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40金币求救a级错误解决方法（已解决）
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我的晶体由于对称原因金属原子和部分N原子占有率为0.5，数据还可以，R1=0.06 各向异性后，check结果有很多 PLAT211_ALERT_2_A ADP of Atom N2 is NPD ..................... ? A级错误,并且无法画椭球图 请问如何解决 [ Last edited by gaoyawen on 2009-4-8 at 10:28 ] |
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2楼2009-04-05 10:17:16
3楼2009-04-05 10:20:35
4楼2009-04-05 10:24:19
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错误提示是这样的，请问以上命令如何用 PLAT211_ALERT_2_A ADP of Atom O1W is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom N2 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom C1 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom C4 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom C5 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom C21 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom C22 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom C23 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom C25 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom C26 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom O6 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom C11 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom C13 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom C14 is NPD ..................... ? PLAT211_ALERT_2_A ADP of Atom C16 is NPD ..................... ? |
5楼2009-04-05 10:26:37
6楼2009-04-05 10:29:42
★ ★
gaoyawen(金币+2,VIP+0):感谢讲解，不是无序的原因 4-5 10:55
gaoyawen(金币+2,VIP+0):感谢讲解，不是无序的原因 4-5 10:55
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Finally we would like to refine with anisotropic displacement parameters because the thermal motion of such solvent molecules is certainly not isotropic, but the refinement will be unstable unless we restrain the anisotropic displacement parameters to behave 'reasonably' by means of rigid bond restraints (DELU) and 'similar Uij' restraints (SIMU); fortunately the program can set up these restraints automatically. DELU restrains the differences in the components of the displacement parameters of two atoms to zero along the 1,2- and 1,3-vector directions; these restraints are derived automatically with the help of the connectivity table. Since the SIMU restraints are much more approximate, we restrict them here to atoms which, because of the disorder, are almost overlapping (i.e. are within 0.7 Å of each other). Note that the SIMU restraints ignore the connectivity table and are based directly on a distance criterion specifically because the connectivity table does not link the disordered atoms. In order to specify a non-standard distance cut-off which is the third SIMU parameter, we must also give the first two parameters, which are the restraint esds for distances involving non-terminal atoms (0.02) and at least one terminal atom (0.04) respectively. The .ins file now contains: HFIX 23 C12 > C15 C22 > C25 ANIS O11 > C25 DELU O11 > C25 SIMU O11 > C25 0.04 0.08 0.7 FVAR ..... 0.75 .... PART 1 SAME O21 > C25 SAME O11 C15 < C12 O11 4 ..... ..... ..... 21 C12 1 ..... ..... ..... 21 C13 1 ..... ..... ..... 21 C14 1 ..... ..... ..... 21 C15 1 ..... ..... ..... 21 PART 2 O21 4 ..... ..... ..... -21 C22 1 ..... ..... ..... -21 C23 1 ..... ..... ..... -21 C24 1 ..... ..... ..... -21 C25 1 ..... ..... ..... -21 PART 0 An alternative type of disorder common for THF molecules and proline residues in proteins is when one atom (say C14) can flip between two positions (i.e. it is the flap of an envelope conformation). If we assign C14 to PART 1, C14' to PART 2, and the remaining ring atoms to PART 0, then the program will be able to generate the correct connectivity, and so we can also generate hydrogen atoms for both disordered components (with AFIX, not HFIX): SIMU C14 C14' ANIS O11 > C14' |
7楼2009-04-05 10:38:07
8楼2009-04-05 10:50:55
xi2004
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9楼2009-04-05 11:47:15
10楼2009-04-05 12:05:34