Re: [ccp4bb] HKL to mtz

[Engin Özkan]

By HKL, I assume you mean an XDS output file. In that case, xdsconv from 
the XDS package works. Pick one of the CCP4 formats (like CCP4_I+F). 
Then, xdsconv essentially tells you to run f2mtz and cad (I think) with 
certain options. It does employ a French-Wilson scheme for converting 
negative intensities, if you like that.


I had been encountering (for a long time) one issue, though. The 
OUTPUT_FILE parameter seems to not take effect (at least in the CCP4_I+F 
format) and defaults to something like output_file.mtz within the 
commands xdsconv instructs you to type. Manually change it.


Engin

On 10/5/17 10:26 PM, Edward A. Berry wrote:

On 10/05/2017 11:01 PM, ameya benz wrote:

Hi,

I want to convert HKL file to mtz. I tried using F2mtz but somehow 
the output mtz is not working. What parameters should I set during 
conversion. Or can anyone suggest alternative to F2mtz?


regards,
Ameya
National chemical laboratory, Pune, India


Hi, Ameya,
F2mtz works.
In order for someone to help you you need to give more information.
What does your HKL file look like (show us the first 10-20 lines)?
Are you running f2mtz from one of the GUIs, or from a a script or 
commandline?
What parameters did you give (or what was your script)? (often the 
FORMAT statement is the problem).
And in what way the output mtz file is not working? maybe use mtzdump 
to show what you got.

Hope that will lead to a speedy resolution!


--
Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu

Re: [ccp4bb] HKL to mtz

[Edward A. Berry]

On 10/05/2017 11:01 PM, ameya benz wrote:

Hi,

I want to convert HKL file to mtz. I tried using F2mtz but somehow the output 
mtz is not working. What parameters should I set during conversion. Or can 
anyone suggest alternative to F2mtz?

regards,
Ameya
National chemical laboratory, Pune, India


Hi, Ameya,
F2mtz works.
In order for someone to help you you need to give more information.
What does your HKL file look like (show us the first 10-20 lines)?
Are you running f2mtz from one of the GUIs, or from a a script or commandline?
What parameters did you give (or what was your script)? (often the FORMAT 
statement is the problem).
And in what way the output mtz file is not working? maybe use mtzdump to show 
what you got.
Hope that will lead to a speedy resolution!

Re: [ccp4bb] HKL to mtz

[Wojtas, Lukasz]

Use XPREP to convert HKL to SCA file  (options D and W) then CCP4 to get MTZ,


Lukasz Wojtas


From: CCP4 bulletin board  on behalf of ameya benz 

Sent: Thursday, October 5, 2017 11:01:35 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] HKL to mtz

Hi,

I want to convert HKL file to mtz. I tried using F2mtz but somehow the output 
mtz is not working. What parameters should I set during conversion. Or can 
anyone suggest alternative to F2mtz?

regards,
Ameya
National chemical laboratory, Pune, India

[ccp4bb] HKL to mtz

[ameya benz]

Hi,

I want to convert HKL file to mtz. I tried using F2mtz but somehow the
output mtz is not working. What parameters should I set during conversion.
Or can anyone suggest alternative to F2mtz?

regards,
Ameya
National chemical laboratory, Pune, India

Re: [ccp4bb] Off topic: denaturing urea gels

[Mohammad Khan]

Dear all,

Thanks for all the replies. I adjusted my volumes and stopped reactions
with 8 M urea and 25 mM EDTA. The gels now run fine :)

-Mohammad

On 05-Oct-2017 7:29 PM, "Phoebe A. Rice"  wrote:

> Even though the protein should be denatured by all that urea, we find such
> gels sometimes look nicer if stop the reaction with SDS and protease K,
> and/or phenol extract the remains of the protein before loading the
> high-urea gel.
>
> ++
>
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> pr...@uchicago.edu
>
>
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Opher
> Gileadi [opher.gile...@sgc.ox.ac.uk]
> Sent: Saturday, September 30, 2017 3:44 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Off topic: denaturing urea gels
>
> In addition to the previous suggestions:
>
> With very small gels, the sample composition and depth (in the well) have
> a strong effect on the resolution.
> Rinse the wells with TBE buffer just before loading, as urea from the gel
> diffuses into the well and may prevent the sample from settling at the
> bottom. Minimize the amount of salt in the samples; try to load very small
> volumes (1-3 ul), even if this means longer exposures later.

Re: [ccp4bb] Off topic: denaturing urea gels

[Phoebe A. Rice]

Even though the protein should be denatured by all that urea, we find such gels 
sometimes look nicer if stop the reaction with SDS and protease K, and/or 
phenol extract the remains of the protein before loading the high-urea gel.

++

Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
pr...@uchicago.edu



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Opher Gileadi 
[opher.gile...@sgc.ox.ac.uk]
Sent: Saturday, September 30, 2017 3:44 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off topic: denaturing urea gels

In addition to the previous suggestions:

With very small gels, the sample composition and depth (in the well) have a 
strong effect on the resolution.
Rinse the wells with TBE buffer just before loading, as urea from the gel 
diffuses into the well and may prevent the sample from settling at the bottom. 
Minimize the amount of salt in the samples; try to load very small volumes (1-3 
ul), even if this means longer exposures later.

[ccp4bb] Beam time available at CHESS

[Doletha Marian Szebenyi]

Beamtime for MX still available at CHESS, Nov. 1 - Dec. 21, 2017


The CHESS/MacCHESS facility, located at Cornell University in Ithaca, NY, 
invites macromolecular crystallographers to apply for time on our F1 station.

This station is well equipped for crystallographic data collection, for MR or 
Se SAD phasing. It features a Dectris Pilatus3 6M detector and an ALS-type 
automounter. We offer remote and mail-in modes of data collection, and our 
expert staff provides exceptional support 24/7. "Non-standard" experiments 
needing some special setup are welcome.

Apply for time on-line at http://userdb.chess.cornell.edu. Applications are 
accepted at any time, and turn-around time can be just a couple of weeks - less 
if you already have a proposal in our system and just need to submit a beamtime 
request.

For more information see the web site http://www.chess.cornell.edu, or contact 
administrator Kathy Dedrick, k...@cornell.edu.

= A special option ==

Pressure cryocooling of (unfrozen) crystals is available by prearrangement. 
This method can reduce the damage induced by cryocooling, often with no need 
for cryoprotectants (Kim et al., Acta Cryst. D61, 881-890 (2005)). In some 
cases, it can reduce initial disorder (high mosaicity, anisotropic diffraction, 
some kinds of twinning). Contact Marian Szebenyi (dm...@cornell.edu) if you 
have questions about pressure cryocooling.

Re: [ccp4bb] PDB search help

[John Berrisford]

Dear Rajesh

 

 

This is possible with our search API

See:

http://www.ebi.ac.uk/pdbe/api/doc/search.html

 

For example 

https://www.ebi.ac.uk/pdbe/search/pdb/select?q=pfam_name:Lipocalin 
 
=json

 

then for each result you will need to compare “number_of_polymer_residues” and 
“max_observed_residues”. This will give you the observed ratio for each 
molecule (results are per molecule, not per PDB entry) in your result.

 

To make your query you can use our standard search page (pdbe.org) and with a 
small amount of reformatting use the same query in our search API. 

For example:

If you did a search on a main page the URL would look something like this:

https://www.ebi.ac.uk/pdbe/entry/search/index?text:hemoglobin 

 
_name:%22Neural%20hemoglobin%22_composition:%22protein%20structure%22_type:Protein

with all the search parameters encoded in the URL.

To use this in the API – take the part after the ? and change & to “ AND “ – 
the spaces are important here. 

i.e. 

text:hemoglobin_name:"Neural%20hemoglobin"_composition:"protein%20structure"_type:Protein

becomes

text:haemoglobin AND molecule_name:"Neural%20hemoglobin" AND 
assembly_composition:"protein%20structure" AND molecule_type:Protein

then append this to our search API URL 
(https://www.ebi.ac.uk/pdbe/search/pdb/select?q=)

https://www.ebi.ac.uk/pdbe/search/pdb/select?q=text:hemoglobin AND 
molecule_name:"Neural%20hemoglobin" AND 
assembly_composition:"protein%20structure" AND molecule_type:Protein

and then if you prefer JSON format to XML add =json to the end.  

https://www.ebi.ac.uk/pdbe/search/pdb/select?q=text:hemoglobin AND 
molecule_name:"Neural%20hemoglobin" AND 
assembly_composition:"protein%20structure" AND molecule_type:Protein=json

By default this will get you 10 result – to get more add =10 to the end 
and change 10 to a larger number. 

 

 

Hope this helps

 

John

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh
Sent: 27 September 2017 23:48
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PDB search help

 

Dear BB,

Sorry for the off topic. 

Does anyone know how to search the PDB for the entries that have the density 
only for part of the protein molecule rather than for the entire length of the 
protein attempted to crystallize?

 

 

Thanks,

Rajesh..