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
1 2 3 4 5 6 7 8
IP fitted, no o 1 0.9270 0.32 0 4481 218 2023 3 1173 7665 2294
IP fitted, no o 2 1.0386 0.28 0 2885 147 1331 3 913 3975 2349
IP fitted, no o 3 0.9685 0.20 0 3014 165 1361 4 962 4698 2353
IP fitted, no o 4 1.0000 0.00 0 2912 124 1345 5 1061 4250 2355
IP fitted, no o 5 0.9894 -0.25 0 2924 139 1333 2 1055 4359 2301
IP fitted, no o 6 0.9720 -0.54 0 2639 136 1214 3 1133 4242 2370
IP fitted, no o 7 0.9489 -0.89 0 2848 127 1275 3 1118 4509 2284
IP fitted, no o 8 0.9700 -1.30 0 3018 145 1316 1 1194 4722 2380
IP fitted, no o 9 0.9275 -1.68 0 2568 136 1175 0 1227 4111 2331
IP fitted, no o 10 0.9619 -2.18 0 2597 144 1173 0 1261 4617 2293
IP fitted, no o 11 0.9295 -2.71 0 2491 135 1089 0 1233 4194 2335
IP fitted, no o 12 0.9589 -3.25 0 2713 155 1194 0 1265 4661 2375
IP fitted, no o 13 0.9533 -3.77 0 2548 167 1110 2 1347 4544 2263
IP fitted, no o 14 0.9683 -4.37 0 2413 170 1067 3 1393 4475 2322
IP fitted, no o 15 0.9639 -4.92 0 2420 141 1090 4 1340 4162 2357
IP fitted, no o 16 0.9386 -5.44 0 2480 167 1024 3 1337 4357 2403
IP fitted, no o 17 0.9576 -5.97 0 2400 144 1043 3 1373 4317 2378
*Von:*张士军[mailto:21620150150...@stu.xmu.edu.cn]
*Gesendet:* Donnerstag, 17. November 2016 13:41
*An:* Schreuder, Herman R&D/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
1 0 13 p+ 254 4.7 68.4 101 479.1
1 0 13 a+ 255 4.7 3117.1 101 479.1
1 0 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
-1 0 -13 n- 251 4.5 20.2 101 491.1
-1 0 -13 a- 252 4.5 2940.5 101 491.1
-1 0 -13 p- 253 4.5 460.7 101 491.1
0 1 -13 a- 89 6.6 2858.2 101 343.0
0 1 -13 p- 90 6.6 612.6 101 343.0
0 1 -13 p- 264 6.1 66.3 101 525.5
0 1 -13 a- 265 6.1 3533.4 101 525.5
0 1 -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
0 1 -15 n- 85 5.1 15.5 101 229.2
0 1 -15 a- 86 5.1 1516.5 101 229.2
0 1 -15 p- 87 5.1 194.3 101 229.2
1 1 -8 n- 275 5.3 0.5 101 136.4
1 1 -8 p- 276 5.3 34.2 101 136.4
1 1 -8 p- 277 5.3 260.0 101 136.4
1 1 -8 a- 278 5.3 517.6 101 136.4
1 1 -8 p- 279 5.3 473.3 101 136.4
1 1 -8 p- 280 5.3 203.4 101 136.4
1 1 -8 p- 281 5.3 78.0 101 136.4
2 -1 7 n+ 285 4.4 32.2 101 280.7
2 -1 7 a+ 286 4.4 1731.7 101 280.7
2 -1 7 p+ 287 4.4 250.6 101 280.7
-----原始邮件-----
*发件人:* herman.schreu...@sanofi.com <mailto: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 <mailto: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
<mailto:21620150150...@stu.xmu.edu.cn>]
*Gesendet:* Donnerstag, 17. November 2016 09:16
*An:* Schreuder, Herman R&D/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 <mailto: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 <mailto:21620150150...@stu.xmu.edu.cn>,
CCP4BB@JISCMAIL.AC.UK <mailto: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 does a 3-dimensional profile fitting
which works better for high-mosaicity (smearing) crystals.
Good luck!
Herman
*Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>] *Im Auftrag von *???
*Gesendet:* Donnerstag, 17. November 2016 08:23
*An:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Betreff:* [ccp4bb] confusing crystal diffraction
Hello guys
I have crystal which was grown in 0.2M ammonium sulfate, 0.1M
sodium cacodylate PH6.6, 40%MPD.I have asked how to resolve the smearing
diffraction problem two month ago ,and got a lot of solutions .After tried most
of the methods ,I can got a better diffraction result now,which was replace the
MPD with glycerol step by step .Unfortunately the diffraction spots still have
a little tailing,and it will smearing badly when the crystal rotated to some
degree .According to this problem ,I have to cutoff some diffraction maps when
I processing the data with HKL2000,but the scale result still has a high
rejection percentage and Rmerge ,maybe I need adjust some parameter of HKL2000
when process ?I haven't any experience about that ,so Any one can give me some
suggestions about the crystal harvest or HKL2000 process experience ? Thanks a
lot !!!!
Best Regard
Shijun
