[ccp4bb] Dave Case gives John Lawrence Seminar- starting now!

[James Holton]

starting now: Dave Case on simulating macromolecular crystals with AMBER :

https://lbnl.zoom.us/j/99255547757?pwd=TWozZm9NNDBZZFpIZER6U0JmMmYvQT09



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/

[ccp4bb] Cryo-EM Researcher positions @ Penn State

[Kenneth Lee]

Membrane Structural Biophysics at The Pennsylvania State University
The laboratory of Dr. Kenneth Lee in the Department of Cellular and Molecular Physiology at the Pennsylvania State University College of Medicine invites applications for new NIH-funded postdoctoral positions to study mechanisms and regulation of membrane transport at structural and functional levels.
Ion channels, transporters and receptors connected to neurological disorders, metabolic diseases and cancer are principal areas of focus. We apply interdisciplinary approaches to investigate their structure, dynamics and function in situ and in vitro.
We are looking for dynamic and driven individuals with a recent (or expected) PhD or MD/PhD degree in biochemistry, biophysics, neuroscience, molecular genetics, cell biology, chemistry or related fields. A track-record of productivity is required. Ideal candidates will possess a strong work ethic, a broad curiosity and a passion for discovery. Expertise in membrane protein biochemistry, cell imaging, electrophysiology, single molecule biophysics, molecular dynamics, cryo-EM/ET or X-ray crystallography will be a plus but not required.
Successful candidates will be immersed in a friendly and inclusive training environment with a diverse and vibrant community of scientists and health professionals. The lab enjoys routine on-site access to superb resources including a newly established state-of-the-art cryo-EM facility housing a 300 kV Titan Krios G3i cryo-TEM equipped with a Volta phase plate, Gatan BioQuantum energy filter and K3 direct electron detector.
For an example of our recent work see Tillinghast et al, Molecular Cell 2021. Visit our website at https://sites.psu.edu/leelab to learn more about us. Interested applicants should submit a cover letter, CV and contact information of three references to Dr. Kenneth Lee (kenneth...@psu.edu).
Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status.




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD data

[Elke De Zitter]

Dear Saha, 

If you are not used to use ccp4 with the command line, you first need to tell 
your computer where to find the ccp4 programs by using the command "source". 
For example, I am working on a Mac, where ccp4 is installed in the Applications 
folder, so in a terminal I just have to run "source 
/Applications/ccp4-8.0/bin/ccp4.setup-sh" and then I can run the ccp4 command 
line toold such as mtzdmp. If you are using another operating system or if you 
have installed ccp4 elsewhere then the path to the setup script will be 
different. 

Also upon installing ccp4, you might also have the program "viewhk" which can 
open an mtz file and show its information. 

Good luck, 
Elke 


De: "Pedro Matias"  
À: CCP4BB@JISCMAIL.AC.UK 
Envoyé: Mardi 10 Mai 2022 15:08:34 
Objet: Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD data 



Shelxc/d/e require text files (either SHELX hkl or SCALEPACK sca format), not 
binary files like mtz. 

You can convert directly the XDS_ASCII.HKL from XDS to SHELX hkl with XDSCONV, 
which you can then input to shelxc to begin the pipeline. You still need to 
supply cell parameters and space group info, though. 


I recommend using the hkl instead of the sca file because you can create an 
unmerged file with all the measured observations and then you get a graphical 
analysis of the anomalous self-correlation. Ideally it should be very high 
(>80-90%) at low resolution and should not fall below 30% below about 2 A 
resolution. If you don't see this type of curve then it is highly unlikely that 
you will be able to solve your structure using S-SAD. Unless you used a very 
long wavelength to collect your data (~ 2A) the anomalous differences arising 
from the sulfur atoms are very small and you need a dataset with very high 
multiplicity to succeed. 

As an alternative, and if your crystals are good enough you can try soaks with 
1M KI before cryocooling your crystal. The iodide ions have a much higher 
anomalous signal, even at the Cu K-alpha wavelength, and even though nearly all 
sites will be only partially occupied, the multiplicity requirements are less 
stringent and it might be enough to solve your structure. 
Em 10/05/2022 13:51, Rituparna Saha escreveu: 



Thank you for the suggestions. I had searched the mtzdump in CCP4i, but didn't 
find any, I only found the mtz2various program. 
I am using the Shelxc/d/e suite. I had converted the ASCII.HKL file (the one 
that I had mentioned before) to mtz using Pointless. Then, when I used this 
file to run Shelxc/d/e, the job failed and I encountered errors each time. For 
this reason, I wanted to view and analyze the mtz file and HKL file. I donot 
know how to solve this problem as well. 
Kindly guide me if I went wrong anywhere here. 

On Tue, May 10, 2022 at 5:49 PM Pedro Matias < [ mailto:mat...@itqb.unl.pt | 
mat...@itqb.unl.pt ] > wrote: 

BQ_BEGIN



Hi there, 

I assume you processed the data with XDS. If so, you can use xdsconv to convert 
the file other formats, including mtz 

To analyze (view?) an mtz file you can use mtzdump. MTZ2Various is a format 
conversion program, just like xdsconv. You can convert directly to SCALEPACK 
format without a USER FORMAT option, and the output from a .sca file created 
from an mtz file with MTZ2various looks like this: 


BQ_BEGIN
1 
-987 
105.794 62.940 110.050 90.000 105.008 90.000 c 1 2 1 <-- cell parameters and SG 
info 
-73 1 3 5.1 5.1 7.5 4.5 <--- h,k,l, I+, sigI+, I-, sigI- (bijvoet mates) 
-73 1 4 -1.4 6.8 3.4 5.3 



What is the software you are using to solve the structure via S-SAD? I 
recomment the shelxc/d/e suite that can be easily run via the hkl2map GUI. 

Best, 

Pedro 
Em 10/05/2022 12:51, Rituparna Saha escreveu: 

BQ_BEGIN

Dear all, 
I am trying to solve a protein structure via S SAD phasing. I have the 
ASCII.HKL file, but whenever I opened the text file I couldn't understand which 
one is the F+ and F- values. 
Also, how can I read and analyze an mtz file? I tried using the MTZ2VARIOUS 
program in CCP4, where I changed it into USER FORMAT, it generated a .sca file, 
and the text file so generated did not have any labels (headers) inside it. It 
just gave me a list of values. 

Kindly guide me through this since I am really a novice in this field. 

-- 
-- 
- 

Regards, 
Rituparna Saha 
Research Scholar 
Bioseparation and Structural Biochemistry Lab 
Department of Biotechnology, IIT Kharagpur 








To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 
BQ_END

-- 
Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : [ mailto:mat...@itqb.unl.pt | mat...@itqb.unl.pt ] [ 

[ccp4bb] you do this

[Eleanor Dodson]

mtzdump hklin a.mtz
end


And you get this output

Look at the BOLD bit
Name of file
Cell and spacegroup

Column labels.
In this case the file I downloaded from the PDB only has F and SIGF
Resolution
etc..



mbat:Paul-5ACs eleanor$
*mtzdump hklin CCP4_JOBS/job_1/1_paul-5acs_obsout_import_merged.mtz*
*end*



 





 ###
 ###
 ###
 ### CCP4 8.0.017: MTZDUMP  version 1.1 : ##
 ###
 User: eleanor  Run date: 10/ 5/2022 Run time: 14:30:13


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67,
235-242.
 as well as any specific reference in the program write-up.





 Optional input follows.

 Keywords: RESO STATS LRESO HEAD NREF START SKIP SYMM
   BATCH FORMAT RUN/GO/END
 RESO max min - resolution limits for listing (default all)
 STATS [NBIN num] [RESO max min] - no. of reso. bins and limits for stats.
 LRESO -  S is given for each listed reflection
 HEAD - print MTZ file header only
 NREF num - number of reflections listed (default 10)
 START H0 K0 L0 - first reflection listed (default first)
 SKIP nskip - no. of refls. skipped before listing (default 0)
 SYMMETRY - list symmetry info
 VALM num - missing data set to this value
 BATCH - list batch orientation blocks

 FORMAT fmt - format of listed refls. .e.g. '(3i4,10f8.2)'
 RUN/GO/END - to start dump

end

 OPENED INPUT MTZ FILE
 Logical Name: HKLIN   Filename:
CCP4_JOBS/job_1/1_paul-5acs_obsout_import_merged.mtz

 * Title:

* Converted from mmCIF block r5achsf*

 * Base dataset:

0 HKL_base
  HKL_base
  HKL_base

 * Number of Datasets = 1








** Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
  1 5ach  r5achsf  r5achsf124.7000
 124.7000  124.7000   90.   90.   90. 0.96500*
 * Number of Columns = 5

 * Number of Reflections = 85015

 * Missing value set to NaN in input mtz file

 * HISTORY for current MTZ file :

 From gemmi-cif2mtz 0.5.2


 * Column Labels :

* H K L F SIGF*

 * Column Types :

* H H H F Q*

 * Associated datasets :

 0 0 0 1 1

 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)

  124.7000  124.7000  124.7000   90.   90.   90.




* *  Resolution Range :0.000580.61035 ( 41.567 -  1.280
A )*
 * Sort Order :

  0 0 0 0 0

* * Space group = 'P 41 3 2' (number 213)*



 OVERALL FILE STATISTICS for resolution range   0.001 -   0.610
 ===


 Col SortMinMaxNum  % Mean Mean   Resolution   Type
Column
 num order   Missing complete  abs.   LowHigh
label

   1 ASC  0  54  0  100.00 15.1 15.1  41.57   1.28   H
 H
   2 NONE 2  97  0  100.00 60.4 60.4  41.57   1.28   H
 K
   3 NONE 0  68  0  100.00 33.2 33.2  41.57   1.28   H
 L
   4 NONE   16.2  3974.1 0  100.00   242.33   242.33  41.57   1.28   F
 F
   5 NONE2.1   118.6 0  100.0012.1912.19  41.57   1.28   Q
 SIGF


 No. of reflections used in FILE STATISTICS85015



 LIST OF REFLECTIONS
 ===

0   3   1  278.29  8.60
0   3   2  342.46  5.19
0   3   3 1010.45 30.00
0   4   0   82.03  3.35
0   4   1 1294.37 19.13
0   4   2  735.01 10.92
0   4   3  748.28 12.81
0   4   4  776.90 23.13
0   5   1  111.05  2.73
0   5   2 1040.74 15.44

 MTZDUMP:   Normal termination of mtzdump
Times: User:   0.1s System:0.0s Elapsed: 0:04






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/

Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD data

[Pedro Matias]

Shelxc/d/e require text files (either SHELX hkl or SCALEPACK sca 
format), not binary files like mtz.


You can convert directly the XDS_ASCII.HKL from XDS to SHELX hkl with 
XDSCONV, which you can then input to shelxc to begin the pipeline. You 
still need to supply cell parameters and space group info, though.


I recommend using the hkl instead of the sca file because you can create 
an unmerged file with all the measured observations and then you get a 
graphical analysis of the anomalous self-correlation. Ideally it should 
be very high (>80-90%) at low resolution and should not fall below 30% 
below about 2 A resolution. If you  don't see this type of curve then it 
is highly unlikely that you will be able to solve your structure using 
S-SAD. Unless you used a very long wavelength to collect your data (~ 
2A) the anomalous differences arising from the sulfur atoms are very 
small and you need a dataset with very high multiplicity to succeed.


As an alternative, and if your crystals are good enough you can try 
soaks with 1M KI before cryocooling your crystal. The iodide ions have a 
much higher anomalous signal, even at the Cu K-alpha wavelength, and 
even though nearly all sites will be only partially occupied, the 
multiplicity requirements are less stringent and it might be enough to 
solve your structure.


Em 10/05/2022 13:51, Rituparna Saha escreveu:
Thank you for the suggestions. I had searched the mtzdump in CCP4i, 
but didn't find any, I only found the mtz2various program.
I am using the Shelxc/d/e suite. I had converted the ASCII.HKL file 
(the one that I had mentioned before) to mtz using Pointless. Then, 
when I used this file to run Shelxc/d/e, the job failed and I 
encountered errors each time. For this reason, I wanted to view and 
analyze the mtz file and HKL file. I donot know how to solve this 
problem as well.

Kindly guide me if I went wrong anywhere here.

On Tue, May 10, 2022 at 5:49 PM Pedro Matias  wrote:

Hi there,

I assume you processed the data with XDS. If so, you can use
xdsconv to convert the file other formats, including mtz

To analyze (view?) an mtz file you can use mtzdump. MTZ2Various is
a format conversion program, just like xdsconv. You can convert
directly to SCALEPACK format without a USER FORMAT option, and the
output from a .sca file created from an mtz file with MTZ2various
looks like this:


    1
 -987
   105.794    62.940   110.050    90.000   105.008 90.000 c 1 2
1   <-- cell parameters and SG info
 -73   1   3 5.1 5.1 7.5 4.5 <--- h,k,l, I+,
sigI+, I-, sigI- (bijvoet mates)
 -73   1   4    -1.4 6.8 3.4 5.3


What is the software you are using to solve the structure via
S-SAD? I recomment the shelxc/d/e suite that can be easily run via
the hkl2map GUI.

Best,

Pedro

Em 10/05/2022 12:51, Rituparna Saha escreveu:

Dear all,
I am trying to solve a protein structure via S SAD phasing. I
have the ASCII.HKL file, but whenever I opened the text file I
couldn't understand which one is the F+ and F- values.
Also, how can I read and analyze an mtz file? I tried using the
MTZ2VARIOUS program in CCP4, where I changed it into USER FORMAT,
it generated a .sca file, and the text file so generated did not
have any labels (headers) inside it. It just gave me a list of
values.

Kindly guide me through this since I am really a novice in this
field.

-- 
-- 
-


Regards,
Rituparna Saha
Research Scholar
Bioseparation and Structural Biochemistry Lab
Department of Biotechnology, IIT Kharagpur







To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1


-- 
Industry and Medicine Applied Crystallography

Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
  (351-21) 446-9669 (direct)
  Fax   : (351-21) 441-1277 or 443-3644

email :mat...@itqb.unl.pt


http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8



--
--
-

Regards,
Rituparna Saha
Research Scholar
Bioseparation and Structural Biochemistry Lab
Department of Biotechnology, IIT Kharagpur





--
Industry and Medicine Applied 

Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD data

[Robbie Joosten]

mtzdump is a command line tool, so you have run it from a terminal. There is 
also a shorthand version for lazy people like me (notice the missing 'u'): 
mtzdmp something.mtz

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of
> Rituparna Saha
> Sent: Tuesday, May 10, 2022 14:51
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD
> data
> 
> Thank you for the suggestions. I had searched the mtzdump in CCP4i, but
> didn't find any, I only found the mtz2various program.
> 
> I am using the Shelxc/d/e suite. I had converted the ASCII.HKL file (the one
> that I had mentioned before) to mtz using Pointless. Then, when I used this
> file to run Shelxc/d/e, the job failed and I encountered errors each time. For
> this reason, I wanted to view and analyze the mtz file and HKL file. I donot
> know how to solve this problem as well.
> 
> Kindly guide me if I went wrong anywhere here.
> 
> 
> On Tue, May 10, 2022 at 5:49 PM Pedro Matias   > wrote:
> 
> 
>   Hi there,
> 
>   I assume you processed the data with XDS. If so, you can use xdsconv
> to convert the file other formats, including mtz
> 
>   To analyze (view?) an mtz file you can use mtzdump. MTZ2Various is
> a format conversion program, just like xdsconv. You can convert directly to
> SCALEPACK format without a USER FORMAT option, and the output from a
> .sca file created from an mtz file with MTZ2various looks like this:
> 
> 
> 
>   1
>-987
>  105.79462.940   110.05090.000   105.00890.000 c 
> 1 2
> 1   <-- cell parameters and SG info
>-73   1   3 5.1 5.1 7.5 4.5 <--- h,k,l, I+, 
> sigI+, I-, sigI-
> (bijvoet mates)
>-73   1   4-1.4 6.8 3.4 5.3
> 
> 
> 
>   What is the software you are using to solve the structure via S-SAD? I
> recomment the shelxc/d/e suite that can be easily run via the hkl2map GUI.
> 
> 
> 
>   Best,
> 
>   Pedro
> 
> 
>   Em 10/05/2022 12:51, Rituparna Saha escreveu:
> 
> 
>   Dear all,
>   I am trying to solve a protein structure via S SAD phasing. I
> have the ASCII.HKL file, but whenever I opened the text file I couldn't
> understand which one is the F+ and F- values.
> 
>   Also, how can I read and analyze an mtz file? I tried using the
> MTZ2VARIOUS program in CCP4, where I changed it into USER FORMAT, it
> generated a .sca file, and the text file so generated did not have any labels
> (headers) inside it. It just gave me a list of values.
> 
>   Kindly guide me through this since I am really a novice in this
> field.
> 
>   --
> 
>   --
> 
>   -
> 
>   Regards,
>   Rituparna Saha
> 
>   Research Scholar
>   Bioseparation and Structural Biochemistry Lab
>   Department of Biotechnology, IIT Kharagpur
> 
> 
> 
> 
> 
> 
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-bin/WA-
> JISC.exe?SUBED1=CCP4BB=1
> 
>   --
>   Industry and Medicine Applied Crystallography
>   Macromolecular Crystallography Unit
>   ___
>   Phones : (351-21) 446-9100 Ext. 1669
>(351-21) 446-9669 (direct)
>Fax   : (351-21) 441-1277 or 443-3644
> 
>   email : mat...@itqb.unl.pt 
> 
>   http://www.itqb.unl.pt/research/biological-chemistry/industry-and-
> medicine-applied-crystallography
>   http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
> 
>   Mailing address :
>   Instituto de Tecnologia Quimica e Biologica António Xavier
>   Universidade Nova de Lisboa
>   Av. da República
>   2780-157 Oeiras
>   PORTUGAL
> 
>   ITQB NOVA, a great choice for your PhD
>   https://youtu.be/de6j-aaTWNQ
> 
>   Master Programme in Biochemistry for Health
>   https://youtu.be/UKstDCFjYI8
> 
> 
> 
> --
> 
> --
> 
> -
> 
> Regards,
> Rituparna Saha
> 
> Research Scholar
> Bioseparation and Structural Biochemistry Lab Department of Biotechnology,
> IIT Kharagpur
> 
> 
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




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/

Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD data

[Rituparna Saha]

Thank you for the suggestions. I had searched the mtzdump in CCP4i, but
didn't find any, I only found the mtz2various program.
I am using the Shelxc/d/e suite. I had converted the ASCII.HKL file (the
one that I had mentioned before) to mtz using Pointless. Then, when I used
this file to run Shelxc/d/e, the job failed and I encountered errors each
time. For this reason, I wanted to view and analyze the mtz file and HKL
file. I donot know how to solve this problem as well.
Kindly guide me if I went wrong anywhere here.

On Tue, May 10, 2022 at 5:49 PM Pedro Matias  wrote:

> Hi there,
>
> I assume you processed the data with XDS. If so, you can use xdsconv to
> convert the file other formats, including mtz
>
> To analyze (view?) an mtz file you can use mtzdump. MTZ2Various is a
> format conversion program, just like xdsconv. You can convert directly to
> SCALEPACK format without a USER FORMAT option, and the output from a .sca
> file created from an mtz file with MTZ2various looks like this:
>
> 1
>  -987
>105.79462.940   110.05090.000   105.00890.000 c 1 2 1   <--
> cell parameters and SG info
>  -73   1   3 5.1 5.1 7.5 4.5 <--- h,k,l, I+, sigI+, I-,
> sigI- (bijvoet mates)
>  -73   1   4-1.4 6.8 3.4 5.3
>
>
> What is the software you are using to solve the structure via S-SAD? I
> recomment the shelxc/d/e suite that can be easily run via the hkl2map GUI.
>
> Best,
>
> Pedro
> Em 10/05/2022 12:51, Rituparna Saha escreveu:
>
> Dear all,
> I am trying to solve a protein structure via S SAD phasing. I have the
> ASCII.HKL file, but whenever I opened the text file I couldn't understand
> which one is the F+ and F- values.
> Also, how can I read and analyze an mtz file? I tried using the
> MTZ2VARIOUS program in CCP4, where I changed it into USER FORMAT, it
> generated a .sca file, and the text file so generated did not have any
> labels (headers) inside it. It just gave me a list of values.
>
> Kindly guide me through this since I am really a novice in this field.
>
> --
> --
> -
>
> Regards,
> Rituparna Saha
> Research Scholar
> Bioseparation and Structural Biochemistry Lab
> Department of Biotechnology, IIT Kharagpur
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> --
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___
> Phones : (351-21) 446-9100 Ext. 1669
>  (351-21) 446-9669 (direct)
>  Fax   : (351-21) 441-1277 or 443-3644
>
> email : mat...@itqb.unl.pt
> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallographyhttp://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
>
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica António Xavier
> Universidade Nova de Lisboa
> Av. da República
> 2780-157 Oeiras
> PORTUGAL
>
> ITQB NOVA, a great choice for your PhDhttps://youtu.be/de6j-aaTWNQ
>
> Master Programme in Biochemistry for Healthhttps://youtu.be/UKstDCFjYI8
>
>

-- 
-- 
-

Regards,
Rituparna Saha
Research Scholar
Bioseparation and Structural Biochemistry Lab
Department of Biotechnology, IIT Kharagpur



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/

Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD data

[Eleanor Dodson]

If you run mtzdump hklin your.mtz
the first output is descriptive.
Have you done that?

You will get "header" information about cell, selected symmetry, etc, and a
list of labels for the columns

That will start H K L then maybe F+ SIGF+ F- SIGF-
or I+ SIGI+ I_ SIGI-
or something else.
Can you send the BB the header you get.. Thn we can be more useful!
Eleanor

On Tue, 10 May 2022 at 13:20, Pedro Matias  wrote:

> Hi there,
>
> I assume you processed the data with XDS. If so, you can use xdsconv to
> convert the file other formats, including mtz
>
> To analyze (view?) an mtz file you can use mtzdump. MTZ2Various is a
> format conversion program, just like xdsconv. You can convert directly to
> SCALEPACK format without a USER FORMAT option, and the output from a .sca
> file created from an mtz file with MTZ2various looks like this:
>
> 1
>  -987
>105.79462.940   110.05090.000   105.00890.000 c 1 2 1   <--
> cell parameters and SG info
>  -73   1   3 5.1 5.1 7.5 4.5 <--- h,k,l, I+, sigI+, I-,
> sigI- (bijvoet mates)
>  -73   1   4-1.4 6.8 3.4 5.3
>
>
> What is the software you are using to solve the structure via S-SAD? I
> recomment the shelxc/d/e suite that can be easily run via the hkl2map GUI.
>
> Best,
>
> Pedro
> Em 10/05/2022 12:51, Rituparna Saha escreveu:
>
> Dear all,
> I am trying to solve a protein structure via S SAD phasing. I have the
> ASCII.HKL file, but whenever I opened the text file I couldn't understand
> which one is the F+ and F- values.
> Also, how can I read and analyze an mtz file? I tried using the
> MTZ2VARIOUS program in CCP4, where I changed it into USER FORMAT, it
> generated a .sca file, and the text file so generated did not have any
> labels (headers) inside it. It just gave me a list of values.
>
> Kindly guide me through this since I am really a novice in this field.
>
> --
> --
> -
>
> Regards,
> Rituparna Saha
> Research Scholar
> Bioseparation and Structural Biochemistry Lab
> Department of Biotechnology, IIT Kharagpur
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> --
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___
> Phones : (351-21) 446-9100 Ext. 1669
>  (351-21) 446-9669 (direct)
>  Fax   : (351-21) 441-1277 or 443-3644
>
> email : mat...@itqb.unl.pt
> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallographyhttp://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
>
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica António Xavier
> Universidade Nova de Lisboa
> Av. da República
> 2780-157 Oeiras
> PORTUGAL
>
> ITQB NOVA, a great choice for your PhDhttps://youtu.be/de6j-aaTWNQ
>
> Master Programme in Biochemistry for Healthhttps://youtu.be/UKstDCFjYI8
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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/

Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD data

[Pedro Matias]

Hi there,

I assume you processed the data with XDS. If so, you can use xdsconv to 
convert the file other formats, including mtz


To analyze (view?) an mtz file you can use mtzdump. MTZ2Various is a 
format conversion program, just like xdsconv. You can convert directly 
to SCALEPACK format without a USER FORMAT option, and the output from a 
.sca file created from an mtz file with MTZ2various looks like this:



    1
 -987
   105.794    62.940   110.050    90.000   105.008    90.000 c 1 2 1   
<-- cell parameters and SG info
 -73   1   3 5.1 5.1 7.5 4.5 <--- h,k,l, I+, sigI+, 
I-, sigI- (bijvoet mates)

 -73   1   4    -1.4 6.8 3.4 5.3

What is the software you are using to solve the structure via S-SAD? I 
recomment the shelxc/d/e suite that can be easily run via the hkl2map GUI.


Best,

Pedro

Em 10/05/2022 12:51, Rituparna Saha escreveu:

Dear all,
I am trying to solve a protein structure via S SAD phasing. I have the 
ASCII.HKL file, but whenever I opened the text file I couldn't 
understand which one is the F+ and F- values.
Also, how can I read and analyze an mtz file? I tried using the 
MTZ2VARIOUS program in CCP4, where I changed it into USER FORMAT, it 
generated a .sca file, and the text file so generated did not have any 
labels (headers) inside it. It just gave me a list of values.


Kindly guide me through this since I am really a novice in this field.

--
--
-

Regards,
Rituparna Saha
Research Scholar
Bioseparation and Structural Biochemistry Lab
Department of Biotechnology, IIT Kharagpur







To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 




--
Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email :mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8



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/

[ccp4bb] Problem with understanding mtz and hkl files of S SAD data

[Rituparna Saha]

Dear all,
I am trying to solve a protein structure via S SAD phasing. I have the
ASCII.HKL file, but whenever I opened the text file I couldn't understand
which one is the F+ and F- values.
Also, how can I read and analyze an mtz file? I tried using the MTZ2VARIOUS
program in CCP4, where I changed it into USER FORMAT, it generated a .sca
file, and the text file so generated did not have any labels (headers)
inside it. It just gave me a list of values.

Kindly guide me through this since I am really a novice in this field.

-- 
-- 
-

Regards,
Rituparna Saha
Research Scholar
Bioseparation and Structural Biochemistry Lab
Department of Biotechnology, IIT Kharagpur



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/

[ccp4bb] Postdoc position at IECB, Bordeaux, France

[Pierre Maisonneuve]

Dear colleagues, 
 
We have an open position for a highly motivated postdoctoral candidate in my 
group at the European Institute of Chemistry and Biology (IECB) to investigate 
the structural basis of the regulation protein kinases and pseudokinases 
receptors in human signaling by using cryo-EM and X-ray crystallography. 
 
Applicants must have a Ph.D. (or due to complete within 6 months) in 
biochemistry, biophysics, life science or related fields. We are seeking a 
person with expertise in protein biochemistry (ideally in membrane protein) and 
with knowledge in single-particle electron microscopy (cryo-EM). Previous 
experience in protein expression in eukaryotic cells (insect and human) is 
preferred but not required.

The position is funded for 2 years, but the candidate is encouraged to apply 
for additional postdoctoral funding.

The candidate will join an exciting and multidisciplinary scientific 
environment with on-site access to cutting-edge facilities in cryo-EM (housing 
a 200kV Arctica equipped with a K2 summit camera and soon to come 200kV 
Cryo-electron microscope equipped with an energy filter and last generation 
direct detector), X-Ray crystallography, NMR, Biochemistry, Biophysics, 
molecular biology and cell biology. The project involved international 
collaborations with cell biologists for complementary characterization of 
protein function in cell and in mice.  

Interested applicants should submit a cover letter, CV and contact information 
of 2 references here:  
https://emploi.cnrs.fr/Offres/CDD/UMR5248-PIEMAI-001/Default.aspx?lang=EN 

 
The deadline for the application is May 30th. The starting date for this 
position is October 1st.

Example of work that we are developing in the lab:
 
Posternak G*, Tang X*, Maisonneuve P*, Jin T*, Lavoie H* et al., Functional 
characterization of a PROTAC directed against BRAF mutant V600E. Nature 
Chemical Biology. 2020 Nov;16(11):1170-1178. *Equal Contribution
 
Lavoie H*, Sahmi M*, Maisonneuve P* et al., MEK drives BRAF activation through 
allosteric control of KSR proteins. Nature. 2018 Feb 22;554(7693):549-553. 
*Equal Contribution

Best,

Pierre

*
Pierre Maisonneuve Ph.D.

Group Leader
UMR 5248 - Chemistry & Biology of Membranes and Nano-Objects
CNRS - Université de Bordeaux

Institut Européen de Chimie et Biologie
Phone: +33(0)5 40 00 35 88
@: p.maisonne...@iecb.u-bordeaux.fr 
2 rue Robert Escarpit, 
33607 Pessac, France
**
Please consider the environment before printing this email.


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/