Re: [ccp4bb] [xds] how to specify measuring angle

2020-10-08 Thread Kay Diederichs 
I agree with Tim that Doo Nam Kim's question appears to be directed towards the 
rotation per frame, 
which is specified in XDS.INP using
 OSCILLATION_RANGE= ! (not OSCILLATION_WIDTH!)
please see the documentation at  
http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#OSCILLATION_RANGE=

best,
Kay

On Thu, 8 Oct 2020 11:04:21 +0200, Tim Gruene  wrote:

>Dear Doo Nam Kim,
>
>the indexing procedure is independent of the starting angle of the
>first frame.
>
>Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree
>per frame during data collection?
>
>Best regards,
>Tim
>
>On Thu, 8 Oct 2020 09:28:07 +0100
>Doo Nam Kim <4e720d49e642-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> I think that my microED data was measured with -60 to 60 rotation
>> angle.
>> 
>> However, 
>> STARTING_ANGLE=  -60.
>> in my XDS.INP
>> 
>> resulted in 
>> ...
>>   #  COORDINATES OF REC. BASIS VECTORREDUCED CELL INDICES
>> 
>> 1   0.0020349 0.0108237 0.0096964 1.00   -0.00   -0.00
>> 2  -0.0056895-0.0002762 0.0015024 0.001.00   -0.00
>> 3   0.0011313-0.0034716 0.0036457 0.00   -0.001.00
>> 
>> 
>>  * REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1
>> * !!! ERROR IN REFINE !!! RETURN CODE IS IER=   0
>> 
>> I assume that rotation angle should be specified in XDS.INP.
>> 
>> Anyone knows how to specify measuring angle in XDS.INP?
>> 
>> If there's no such option in XDS.INP, please let me know as well.
>> Then, my other part of XDS.INP should be corrected.
>> 
>> Thank you
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
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>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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>
>
>
>-- 
>--
>Tim Gruene
>Head of the Centre for X-ray Structure Analysis
>Faculty of Chemistry
>University of Vienna
>
>Phone: +43-1-4277-70202
>
>GPG Key ID = A46BEE1A
>
>
>
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Re: [ccp4bb] Downloading older CCP4 version

2020-10-08 Thread Debanu Das 
Hi All,
No more responses required, thank you.
Best,
Debanu

On Thu, Oct 8, 2020 at 8:54 AM Debanu Das  wrote:

> Hello CCP4BB-ers,
> Posting this here as I have been unable to get a response yet from the
> CCP4 help desk:
> Can anyone point to how (specific download link for this version) I can
> download ccp4 7.0.72?
> It appears challenging now to access legacy CCP4 versions.
> Thanks,
> Debanu
>



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[ccp4bb] Downloading older CCP4 version

2020-10-08 Thread Debanu Das 
Hello CCP4BB-ers,
Posting this here as I have been unable to get a response yet from the CCP4
help desk:
Can anyone point to how (specific download link for this version) I can
download ccp4 7.0.72?
It appears challenging now to access legacy CCP4 versions.
Thanks,
Debanu



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[ccp4bb] Tenure Track Faculty Position in Biochemistry, Samford University

2020-10-08 Thread Brad Bennett 
Greetings all-
The Chemistry and Biochemistry Department at Samford University
(Birmingham, AL) is seeking an Assistant Professor on a 9 month tenure
track appointment to teach courses that include and lead an undergraduate
research program in biochemistry.

Details of the position and the materials required in the application
package can be found at:
https://www.samford.edu/employee/faculty-employment-opportunities/Assistant-Professor-Department-of-Chemistry-and-Biochemistry-9-Mo-TT-Appointment.pdf

Review of applications has begun and will continue until October 30. Please
direct all inquiries to Dr. Chris Pursell, chair of the search committee
and the department, at chris.purs...@samford.edu.

Thank you-

Brad Bennett, Ph.D.
Search Committee Member
Assistant Professor of Biology
Samford University
bbenn...@samford.edu
205-726-4523



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Re: [ccp4bb] [xds] how to specify measuring angle

2020-10-08 Thread Tim Gruene 
Dear Doo Nam Kim,

the indexing procedure is independent of the starting angle of the
first frame.

Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree
per frame during data collection?

Best regards,
Tim

On Thu, 8 Oct 2020 09:28:07 +0100
Doo Nam Kim <4e720d49e642-dmarc-requ...@jiscmail.ac.uk> wrote:

> I think that my microED data was measured with -60 to 60 rotation
> angle.
> 
> However, 
> STARTING_ANGLE=  -60.
> in my XDS.INP
> 
> resulted in 
> ...
>   #  COORDINATES OF REC. BASIS VECTORREDUCED CELL INDICES
> 
> 1   0.0020349 0.0108237 0.0096964 1.00   -0.00   -0.00
> 2  -0.0056895-0.0002762 0.0015024 0.001.00   -0.00
> 3   0.0011313-0.0034716 0.0036457 0.00   -0.001.00
> 
> 
>  * REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1
> * !!! ERROR IN REFINE !!! RETURN CODE IS IER=   0
> 
> I assume that rotation angle should be specified in XDS.INP.
> 
> Anyone knows how to specify measuring angle in XDS.INP?
> 
> If there's no such option in XDS.INP, please let me know as well.
> Then, my other part of XDS.INP should be corrected.
> 
> Thank you
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/



-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Description: OpenPGP digital signature

[ccp4bb] [xds] how to specify measuring angle

2020-10-08 Thread Doo Nam Kim 
I think that my microED data was measured with -60 to 60 rotation angle.

However, 
STARTING_ANGLE=  -60.
in my XDS.INP

resulted in 
...
  #  COORDINATES OF REC. BASIS VECTORREDUCED CELL INDICES

1   0.0020349 0.0108237 0.0096964 1.00   -0.00   -0.00
2  -0.0056895-0.0002762 0.0015024 0.001.00   -0.00
3   0.0011313-0.0034716 0.0036457 0.00   -0.001.00


 * REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1 *
  !!! ERROR IN REFINE !!! RETURN CODE IS IER=   0

I assume that rotation angle should be specified in XDS.INP.

Anyone knows how to specify measuring angle in XDS.INP?

If there's no such option in XDS.INP, please let me know as well.
Then, my other part of XDS.INP should be corrected.

Thank you



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[ccp4bb] Data curation post for EMDB and EMPIAR

2020-10-08 Thread Ardan Patwardhan 
Dear all

We have extended the application deadline for this post to the 20th of October 
2020 -  a post opening at EMBL-EBI, Hinxton UK to work on EMDB and EMPIAR data 
curation at a very exciting time when the archives are expanding rapidly both 
in volume and richness of content: 
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01684=1%5B%5D=0%5B%5D=2
 


Many thanks and best wishes

Ardan

Ardan Patwardhan
Team Leader - Cellular Structure & 3D Bioimaging
EMDB & EMPIAR
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology 
Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD


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