一:图像面板
:Zoom in or out 图像缩放工具
:fit image 图像自动调节工具。
: Contrast 调整对比度工具
:show beam centre。显示光束中心。
: show spots 显示实验衍射点
: show predictions 显示预测理论衍射点
:show masks areas (include backstop)显示已屏蔽的区域
:show spotfinding search area显示衍射点搜索区域(无底色)和背景区域(红色)
:show resolution limits 显示最高分辨率与最低分辨率所跨越的衍射点区域。
:Hide active mask on Rigaku detector。隐藏理学探测器需排除的范围。
:Zoom tool 放大工具
:Panning tool 移动图像工具
:Selection tool for editing search area, processing limit and masks。移动光束中心、调整剔除区域大小,调整分辨率范围,调整背景区域的工具。
: Manual add spots 手动添加衍射点
:masking tool 用于剔除无衍射点区域。
:Circle fitting
:Fit circle to update direct beam position用于标记光束周边的衍射点。
fit circle to update beamstop shadow根据标记的衍射点,确定可能的光束中心。
delete all points删除标记点
:spots and mask eraser 擦除工具,用于擦除对衍射点的标记和对屏蔽区域的标记。
二:indexing面板:
(1)
:new, open, save the file创建、打开、保存文件
: beam x position 光束中心的x坐标
: beam y position 光束中心的y坐标
: crystal to detector distance 晶体与探测器的距离
: spot finding threshold衍射点的阈值,只有强度高于该阈值的斑点才被认为是衍射点。
:spot size limit 衍射点的尺度限制
:min spot separation in x。在x轴方向,区分两相邻衍射点的最小距离。
:min spot separation in y。在y轴方向,区分两相邻衍射点的最小距离。
:max within spot peak separation(splitting)
:I/sig(I) threshold for including spots in indexing在进行indexing时所考虑衍射点的最小I/sig(I)值。
:Exclude any spot rings during indexing。用来排除冰带来的衍射环。
:Fix distance during indexing固定晶体与探测器之间的距离。
:Fix cell during indexing 固定晶胞参数
:Fix the maximum cell edge:固定最大的晶胞范围
:Max cell edge:设置最大的晶胞范围
:Sigma cutoff during refinement:在进行优化时,所能允许对标准偏差的阈值。
(2)备注:
1> The list of solutions, sorted by increasing penalty score and the preferred soltution is that with the highest symmetry from the group with low penalty values.
Usually, the penalty will be less than 20,the rms error (rmsd ) in predicted spots positions (σ(x,y) in mm) are less than 0.3 and the rms error in (σ(Ψ) in degrees) are less than 1.0
输出结果将按惩罚度的高低排序(Pen.)。
较好的结果应该具有最高的对称性(lat.)以及最低的惩罚度和马赛克水平(Mosaicity)。
一般而言,惩罚度应小于20,预测衍射点与真实衍射点的均方根偏差在距离上小于0.3mm,在角度上小于1度。
2> If the indexing fails: Direct beam search
如果indexing失败,可以进行光束中心的自动搜索
3> If the indexing fails: Other parameters.
(1)Weak images
MOSFLM automatically reduces the I/σ(I) threshold for weak images, and it may also reduce the resolution to 4A, but lower values can be tried. It is important not to include spots that are not "real", a small number of false spots can prevent the indexing from working.
(2) Include more images in the indexing.
(3) In case the crystal orientation has changed, try indexing using only one image.
(4) If there are ice rings/spots, use the ice/ring exclusion option. If the cell parameters are known, reduce the maximum allowed cell edge to the known maximum cell edge. This can sometimes help filter incorrect solutions.
(5)If the detector distance is uncertain, and the images are high resolution (eg 2A), allow the detector distance to refine during cell refinement.
如果还是失败可以进行如下尝试,
(1) 衍射点太弱,则减少I/σ(I) 的阈值。
(2) 使用更多的图像来进行indexing。
(3) 如果晶体的取向有可能改变,那么只使用一张图片进行indexing
(4) 如果晶体中有冰,可以使用 排除冰环。
(5) 如果晶体与探测器之间的距离未知,而且图像的分辨率在2A以上,可以在晶胞优化时对距离进行优化。
4> Space group selection
The correct Laue group is difficult to determine by imosflm. So in the absence of additional information, the lower symmetry should be chosen to ensure that a complete dataset is collected. The space group can be distinguished by running POINTLESS when integration is completed.
imosflm 并不能直接确定空间群,所以在进行积分之前,尽量选择同类空间群中最低对称性的空间群(如P21 与P2可选,则选择P2)。
如果要唯一地确定空间群,那么请使用POINTLESS对imosflm 输出的的mtz文件进行进一步处理。
5> Mosaicity estimation
Use to estimation mosaic block size. The smaller the better, Usually blew 1.
表示要用多大的框框才能框住衍射点,自然越小越好,1以下吧。
三:Data collection strategy面板