Re: [ccp4bb] AW: AW: AW: [ccp4bb] confusing crystal diffraction

2016-11-17 Thread Edward A. Berry 

On 11/17/2016 08:36 AM, herman.schreu...@sanofi.com wrote:

Dear Shijun,

The reject.hkl file is the file with all rejected reflections. The first three 
numbers are h, k and l. For the other items you have to consult the HKL manual. 
As I said, I am not familiar with HKL2000. However, in your case, I would look 
in the log files instead of the .hkl files and see if you can find somewhere 
how many reflections were rejected for what reason. With XDS, I know where to 
find these numbers, for HKL2000 you have to ask a HKL2000 expert. For that 
reason I CC’d this email to the bulletin board.

Best,

Herman

The log file has a table listing rejected reflections for each frame.
I need to consult the manual for the meaning of #2 "zero sigma or profile test" 
-
 Others are pretty self-explanatory.

 1 - count of observations deleted manually
 2 - count of observations deleted due to zero sigma or profile test
 3 - count of non-complete profiles (e.g. overloaded) observations
 4 - count of observations deleted due to sigma cutoff
 5 - count of observations deleted below low resolution limit,
 6 - count of observations deleted above high resolution limit,
 7 - count of partial observations
 8 - count of fully recorded observations used in scaling

  12345678
 IP fitted, no o 1  0.92700.320 4481  218 20233 1173 7665 2294
 IP fitted, no o 2  1.03860.280 2885  147 13313  913 3975 2349
 IP fitted, no o 3  0.96850.200 3014  165 13614  962 4698 2353
 IP fitted, no o 4  1.0.000 2912  124 13455 1061 4250 2355
 IP fitted, no o 5  0.9894   -0.250 2924  139 13332 1055 4359 2301
 IP fitted, no o 6  0.9720   -0.540 2639  136 12143 1133 4242 2370
 IP fitted, no o 7  0.9489   -0.890 2848  127 12753 1118 4509 2284
 IP fitted, no o 8  0.9700   -1.300 3018  145 13161 1194 4722 2380
 IP fitted, no o 9  0.9275   -1.680 2568  136 11750 1227 4111 2331
 IP fitted, no o10  0.9619   -2.180 2597  144 11730 1261 4617 2293
 IP fitted, no o11  0.9295   -2.710 2491  135 10890 1233 4194 2335
 IP fitted, no o12  0.9589   -3.250 2713  155 11940 1265 4661 2375
 IP fitted, no o13  0.9533   -3.770 2548  167 11102 1347 4544 2263
 IP fitted, no o14  0.9683   -4.370 2413  170 10673 1393 4475 2322
 IP fitted, no o15  0.9639   -4.920 2420  141 10904 1340 4162 2357
 IP fitted, no o16  0.9386   -5.440 2480  167 10243 1337 4357 2403
 IP fitted, no o17  0.9576   -5.970 2400  144 10433 1373 4317 2378




*Von:*张士军[mailto:21620150150...@stu.xmu.edu.cn]
*Gesendet:* Donnerstag, 17. November 2016 13:41
*An:* Schreuder, Herman R/DE
*Betreff:* Re: AW: AW: [ccp4bb] confusing crystal diffraction


Dear Herman

This is the rejection file ,I can not understand that.Does anyone familiar with 
HKL2000 tell me what those mean ?
reject hkl
   10   13 p+   254   4.7   68.4  101  479.1
   10   13 a+   255   4.7 3117.1  101  479.1
   10   13 p+   256   4.7  263.7  101  479.1
   0   -1   13 n+   268   6.2   42.3  101  495.4
   0   -1   13 a+   269   6.2 3330.3  101  495.4
   0   -1   13 p+   270   6.2  881.7  101  495.4
  -10  -13 n-   251   4.5   20.2  101  491.1
  -10  -13 a-   252   4.5 2940.5  101  491.1
  -10  -13 p-   253   4.5  460.7  101  491.1
   01  -13 a-89   6.6 2858.2  101  343.0
   01  -13 p-90   6.6  612.6  101  343.0
   01  -13 p-   264   6.1   66.3  101  525.5
   01  -13 a-   265   6.1 3533.4  101  525.5
   01  -13 p-   266   6.1  796.9  101  525.5
   0   -1   15 p+81   4.6  786.8  101  247.5
   0   -1   15 a+82   4.6  916.5  101  247.5
   01  -15 n-85   5.1   15.5  101  229.2
   01  -15 a-86   5.1 1516.5  101  229.2
   01  -15 p-87   5.1  194.3  101  229.2
   11   -8 n-   275   5.30.5  101  136.4
   11   -8 p-   276   5.3   34.2  101  136.4
   11   -8 p-   277   5.3  260.0  101  136.4
   11   -8 a-   278   5.3  517.6  101  136.4
   11   -8 p-   279   5.3  473.3  101  136.4
   11   -8 p-   280   5.3  203.4  101  136.4
   11   -8 p-   281   5.3   78.0  101  136.4
   2   -17 n+   285   4.4   32.2  101  280.7
   2   -17 a+   286   4.4 1731.7  101  280.7
   2   -17 p+   287   4.4  250.6  101  280.7

-原始邮件-
*发件人:* herman.schreu...@sanofi.com

[ccp4bb] AW: AW: AW: [ccp4bb] confusing crystal diffraction

2016-11-17 Thread Herman . Schreuder 
Dear Shijun,

The reject.hkl file is the file with all rejected reflections. The first three 
numbers are h, k and l. For the other items you have to consult the HKL manual. 
As I said, I am not familiar with HKL2000. However, in your case, I would look 
in the log files instead of the .hkl files and see if you can find somewhere 
how many reflections were rejected for what reason. With XDS, I know where to 
find these numbers, for HKL2000 you have to ask a HKL2000 expert. For that 
reason I CC’d this email to the bulletin board.

Best,
Herman

Von: 张士军 [mailto:21620150150...@stu.xmu.edu.cn]
Gesendet: Donnerstag, 17. November 2016 13:41
An: Schreuder, Herman R/DE
Betreff: Re: AW: AW: [ccp4bb] confusing crystal diffraction


Dear Herman

This is the rejection file ,I can not understand that.Does anyone familiar with 
HKL2000 tell me what those mean ?
reject hkl
  10   13 p+   254   4.7   68.4  101  479.1
  10   13 a+   255   4.7 3117.1  101  479.1
  10   13 p+   256   4.7  263.7  101  479.1
  0   -1   13 n+   268   6.2   42.3  101  495.4
  0   -1   13 a+   269   6.2 3330.3  101  495.4
  0   -1   13 p+   270   6.2  881.7  101  495.4
 -10  -13 n-   251   4.5   20.2  101  491.1
 -10  -13 a-   252   4.5 2940.5  101  491.1
 -10  -13 p-   253   4.5  460.7  101  491.1
  01  -13 a-89   6.6 2858.2  101  343.0
  01  -13 p-90   6.6  612.6  101  343.0
  01  -13 p-   264   6.1   66.3  101  525.5
  01  -13 a-   265   6.1 3533.4  101  525.5
  01  -13 p-   266   6.1  796.9  101  525.5
  0   -1   15 p+81   4.6  786.8  101  247.5
  0   -1   15 a+82   4.6  916.5  101  247.5
  01  -15 n-85   5.1   15.5  101  229.2
  01  -15 a-86   5.1 1516.5  101  229.2
  01  -15 p-87   5.1  194.3  101  229.2
  11   -8 n-   275   5.30.5  101  136.4
  11   -8 p-   276   5.3   34.2  101  136.4
  11   -8 p-   277   5.3  260.0  101  136.4
  11   -8 a-   278   5.3  517.6  101  136.4
  11   -8 p-   279   5.3  473.3  101  136.4
  11   -8 p-   280   5.3  203.4  101  136.4
  11   -8 p-   281   5.3   78.0  101  136.4
  2   -17 n+   285   4.4   32.2  101  280.7
  2   -17 a+   286   4.4 1731.7  101  280.7
  2   -17 p+   287   4.4  250.6  101  280.7
-原始邮件-
发件人: herman.schreu...@sanofi.com
发送时间: 2016年11月17日 星期四
收件人: 21620150150...@stu.xmu.edu.cn
抄送:
主题: AW: AW: [ccp4bb] confusing crystal diffraction
Dear Shijun,

You should be able to processes this data. I have seen far worse diffraction 
patterns. What is the reason the reflections get rejected? HKL2000 should have 
nice graphical facilities that allow you to see whether the observed 
reflections fit in the predicted boxes.

Good luck!
Herman



Von: 张士军 
[mailto:21620150150...@stu.xmu.edu.cn]
Gesendet: Donnerstag, 17. November 2016 09:16
An: Schreuder, Herman R/DE
Betreff: Re: AW: [ccp4bb] confusing crystal diffraction


Dear Herman

  yes ,I sent some smearing picture now ,and I will try XDS to check whether it 
can work or not


yours


 shijun
-原始邮件-
发件人: herman.schreu...@sanofi.com
发送时间: 2016年11月17日 星期四
收件人: 21620150150...@stu.xmu.edu.cn, 
CCP4BB@JISCMAIL.AC.UK
抄送:
主题: AW: [ccp4bb] confusing crystal diffraction
Dear

Could you send us some images of badly smearing spots? The images you sent us 
are absolutely fine and should not pose any problems processing.

Also, what is the reason the reflections get rejected? I have no experience 
with HKL2000 but I am sure it will produce in the output a table with numbers 
of rejected reflections together with a reason why they were rejected. Reasons 
could e.g. be: overloads, spot too far from predicted position, overlapping 
reflections, bad scaling statistics etc. Did you impose any specific space 
group for processing?

Judging from the images you send us, I would try processing in P1 (no space 
group imposed) and try to get the predicted spots as close as possible to the 
observed spots. If the spots at some other rotation angles are really smearing, 
I would switch to XDS, since XDS