁克海文蛋白质数据库里据认为一半的结构数据是错误的。你可以经常看到结晶学家在进行纠错通知，施一公也在此列。

另外蛋白质晶体解构并不是你说的那么神，一个蛋白质晶体的成功制备同当时的特殊溶液条件有关，并不能真实反映这个蛋白质在体内的和溶液内的真正构象。所以搞蛋白质结构分析目前大量使用nmr解析方法作为辅助手段。

至于你感到神奇的40mg的药物可以治病的能力，对我们来讲不算什么，有1mg级别的口服药呢。药物工作人员追求的药物-受体靶位之间的亲和力达到fm水平的都是司空惯见的。
 0.000 001 纳米(nm) = 1 飞米

空间群No12：国际空间群表和晶体学数据
已有 6101 次阅读 2010-4-26 10:03 |个人分类:晶体学和空间群|系统分类:科研笔记|关键词:原子坐标，空间群
空间群No12：国际空间群表和晶体学数据
美国有个海军，海军有个什么实验室，这个实验室有个晶体学启蒙网站。

在中国，这个网站有时可以打开，有时打不开。也不知道是谁在捣蛋，是老美在捣蛋？还是本拉登在捣蛋？还是什么第三者在捣蛋？咱中国人是不会干这种缺德的事情！
老美财大气粗，特别是老美的海军，更是财大气粗中的财大气粗。他们对于案例中涉及到的晶体结构，都给出了三维动画演示，他们的原子坐标是用矢量法表示的。
我也分析了很多的晶体结构，但是我只能给出数字表示。他们是一帮人，我就我自己。他们财大气粗，有个专门的网站，我只有靠科学网这个平台，才可以把我的结果贴出来。
为什么要贴出来呢？
为了梦中的橄榄树！

老的PDF数据没有给出原子坐标。

这个数据给出了原子坐标，如果没有绿色框之中的信息，数据仍然是不完备的。

这是12号国际空间群表的表头，我喜欢使用No.12和C2h（3）符号。不幸的是，编号为12的空间群有很多种表达方法，这给我们解读晶体学数据（如求键络）带来很多麻烦。
No.12空间群的点群为C2h，有一个C2轴，还有一个镜面m垂直于这个2次轴，还有一个反演中心i，加上单位元素，组成一个4阶点群（C2h）。
这个唯一的对称轴C2就是UNIQUE AXIS。
如果把晶体的对称轴C2给了（置于）b轴（Y轴），就是所谓的UNIQUE AXIS b；
如果把晶体的对称轴C2给了（置于）c轴（Z轴），就是所谓的UNIQUE AXIS c；
当然了，也可以把晶体的对称轴C2给了（置于）a轴（X轴），就是所谓的UNIQUE AXIS a；
 
除了空间群表的6种表示外，还有其他6种表示符号。
C12/m1，A12/m1，I12/m1；对应选择UNIQUE AXIS b；
A112/m，B112/m，I112/m；对应选择UNIQUE AXIS c；
A2/m,C2/a,C2/m11,C2/m,F2/m,I2/m这也是No.12空间群的表示符号。

教科书上单斜晶系的晶胞参数是：a≠b≠c，α＝γ＝90o，β≠90o。
这种写法是有条件的，即把实际晶体的UNIQUE AXIS给了b。
当然了，也可以把晶体的UNIQUE AXIS给了c，也可以把晶体的UNIQUE AXIS给了a。
相对于晶体来说，a，b，c的安放就相当于参照坐标系的选择，可以是随意的。
国际空间群表只约定了两种：
把晶体的UNIQUE AXIS给了b和把晶体的UNIQUE AXIS给了c。
此外，国际空间群表中的No.12空间群，给出了6种原子坐标，即所谓的CELL CHOICE，这都是由于不同的人的习惯不同，结果弄出6种摆放原子的模式。无论怎么描述原子的摆放，每个原子的环境是不能变的。
如何来描述原子的环境呢？
有点法、线法和面法。各种化学键理论和电子密度理论都需要知道原子的环境。
化合物AlCeCo的原子环境：
"a=",11.098,"b=",4.41,"c=",4.807,"Delta=",.005
1,"  ","4i-Co","---","4i-Ce","      d===",2.4613
"4i-Co",":",-5.3604,14.0361,-2.205,"          Z=",1
"  SP coordinates=",1.807,0,.146
"     配位原子：","4i-Ce",": ",-2.9939,14.7126,-2.205
"            SP coordinates=",1.87,0,.675
"4i-Ce",":",-2.9939,14.7126,-2.205,"          Z=",1
"  SP coordinates=",1.87,0,.675
"     配位原子：","4i-Co",":  ",-5.3604,14.0361,-2.205
"             SP coordinates=",1.807,0,.146
 
2,"  ","4i-Al","---","4i-Co","      d===",2.488
"4i-Al",":",.1502,-6.2931,-4.41,"          Z=",2
"  SP coordinates=",-.086,-.5,.19
"     配位原子：","4i-Co",": ",.2383,-7.4422,-6.615
"            SP coordinates=",-.193,-1,.146
"     配位原子：","4i-Co",": ",.2383,-7.4422,-2.205
"            SP coordinates=",-.193,0,.146
"4i-Co",":",.2383,-7.4422,-6.615,"          Z=",2
"  SP coordinates=",-.193,-1,.146
"     配位原子：","4i-Al",":  ",.1502,-6.2931,-8.82
"             SP coordinates=",-.086,-1.5,.19
"     配位原子：","4i-Al",":  ",.1502,-6.2931,-4.41
"             SP coordinates=",-.086,-.5,.19
 
3,"  ","4i-Co","---","4i-Ce","      d===",2.5325
"4i-Co",":",2.5611,-3.2969,2.205,"          Z=",1
"  SP coordinates=",.193,1,.854
"     配位原子：","4i-Ce",": ",5.0015,-3.9735,2.205
"            SP coordinates=",.13,1,1.325
"4i-Ce",":",5.0015,-3.9735,2.205,"          Z=",1
"  SP coordinates=",.13,1,1.325
"     配位原子：","4i-Co",":  ",2.5611,-3.2969,2.205
"             SP coordinates=",.193,1,.854
 
4,"  ","4i-Al","---","4i-Co","      d===",2.574
"4i-Al",":",-3.5576,.9236,-2.205,"          Z=",1
"  SP coordinates=",.586,0,-.19
"     配位原子：","4i-Co",": ",-2.5611,3.2969,-2.205
"            SP coordinates=",.807,0,.146
"4i-Co",":",-2.5611,3.2969,-2.205,"          Z=",1
"  SP coordinates=",.807,0,.146
"     配位原子：","4i-Al",":  ",-3.5576,.9236,-2.205
"             SP coordinates=",.586,0,-.19
 
5,"  ","4i-Co","---","4i-Co","      d===",2.7453
"4i-Co",":",1.1614,2.0727,0,"          Z=",2
"  SP coordinates=",.693,.5,.854
"     配位原子：","4i-Co",": ",2.2459,3.2969,-2.205
"            SP coordinates=",.807,0,1.146
"     配位原子：","4i-Co",": ",2.2459,3.2969,2.205
"            SP coordinates=",.807,1,1.146
"4i-Co",":",2.2459,3.2969,-2.205,"          Z=",2
"  SP coordinates=",.807,0,1.146
"     配位原子：","4i-Co",":  ",1.1614,2.0727,-4.41
"             SP coordinates=",.693,-.5,.854
"     配位原子：","4i-Co",":  ",1.1614,2.0727,0
"             SP coordinates=",.693,.5,.854
 
6,"  ","4i-Al","---","4i-Al","      d===",2.9562
"4i-Al",":",2.6491,-4.446,0,"          Z=",1
"  SP coordinates=",.086,.5,.81
"     配位原子：","4i-Al",": ",4.9572,-6.2931,0
"            SP coordinates=",-.086,.5,1.19
"4i-Al",":",4.9572,-6.2931,0,"          Z=",1
"  SP coordinates=",-.086,.5,1.19
"     配位原子：","4i-Al",":  ",2.6491,-4.446,0
"             SP coordinates=",.086,.5,.81
 
7,"  ","4i-Al","---","4i-Al","      d===",3.1074
"4i-Al",":",-1.2494,-.9236,-2.205,"          Z=",1
"  SP coordinates=",.414,0,.19
"     配位原子：","4i-Al",": ",1.2494,.9236,-2.205
"            SP coordinates=",.586,0,.81
"4i-Al",":",1.2494,.9236,-2.205,"          Z=",1
"  SP coordinates=",.586,0,.81
"     配位原子：","4i-Al",":  ",-1.2494,-.9236,-2.205
"             SP coordinates=",.414,0,.19
 
8,"  ","4i-Al","---","4i-Ce","      d===",3.2007
"4i-Al",":",.7582,9.8156,2.205,"          Z=",2
"  SP coordinates=",1.414,1,1.19
"     配位原子：","4i-Ce",": ",.8025,12.1352,0
"            SP coordinates=",1.63,.5,1.325
"     配位原子：","4i-Ce",": ",.8025,12.1352,4.41
"            SP coordinates=",1.63,1.5,1.325
"4i-Ce",":",.8025,12.1352,4.41,"          Z=",2
"  SP coordinates=",1.63,1.5,1.325
"     配位原子：","4i-Al",":  ",.7582,9.8156,2.205
"             SP coordinates=",1.414,1,1.19
"     配位原子：","4i-Al",":  ",.7582,9.8156,6.615
"             SP coordinates=",1.414,2,1.19
 
9,"  ","4i-Ce","---","4i-Co","      d===",3.2115
"4i-Ce",":",-6.4012,9.3431,4.41,"          Z=",2
"  SP coordinates=",1.37,1.5,-.325
"     配位原子：","4i-Co",": ",-5.0453,7.4422,2.205
"            SP coordinates=",1.193,1,-.146
"     配位原子：","4i-Co",": ",-5.0453,7.4422,6.615
"            SP coordinates=",1.193,2,-.146
"4i-Co",":",-5.0453,7.4422,2.205,"          Z=",2
"  SP coordinates=",1.193,1,-.146
"     配位原子：","4i-Ce",":  ",-6.4012,9.3431,0
"             SP coordinates=",1.37,.5,-.325
"     配位原子：","4i-Ce",":  ",-6.4012,9.3431,4.41
"             SP coordinates=",1.37,1.5,-.325
 
10,"  ","4i-Ce","---","4i-Al","      d===",3.2587
"4i-Ce",":",-5.0015,3.9735,-2.205,"          Z=",2
"  SP coordinates=",.87,0,-.325
"     配位原子：","4i-Al",": ",-2.6491,4.446,-4.41
"            SP coordinates=",.914,-.5,.19
"     配位原子：","4i-Al",": ",-2.6491,4.446,0
"            SP coordinates=",.914,.5,.19
"4i-Al",":",-2.6491,4.446,0,"          Z=",2
"  SP coordinates=",.914,.5,.19
"     配位原子：","4i-Ce",":  ",-5.0015,3.9735,-2.205
"             SP coordinates=",.87,0,-.325
"     配位原子：","4i-Ce",":  ",-5.0015,3.9735,2.205
"             SP coordinates=",.87,1,-.325
 
11,"  ","4i-Al","---","4i-Ce","      d===",3.3331
"4i-Al",":",-1.2494,-.9236,2.205,"          Z=",2
"  SP coordinates=",.414,1,.19
"     配位原子：","4i-Ce",": ",1.2051,-1.3961,0
"            SP coordinates=",.37,.5,.675
"     配位原子：","4i-Ce",": ",1.2051,-1.3961,4.41
"            SP coordinates=",.37,1.5,.675
"4i-Ce",":",1.2051,-1.3961,0,"          Z=",2
"  SP coordinates=",.37,.5,.675
"     配位原子：","4i-Al",":  ",-1.2494,-.9236,-2.205
"             SP coordinates=",.414,0,.19
"     配位原子：","4i-Al",":  ",-1.2494,-.9236,2.205
"             SP coordinates=",.414,1,.19
 
12,"  ","4i-Ce","---","4i-Al","      d===",3.3744
"4i-Ce",":",-.1945,3.9735,6.615,"          Z=",1
"  SP coordinates=",.87,2,.675
"     配位原子：","4i-Al",": ",1.2494,.9236,6.615
"            SP coordinates=",.586,2,.81
"4i-Al",":",1.2494,.9236,6.615,"          Z=",1
"  SP coordinates=",.586,2,.81
"     配位原子：","4i-Ce",":  ",-.1945,3.9735,6.615
"             SP coordinates=",.87,2,.675
 
13,"  ","4i-Co","---","4i-Ce","      d===",3.469
"4i-Co",":",3.9607,-8.6665,-4.41,"          Z=",1
"  SP coordinates=",-.307,-.5,.854
"     配位原子：","4i-Ce",": ",4.0045,-12.1352,-4.41
"            SP coordinates=",-.63,-.5,.675
"4i-Ce",":",4.0045,-12.1352,-4.41,"          Z=",1
"  SP coordinates=",-.63,-.5,.675
"     配位原子：","4i-Co",":  ",3.9607,-8.6665,-4.41
"             SP coordinates=",-.307,-.5,.854
 
14,"  ","4i-Ce","---","4i-Ce","      d===",3.5393
"4i-Ce",":",.8025,12.1352,-4.41,"          Z=",2
"  SP coordinates=",1.63,-.5,1.325
"     配位原子：","4i-Ce",": ",1.8131,14.7126,-6.615
"            SP coordinates=",1.87,-1,1.675
"     配位原子：","4i-Ce",": ",1.8131,14.7126,-2.205
"            SP coordinates=",1.87,0,1.675
"4i-Ce",":",1.8131,14.7126,-6.615,"          Z=",2
"  SP coordinates=",1.87,-1,1.675
"     配位原子：","4i-Ce",":  ",.8025,12.1352,-8.82
"             SP coordinates=",1.63,-1.5,1.325
"     配位原子：","4i-Ce",":  ",.8025,12.1352,-4.41
"             SP coordinates=",1.63,-.5,1.325
 
15,"  ","4i-Ce","---","4i-Ce","      d===",3.6797
"4i-Ce",":",-.1945,3.9735,-2.205,"          Z=",1
"  SP coordinates=",.87,0,.675
"     配位原子：","4i-Ce",": ",2.2022,6.7657,-2.205
"            SP coordinates=",1.13,0,1.325
"4i-Ce",":",2.2022,6.7657,-2.205,"          Z=",1
"  SP coordinates=",1.13,0,1.325
"     配位原子：","4i-Ce",":  ",-.1945,3.9735,-2.205
"             SP coordinates=",.87,0,.675
 
16,"  ","4i-Ce","---","4i-Ce","      d===",3.6885
"4i-Ce",":",.8025,12.1352,-4.41,"          Z=",1
"  SP coordinates=",1.63,-.5,1.325
"     配位原子：","4i-Ce",": ",3.2128,9.3431,-4.41
"            SP coordinates=",1.37,-.5,1.675
"4i-Ce",":",3.2128,9.3431,-4.41,"          Z=",1
"  SP coordinates=",1.37,-.5,1.675
"     配位原子：","4i-Ce",":  ",.8025,12.1352,-4.41
"             SP coordinates=",1.63,-.5,1.325
 
17,"  ","4i-Al","---","4i-Al","      d===",4.2538
"4i-Al",":",2.6491,-4.446,0,"          Z=",2
"  SP coordinates=",.086,.5,.81
"     配位原子：","4i-Al",": ",3.5576,-.9236,-2.205
"            SP coordinates=",.414,0,1.19
"     配位原子：","4i-Al",": ",3.5576,-.9236,2.205
"            SP coordinates=",.414,1,1.19
"4i-Al",":",3.5576,-.9236,2.205,"          Z=",2
"  SP coordinates=",.414,1,1.19
"     配位原子：","4i-Al",":  ",2.6491,-4.446,0
"             SP coordinates=",.086,.5,.81
"     配位原子：","4i-Al",":  ",2.6491,-4.446,4.41
"             SP coordinates=",.086,1.5,.81
 
18,"  ","4i-Ce","---","4i-Ce","      d===",4.41
"4i-Ce",":",-5.0015,3.9735,2.205,"          Z=",2
"  SP coordinates=",.87,1,-.325
"     配位原子：","4i-Ce",": ",-5.0015,3.9735,-2.205
"            SP coordinates=",.87,0,-.325
"     配位原子：","4i-Ce",": ",-5.0015,3.9735,6.615
"            SP coordinates=",.87,2,-.325
"4i-Ce",":",-5.0015,3.9735,6.615,"          Z=",2
"  SP coordinates=",.87,2,-.325
"     配位原子：","4i-Ce",":  ",-5.0015,3.9735,2.205
"             SP coordinates=",.87,1,-.325
"     配位原子：","4i-Ce",":  ",-5.0015,3.9735,11.025
"             SP coordinates=",.87,3,-.325
 
19,"  ","4i-Al","---","4i-Al","      d===",4.41
"4i-Al",":",4.0488,-9.8156,2.205,"          Z=",2
"  SP coordinates=",-.414,1,.81
"     配位原子：","4i-Al",": ",4.0488,-9.8156,-2.205
"            SP coordinates=",-.414,0,.81
"     配位原子：","4i-Al",": ",4.0488,-9.8156,6.615
"           SP coordinates=",-.414,2,.81
"4i-Al",":",4.0488,-9.8156,6.615,"          Z=",2
"  SP coordinates=",-.414,2,.81
"     配位原子：","4i-Al",":  ",4.0488,-9.8156,2.205
"             SP coordinates=",-.414,1,.81
"     配位原子：","4i-Al",":  ",4.0488,-9.8156,11.025
"             SP coordinates=",-.414,3,.81
 
20,"  ","4i-Co","---","4i-Co","      d===",4.41
"4i-Co",":",5.3604,-14.0361,2.205,"          Z=",2
"  SP coordinates=",-.807,1,.854
"     配位原子：","4i-Co",": ",5.3604,-14.0361,-2.205
"            SP coordinates=",-.807,0,.854
"     配位原子：","4i-Co",": ",5.3604,-14.0361,6.615
"            SP coordinates=",-.807,2,.854
"4i-Co",":",5.3604,-14.0361,6.615,"          Z=",2
"  SP coordinates=",-.807,2,.854
"     配位原子：","4i-Co",":  ",5.3604,-14.0361,2.205
"             SP coordinates=",-.807,1,.854
"     配位原子：","4i-Co",":  ",5.3604,-14.0361,11.025
"             SP coordinates=",-.807,3,.854
 
21,"  ","4i-Co","---","4i-Al","      d===",4.4195
"4i-Co",":",-1.1614,-2.0727,0,"          Z=",1
"  SP coordinates=",.307,.5,.146
"     配位原子：","4i-Al",": ",.1502,-6.2931,0
"            SP coordinates=",-.086,.5,.19
"4i-Al",":",.1502,-6.2931,0,"          Z=",1
"  SP coordinates=",-.086,.5,.19
"     配位原子：","4i-Co",":  ",-1.1614,-2.0727,0
"             SP coordinates=",.307,.5,.146
 
22,"  ","4i-Co","---","4i-Al","      d===",4.425
"4i-Co",":",2.5611,-3.2969,2.205,"          Z=",2
"  SP coordinates=",.193,1,.854
"     配位原子：","4i-Al",": ",4.9572,-6.2931,0
"            SP coordinates=",-.086,.5,1.19
"     配位原子：","4i-Al",": ",4.9572,-6.2931,4.41
"            SP coordinates=",-.086,1.5,1.19
"4i-Al",":",4.9572,-6.2931,4.41,"          Z=",2
"  SP coordinates=",-.086,1.5,1.19
"     配位原子：","4i-Co",":  ",2.5611,-3.2969,2.205
"             SP coordinates=",.193,1,.854
"     配位原子：","4i-Co",":  ",2.5611,-3.2969,6.615
"             SP coordinates=",.193,2,.854
 
23,"  ","4i-Al","---","4i-Co","      d===",4.433
"4i-Al",":",-3.2571,-11.6627,6.615,"          Z=",2
"  SP coordinates=",-.586,2,-.81
"     配位原子：","4i-Co",": ",-.8463,-8.6665,4.41
"            SP coordinates=",-.307,1.5,-.146
"     配位原子：","4i-Co",": ",-.8463,-8.6665,8.82
"            SP coordinates=",-.307,2.5,-.146
"4i-Co",":",-.8463,-8.6665,4.41,"          Z=",2
"  SP coordinates=",-.307,1.5,-.146
"     配位原子：","4i-Al",":  ",-3.2571,-11.6627,2.205
"             SP coordinates=",-.586,1,-.81
"     配位原子：","4i-Al",":  ",-3.2571,-11.6627,6.615
"             SP coordinates=",-.586,2,-.81
 
24,"  ","4i-Al","---","4i-Co","      d===",4.4891
"4i-Al",":",-7.4561,4.446,0,"          Z=",1
"  SP coordinates=",.914,.5,-.81
"     配位原子：","4i-Co",": ",-3.6456,2.0727,0
"            SP coordinates=",.693,.5,-.146
"4i-Co",":",-3.6456,2.0727,0,"          Z=",1
"  SP coordinates=",.693,.5,-.146
"     配位原子：","4i-Al",":  ",-7.4561,4.446,0
"             SP coordinates=",.914,.5,-.81
 
25,"  ","4i-Co","---","4i-Co","      d===",4.4964
"4i-Co",":",-4.5687,-7.4422,2.205,"          Z=",2
"  SP coordinates=",-.193,1,-.854
"     配位原子：","4i-Co",": ",-.8463,-8.6665,0
"            SP coordinates=",-.307,.5,-.146
"     配位原子：","4i-Co",": ",-.8463,-8.6665,4.41
"            SP coordinates=",-.307,1.5,-.146
"4i-Co",":",-.8463,-8.6665,4.41,"          Z=",2
"  SP coordinates=",-.307,1.5,-.146
"     配位原子：","4i-Co",":  ",-4.5687,-7.4422,2.205
"             SP coordinates=",-.193,1,-.854
"     配位原子：","4i-Co",":  ",-4.5687,-7.4422,6.615
"             SP coordinates=",-.193,2,-.854
 
26,"  ","4i-Ce","---","4i-Co","      d===",4.5149
"4i-Ce",":",-6.0121,1.3961,0,"          Z=",2
"  SP coordinates=",.63,.5,-.675
"     配位原子：","4i-Co",": ",-2.5611,3.2969,-2.205
"            SP coordinates=",.807,0,.146
"     配位原子：","4i-Co",": ",-2.5611,3.2969,2.205
"            SP coordinates=",.807,1,.146
"4i-Co",":",-2.5611,3.2969,-2.205,"          Z=",2
"  SP coordinates=",.807,0,.146
"     配位原子：","4i-Ce",":  ",-6.0121,1.3961,-4.41
"             SP coordinates=",.63,-.5,-.675
"     配位原子：","4i-Ce",":  ",-6.0121,1.3961,0
"             SP coordinates=",.63,.5,-.675
 
27,"  ","4i-Al","---","4i-Ce","      d===",4.54
"4i-Al",":",2.6491,-4.446,0,"          Z=",1
"  SP coordinates=",.086,.5,.81
"     配位原子：","4i-Ce",": ",6.0121,-1.3961,0
"            SP coordinates=",.37,.5,1.675
"4i-Ce",":",6.0121,-1.3961,0,"          Z=",1
"  SP coordinates=",.37,.5,1.675
"     配位原子：","4i-Al",":  ",2.6491,-4.446,0
"             SP coordinates=",.086,.5,.81
 
28,"  ","4i-Co","---","4i-Co","      d===",4.7517
"4i-Co",":",-3.9607,8.6665,0,"          Z=",1
"  SP coordinates=",1.307,.5,.146
"     配位原子：","4i-Co",": ",-1.6379,12.8118,0
"            SP coordinates=",1.693,.5,.854
"4i-Co",":",-1.6379,12.8118,0,"          Z=",1
"  SP coordinates=",1.693,.5,.854
"     配位原子：","4i-Co",":  ",-3.9607,8.6665,0
"             SP coordinates=",1.307,.5,.146
 
29,"  ","4i-Ce","---","4i-Ce","      d===",4.807
"4i-Ce",":",-5.0015,3.9735,2.205,"          Z=",2
"  SP coordinates=",.87,1,-.325
"     配位原子：","4i-Ce",": ",-9.8085,3.9735,2.205
"            SP coordinates=",.87,1,-1.325
"     配位原子：","4i-Ce",": ",-.1945,3.9735,2.205
"            SP coordinates=",.87,1,.675
"4i-Ce",":",-.1945,3.9735,2.205,"          Z=",2
"  SP coordinates=",.87,1,.675
"     配位原子：","4i-Ce",":  ",-5.0015,3.9735,2.205
"             SP coordinates=",.87,1,-.325
"     配位原子：","4i-Ce",":  ",4.6125,3.9735,2.205
"             SP coordinates=",.87,1,1.675
 
30,"  ","4i-Co","---","4i-Co","      d===",4.807
"4i-Co",":",-2.5611,3.2969,-2.205,"          Z=",2
"  SP coordinates=",.807,0,.146
"     配位原子：","4i-Co",": ",-7.3681,3.2969,-2.205
"            SP coordinates=",.807,0,-.854
"     配位原子：","4i-Co",": ",2.2459,3.2969,-2.205
"            SP coordinates=",.807,0,1.146
"4i-Co",":",2.2459,3.2969,-2.205,"          Z=",2
"  SP coordinates=",.807,0,1.146
"     配位原子：","4i-Co",":  ",-2.5611,3.2969,-2.205
"             SP coordinates=",.807,0,.146
"     配位原子：","4i-Co",":  ",7.0529,3.2969,-2.205
"             SP coordinates=",.807,0,2.146
 
31,"  ","4i-Al","---","4i-Al","      d===",4.807
"4i-Al",":",-1.2494,-.9236,-2.205,"          Z=",2
"  SP coordinates=",.414,0,.19
"     配位原子：","4i-Al",": ",-6.0564,-.9236,-2.205
"            SP coordinates=",.414,0,-.81
"     配位原子：","4i-Al",": ",3.5576,-.9236,-2.205
"            SP coordinates=",.414,0,1.19
"4i-Al",":",3.5576,-.9236,-2.205,"          Z=",2
"  SP coordinates=",.414,0,1.19
"     配位原子：","4i-Al",":  ",-1.2494,-.9236,-2.205
"             SP coordinates=",.414,0,.19
"     配位原子：","4i-Al",":  ",8.3646,-.9236,-2.205
"             SP coordinates=",.414,0,2.19
 
32,"  ","4i-Co","---","4i-Co","      d===",4.8327
"4i-Co",":",2.5611,-3.2969,-2.205,"          Z=",1
"  SP coordinates=",.193,0,.854
"     配位原子：","4i-Co",": ",5.0453,-7.4422,-2.205
"            SP coordinates=",-.193,0,1.146
"4i-Co",":",5.0453,-7.4422,-2.205,"          Z=",1
"  SP coordinates=",-.193,0,1.146
"     配位原子：","4i-Co",":  ",2.5611,-3.2969,-2.205
"             SP coordinates=",.193,0,.854
 


http://blog.sciencenet.cn/blog-2321-316183.html  此文来自科学网李世春博客，转载请注明出处。
上一篇：人文观点：美国的地震科学VS中国的地震科学
下一篇：大树说：不是谁都可以仰望天空


[14]王晓明  2013-2-19 23:38

"蛋白质结构研究，研究的分子的结构"属于没事找抽型，俺也不再论，回头继续俺的纠错系列。

[13]徐晓  2013-2-19 01:56
晶体，俺懂；高分子结晶，俺也懂；吴飞鹏兄讲得，我也懂。其余的，俺看不懂。
是不是因为
“就“是”论事儿，就“事儿”论是，就“事儿”论“事儿”。”
把我搞疯了？

[12]mirrorliwei  2013-2-18 09:11
to 1 楼【晶体结构可以认为是“分子间”结构与“分子内”结构的总和】的提法不错。已经有人在40-50年前提过这个事情，分为第一级结构分析和第二级。第一级是解决分子的结构，第二级是分子、原子之间的、作为材料的晶体结构评价。小分子的结构分析，已经实现了自动化，不需要人去思考结构了。大分子的计算复原仍然需要人的干涉、调控。学习晶体学的知识，就是为了在计算时的人工干涉、调控，加快计算速度。说蛋白数据库的错误率有一半或许多了些，10-20%很有可能。

[11]mirrorliwei  2013-2-18 06:31
to 9 楼：“蛋白质晶体并不能真实反映这个蛋白质在体内的和溶液内的真正构象。所以搞蛋白质结构分析目前大量使用nmr解析方法作为辅助手段”的说法是偏见，是对物理根本就没有理解的偏见。因为人们所谓的液体的概念是宏观的，而蛋白质的环境则是微观的。微观世界里的“液体”是什么样子想过么？

[10]mirrorliwei  2013-2-18 06:25
to 8楼：【所以说，蛋白质结构研究，最直接的就是研究晶体结构，】属于无病呻吟的说法，不再论。

[9]yuelushan1  2013-2-17 23:51
镜子大概不是搞晶体X射线衍射的。

布鲁克海文蛋白质数据库里据认为一半的结构数据是错误的。你可以经常看到结晶学家在进行纠错通知，施一公也在此列。

另外蛋白质晶体解构并不是你说的那么神，一个蛋白质晶体的成功制备同当时的特殊溶液条件有关，并不能真实反映这个蛋白质在体内的和溶液内的真正构象。所以搞蛋白质结构分析目前大量使用nmr解析方法作为辅助手段。

至于你感到神奇的40mg的药物可以治病的能力，对我们来讲不算什么，有1mg级别的口服药呢。药物工作人员追求的药物-受体靶位之间的亲和力达到fm水平的都是司空惯见的。

[8]王晓明  2013-2-17 22:32
镜先生又在胡搅蛮缠了。let me walk you through this...
所谓的蛋白质结构研究，第一步是得到晶体结构，然后推知蛋白质的（分子）结构，然后再进一步与其作用机能建立correlation，最后的目的是帮助开发新药。

所以说，蛋白质结构研究，最直接的就是研究晶体结构，如果你要讲big picture，那就是帮助开发新药。你非要从这个链的中间拿出个分子结构说事儿，没有任何意义。当然从严格的定义来讲，我不能说你错，但是你要说蛋白质结构研究，研究的只是分子结构而不是晶体结构，那就属于胡搅蛮缠了。

[7]吴国胜  2013-2-17 21:42
To 【5】楼：【6】楼里面的链接显示，有18个药物的作用机理都是新的。

[6]吴国胜  2013-2-17 21:40
"New Drug Approvals Hit 16-Year High In 2012"
http://cen.acs.org/articles/91/i5/New-Drug-Approvals-Hit-16.html
从PDB数据库里面检索其中很多蛋白的名字，可以查到大量的蛋白晶体结构， 比如VEGF, ABL, PDE5， JAK, Factor Xa, 等等。

[5]mirrorliwei  2013-2-17 21:30
to 4楼：新药，是全新的呢？还是改良的新、为了贩卖战术的新呢？

[4]吴国胜  2013-2-17 21:24
FDA在去年一年就批了39个新药，那是16年来的最高峰：绝大多数都是有机小分子，而且很多药物一看就可以猜出是在蛋白质结构的辅助下设计出来的

[3]mirrorliwei  2013-2-17 21:02
to 2楼：【伴随着各种能量和物质传递的过程，蛋白分子的构象和构型都在不断的变化】不假。但是不会变化很大，因为各种物理法则的约束。有机化学成功的范式不变，他们的努力也就不会没有意义。最坏的结果也是个做数据库。

确定蛋白分子结构的结构生物学是个实在的学术，而且有“创药”这种好听的胡萝卜的诱惑，会有个不错的前景。

[2]吴飞鹏  2013-2-17 19:48
他们啥也不想得到，只想得到钱和官位。
生物体内蛋白质根本不会以晶体的形式存在，而伴随着各种能量和物质传递的过程，蛋白分子的构象和构型都在不断的变化，不可能有在晶体内一样的结构，这点他们不是不懂，故意忽略这个生物最重要特征的目的，就是为了通过搞点伪科学捞钱，捞地位和名声。
目前为止用晶体确定蛋白分子结构的结构生物学是最标准的伪科学。

[1]吴国胜  2013-2-17 19:29
为方便说明，姑且称分子结构为“分子内”结构，那么晶体结构和分子结构的关系就不至于那么紧张了，因为晶体结构可以认为是“分子间”结构与“分子内”结构的总和。

当然，有的人可能会认为晶体结构仅仅是女友的钻戒那般宏观的多面外形，而不能理会到分子之间也会摆出不同的POSE, 从而形成不同的晶体。水的不同晶体结构（如冰雪霜）其实是大家都见过的，而不常见的还有CO2 （干冰也可能有不同的晶体结构，看到王晓明的文章之后，我搜索了一下CCDC, 只找到2个和他文章里面不同的结构），蛋白，等等。实验条件的摸索和分子间作用的调控等等都是获得优良晶体的高技术活，当然有人不屑，以为只是一门手艺，却不自己去试试，否则炸药奖也是大把大把地拿了
 
 
 
 
 
搞蛋白质结构研究的到底是想要得到什么？
已有 3270 次阅读 2013-2-17 16:40 |个人分类:镜子医疗卫生专栏|系统分类:科普集锦|关键词:蛋白质 结构
搞蛋白质结构研究的到底是想要得到什么？
作者: mirror (*)
日期: 02/16/2013 20:27:39

春节过后，气象反常。有人要给镜某上课了。能上课很好，只是小心一点，别露了 怯。

镜某说过：搞蛋白质结构分析的人几乎都认为他们是在做晶体的结构分析。这是个错误的提法。因为他们要知道的是分子的结构，不是晶体的。对此主张，有人说：蛋白质结构研究，研究的正是晶体的结构，不是分子的结构。
这可以说是针锋相对的两个主张。的确，搞蛋白质结构分析的人几乎几乎占领了国际晶体学学会。这个学会曾经是半导体的、各类材料学科的势力范围。如今已经改朝换代了。但是这应该是个值得庆贺的事儿，因为有新的领域融入了这个个古老的研究领域。

为什么搞蛋白质结构分析的人要用晶体？做这个研究的人都知道，好晶体的采得的数据质量好，解析起来的结果好。所以，这个领域里做出好晶体是最重要的，在目前。在以前并非如此。因为所谓晶体的好坏都是相对于所处的实验条件、实验技术环境而言的，今天的好晶体在昨天看就不好。比如说不够大。今天几个微米的晶体就可以拍出X光照片来了，过去要毫米级的。这要是换在婚戒钻石的尺度上说，就是1克拉和几百克拉的差别。

研究晶体学，大约可以有这样几个分类。一类是数理上的。有那么几个聪明人，推算出来有有限的空间群，所有的实在晶体都被包括在这些空间群里。在科网里，对晶体学的数理有造诣的，镜某以为李世春可算一位。还有厦门大学的有位老先生，对这些事情很门儿清。这个东西需要有些悟性，不是说是个人就可以学会。另一类是材料上的。晶体对这些人不单是手段、更是目的。因为他们要用的就是这些晶体。要理解材料的特性，所以要学晶体学。另一类是想知道分子结构的人们研究晶体学，这类人数量最多。晶体学对他们来说，不过就是个“中介”，他们最想知道的是分子的构造。

依照数理的结构，有些聪明人做出了计算的软件、排列的图像软件，然后就是用这些软件的人了。应该说，很多人不能理解晶体学的数理。但是并不妨碍他们做晶体学的结构分析。打个比方：会开车的人很多，但是能知道汽车机理、结构的人就少多了，会设计车的人就更少了。多数做结构分析的人是属于会开车的档次。这很正常，因为很多人要用车。不知道车的结构也没有什么不好意思的。

搞蛋白质结构研究的到底是想要得到什么？他们是想知道蛋白质分子的结构，并且试图通过结构去理解机能和生命现象。这种方法在材料领域里已经是常识、已经形成了成功的范式。这个范式的思考，也影响着结构生物学的人们。

开发新药，治所有的病。这是搞结构生物学的理想。的确，40kg的体重的流感患者只需摄入40mg的药物就可以在24小时之内见效，除了“魔术”一词儿之外没有更好的说法了。这就是结构生物学给人们带来的“福音”。因此，镜某说这是现代的“炼丹术”。

治流感的特效药可以成功，治疗癌症的也会有的。乐观的人们都会这样看。镜某比较悲观，总是想，如果“炼丹”成功了，人不死的话，也就意味着不能有人出生了。因为只生不死，人口就要爆炸了。

----------
就“是”论事儿，就“事儿”论是，就“事儿”论“事儿”。
。
Posted by at

No comments:

Post a Comment

Subscribe to: Post Comments (Atom)