Dear Jürgen and Lu,
I am not sure IDXREF found the correct solution (taken from IDXREF.LP):
***** INDEXING OF OBSERVED SPOTS IN SPACE GROUP # 3 *****
2372 OUT OF 40947 SPOTS INDEXED.
3 REJECTED REFLECTIONS (REASON: OVERLAP)
38572 REJECTED REFLECTIONS (REASON: TOO FAR FROM IDEAL POSITION)
EXPECTED ERROR IN SPINDLE POSITION 1.159 DEGREES
EXPECTED ERROR IN DETECTOR POSITION 1.67 PIXELS
Only ~2,000 reflections out of ~40,000 indexed with a relatively large error in
spindle position and detector position. I would check that the direct beam
position in XDS.INP is correct and maybe try to only index the first 30° of
data or so to get the orientation. This orientation can then be used to process
the full data set. You may also try to give the cell parameters obtained from
HKL2000 into your input file. In the XDS wiki should be many tips and tricks
what you could do. You may even process with Mosflm and see what comes out here.
Best,
Herman
Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Jurgen
Bosch
Gesendet: Montag, 11. Mai 2015 15:57
An: [email protected]
Betreff: Re: [ccp4bb] XDS INP
Edit your XDS.INP file to look like this:
!JOB= XYCORR INIT COLSPOT IDXREF
JOB=DEFPIX INTEGRATE CORRECT
Then rerun ads and be happy thereafter.
and RTFM !
Jürgen
......................
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742<tel:%2B1-410-614-4742>
Lab: +1-410-614-4894<tel:%2B1-410-614-4894>
Fax: +1-410-955-2926<tel:%2B1-410-955-2926>
http://lupo.jhsph.edu
On May 11, 2015, at 9:19 AM, Harry Powell
<[email protected]<mailto:[email protected]>> wrote:
Hi Lu
Mosflm indexes your image using all defaults without any problems ;-)
XDS shouldn't have any difficulties with indexing this.
I suspect your crystal only diffracts to ~3.0 - 3.5 Å so you could do a better
experiment by moving the detector back to ~ 900mm...
BUT - PLEASE don't attach your original images to messages to the BB - anyone
on a slow data link will be considerably indisposed by having an 8Mb attachment
that they (most probably) really don't want to have.
On 11 May 2015, at 12:56, luzuok wrote:
Dear Karine and Jürgen,
The XDS terminated in IDXREF with error message:
!! ERROR !!! INSUFFICIENT PERCENTAGE (< 50%) OF INDEXED REFLECTIONS
In the COLSPOT, I can see
NUMBER OF DIFFRACTION SPOTS LOCATED 53669
IGNORED BECAUSE OF SPOT MAXIMUM OUT OF CENTER 174
IGNORED BECAUSE OF SPOT CLOSE TO UNTRUSTED REGION 450
WEAK SPOTS OMITTED 11753
NUMBER OF DIFFRACTION SPOTS ACCEPTED 41292
It seems that the accepted spots are enough. But I don't know why there are so
many spots which cannot be indexed.
Best wishes!
LU
--
卢作焜
南开大学新生物站A202
在 2015-05-11 16:49:53，"Karine Sparta"
<[email protected]<mailto:[email protected]>>
写道：
Dear Lu,
I'm sorry to read that you couldn't process your data with XDSAPP.
I've been busy last week updating our webpage, the latest version of XDSAPP is
now available for download since friday (an official announcement will be made
tomorrow).
Maybe it will help with your data set, if not, I would be interested in the
reason for the failure (IDXREF.LP), I may learn something from it to improve
the next version.
Best regards,
Karine Sparta
On 05/10/15 10:30, luzuok wrote:
Dear all,
Thank you for all your excellent suggestions! The XDS package now works
smoothly in xdsapp in my Linux.
Unfortunately, due to the data quality or maybe my ability, the process was
failed.
Best wishes!
Lu Zuokun
--
卢作焜
南开大学新生物站A202
At 2015-05-08 03:39:07, "Clemens Vonrhein"
<[email protected]<mailto:[email protected]>> wrote:
>Dear Lu,
>
>apart from the other excellent advice you got: autoPROC is another
>pipeline that uses XDS under the hood (among other tools) and tries to
>take most of the pain out of getting started with XDS. For free (to
>academics) licences/download please see
>
> http://www.globalphasing.com/autoproc/
>
>Cheers
>
>Clemens
>
>On Thu, May 07, 2015 at 04:33:38PM +0800, luzuok wrote:
>> Dear all,
>> I'm a XDS beginner and the first problem I encounter was the INP file.
>> The detector type is MX300. Is the detector supported by XDS? How to
>> modified the INP file?
>> The sitefile of HKL2000 was attached.
>> Can anyone provide some tutorial to use XDS?
>>
>> Best wishes!
>>
>> Lu zuokun
>>
>>
>>
>>
>>
>>
>>
>> --
>> 卢作焜
>> 南开大学新生物站A202
>
>> [-- octet-filter file type: "ASCII text" --]
>>
>> HKLSuite0.95SITE
>> {alig,1} {180}
>> {beamline_name} {BL17B}
>> {cass,rotx} {-0.119}
>> {cass,roty} {-0.167}
>> {crossx} {0.044}
>> {crossxy} {0.009}
>> {crossy} {0.001}
>> {detec} {CCD unsupported-m300}
>> {extension} {*.mccd}
>> {last_saved,chix} {3.24}
>> {last_saved,chiy} {1.65}
>> {last_saved,date} {17:11:17 Apr 19, 2015}
>> {last_saved,user} {17bdata1}
>> {polar} {0.99}
>> {rotation_axis} {Phi}
>> {synchrotron_name} {SSRF}
>> {xbeam} {149.336}
>> {y_scale} {1}
>> {ybeam} {145.711}
>
>
>--
>
>***************************************************************
>* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
>*
>* Global Phasing Ltd.
>* Sheraton House, Castle Park
>* Cambridge CB3 0AX, UK
>*--------------------------------------------------------------
>* BUSTER Development Group
>(http://www.globalphasing.com<http://www.globalphasing.com/>)
>***************************************************************
--
Dr. Karine Sparta
Soft Matter and Functional Materials
Macromolecular Crystallography (BESSY-MX)
Elektronenspeicherring BESSY II
Albert-Einstein-Str. 15, D-12489 Berlin, Germany
Fon: +49 30 8062 14869
http://de.linkedin.com/pub/karine-sparta/2a/48/1b3/en
________________________________
Helmholtz-Zentrum Berlin für Materialien und Energie GmbH
Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.
Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv.
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking
Sitz Berlin, AG Charlottenburg, 89 HRB 5583
Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin
http://www.helmholtz-berlin.de<http://www.helmholtz-berlin.de/>
<IDXREF.LP><hg6_L1_1_00001.mccd><SPOT.XDS>
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of International Union of Crystallography Commission on
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic
Computing)
