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CheckCIF-PLAT300-310

2020-05-12 07:42 作者:DJ_Tokyo  | 我要投稿

PLAT300 Type_4 Test for Fixed Partial Occupancy

This site is expected to be fully occupied but has been constrained (e.g. with a SHELXL FVAR variable) or fixed at a value less than 1.0. Please check for incomplete (substitutional) disorder handling.

(http://journals.iucr.org/services/cif/checking/PLAT300.html)

警告原因:某個(gè)原子的占有率被限定成了固定值。

解決策略:原子占有率最好按自由變量精修,除非有合理的解釋(如在對(duì)稱元素上或者已通過TG等試驗(yàn)確定)。

PLAT301 Type_3 Test for main residue(s) disorder %

Atom sites that are not fully occupied are counted. A large fraction of disordered atoms may be both a signal for serious structure analysis problems or less reliable/interesting results.

(http://journals.iucr.org/services/cif/checking/PLAT301.html)

警告原因:分子主體存在無序。

解決策略:無需解決,無序處理有合理解釋即可。

PLAT302 Type_4 Test for (anion/solvent) disorder %

Atom sites that are not fully occupied are counted.

(http://journals.iucr.org/services/cif/checking/PLAT302.html)

警告原因:游離離子或者溶劑存在無序。

解決策略:無需解決,無序處理有合理解釋即可。

PLAT303 Type_2 Test for more than 1 connection to Hydrogen Atoms

Hydrogen atoms are generally connected to only one other atom. A hydrogen atom between two oxygen atoms is a special case. Investigate whether this hydrogen atom is better described with a disorder model with two partially occupied sites. A difference map might show a double-well density.

(http://journals.iucr.org/services/cif/checking/PLAT303.html)

例:PLAT303_ALERT_2_B Full Occupancy H-Atom H8A with # Connections 3.00

解決策略:H8A重新加氫。H8A是否位于對(duì)稱位置?請(qǐng)仔細(xì)考察其存在情況,在某一位置的任何原子的總占有率不能超過1。

PLAT304 Type_4 Test for non-integer number of atoms in residue

A non-integer number of atoms has been found in a residue.

某殘基中發(fā)現(xiàn)了非整數(shù)個(gè)原子。

(http://journals.iucr.org/services/cif/checking/PLAT304.html)

警告原因:結(jié)構(gòu)中某個(gè)(或某些)原子個(gè)數(shù)為非整數(shù)。

解決策略:檢查是否占有率定錯(cuò),改正即可。否則需要給出合理解釋。

PLAT305 Type_2 Test for isolated Hydrogen Atoms

This test reports on hydrogen atoms that are not on bonding distance to any atom. This ALERT may indicate that the hydrogen atom refined to a non-bonding position or needs a symmetry operation to bring it to bonding distance. It also may indicate a problem with incompatible population parameters (e.g. C - H with population 0.8 and 0.9 respectively).

此檢查報(bào)告結(jié)構(gòu)中存在不處于與任何原子鍵合距離內(nèi)的氫原子。此警告可能表明氫原子精修至一個(gè)非鍵合位置,或需要對(duì)稱操作才能使其到達(dá)鍵合距離。它也可能表示存在不兼容的總體參數(shù)問題(例如C-H鍵長(zhǎng)總體分別為0.8和0.9)。

(http://journals.iucr.org/services/cif/checking/PLAT305.html)

警告原因:結(jié)構(gòu)中存在孤立氫原子。

解決策略:檢查是否某原子上的氫原子由于不穩(wěn)定而散架,刪除該孤立氫原子后對(duì)有問題的原子重新加氫。

PLAT306 Type_2 Test for isolated Oxygen Atoms

This test reports on oxygen atoms that are not within bonding distance to any other atom in the structure. A common reason may be that no hydrogen atoms are given for a water molecule. Attempts should be made to locate those hydrogen atoms from a difference map.

(http://journals.iucr.org/services/cif/checking/PLAT306.html)

警告原因:存在游離的氧原子。

解決策略:一般都是游離的水分子,將水上加氫即可,如無法找到氫鍵受體需給出合理解釋。

PLAT307 Type_2 Test for isolated Metal Atoms

This test reports on metal atoms that are not bonded or at coordination distance of other atoms. Isolated ions are very unusual (or non-existent ?)

(http://journals.iucr.org/services/cif/checking/PLAT307.html)

警告原因:存在游離的金屬原子。

解決策略:檢查原子類型是否定錯(cuò)。

PLAT308 Type_2 Test for single bonded Metal Atoms

This test reports on single bonded (coordinated) metal atoms/ions. This represents a very unusual situation. There are literature examples where such a 'single bonded metal' was shown to be a halogen.

此檢查報(bào)告單鍵(配位的)金屬原子/離子。這是一個(gè)極不尋常的情況。有一個(gè)例子是某文獻(xiàn)報(bào)道的這種“單鍵金屬”后被證明其實(shí)是鹵素。

(http://journals.iucr.org/services/cif/checking/PLAT308.html)

警告原因:存在單配位的金屬原子。

解決策略:檢查原子類型是否定錯(cuò)。

PLAT309 Type_2 Test for single bonded Oxygen Atoms

Single bonded Oxygen with C-O > 1.3 Angstrom. Missing H-Atom ? Check

(http://journals.iucr.org/services/cif/checking/PLAT309.html)

警告原因:C-O鍵鍵長(zhǎng)過長(zhǎng),應(yīng)為單鍵。

解決策略:若確定為單鍵,則給氧上加氫。若確定為雙鍵,則限制其鍵長(zhǎng)落在碳氧雙鍵鍵長(zhǎng)范圍內(nèi)。否則需給出合理解釋。

PLAT310 Type_2 Test for 'too close' (symmetry related) full weight atoms

This test identifies (very) short contacts between atoms that only becomes apparent after the application of symmetry on the primary coordinate set.

此檢查識(shí)別原子之間(非常)短的接觸,這種接觸只有在主體坐標(biāo)系上應(yīng)用對(duì)稱性之后才變得明顯。

(http://journals.iucr.org/services/cif/checking/PLAT310.html)

警告原因:結(jié)構(gòu)中存在距離過近的原子(通常需要進(jìn)行對(duì)稱操作才能發(fā)現(xiàn))。

解決策略:通過限制其距離進(jìn)行解決。若不能解決,給出合理解釋即可。


CheckCIF-PLAT300-310的評(píng)論 (共 條)

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