Re: [ccp4bb] Convert .cif to mtz
Hi Madhu, You don't need to use scala, d*trek can do the job as well. The easiest thing to do is to continue with d*trek to scale and merge your data and then input this scaled and merged file into Dtrek2mtz. Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Fri, 24 Jun 2011, Madhu shankar Madhu shankar wrote: HI Eric, I havent yet done the scala ,i have just indexed and integrated the data in d*trek. I tried converting the .cif in Dtrek2mtz but thats failed. Thanks Madhu
Re: [ccp4bb] Convert .cif to mtz
The preferred general route into CCP4 for unmerged data for scaling and merging
(if that is what you want to do) is through Pointless into Scala (or in future
Aimless as a Scala replacement, or the future merged Pointless/Aimless
("nameless")).
At present Pointless will accept data from Mosflm, XDS, and Saint for further
scaling or just merging, and Scalepack or ShelX format for merging (though I
have no reason to suppose that there is anything wrong with the scaling in
other packages, nor that Scala is any better)
As far as I can see the correct CCP4 program for getting unmerged d*trek data
into Scala is dtrek2scala. dtrek2mtz is for already scaled & merged data (I
haven't tried either of them)
Phil
On 24 Jun 2011, at 05:08, Madhu shankar Madhu shankar wrote:
> HI Eric,
> I havent yet done the scala ,i have just indexed and integrated the
> data in d*trek. I tried converting the .cif in Dtrek2mtz but thats failed.
> Thanks Madhu
Re: [ccp4bb] Convert .cif to mtz
HI Eric, I havent yet done the scala ,i have just indexed and integrated the data in d*trek. I tried converting the .cif in Dtrek2mtz but thats failed. Thanks Madhu
Re: [ccp4bb] Convert .cif to mtz
Madhu, I just noticed that your message said you "indexed and integrated" your data. Did you scale it with d*trek too (that needs to be done before using Dtrek2mtz) or are you looking to use the integrated d*trek reflections for subsequent scaling in ccp4 with scala? Eric On Thu, 23 Jun 2011, Eric Larson wrote: Hi Madhu, D*trek is what you processed your data with. In the ccp4i gui, select the program "Dtrek2mtz" and then in the field that says "convert scaled data output from ... ", select "d*trek" from the pull down menu. Go to http://www.ccp4.ac.uk/html/dtrek2mtz.html for more information. good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Fri, 24 Jun 2011, Madhu shankar Madhu shankar wrote: HI, I indexed and integrated data from RAXIS(Rigaku) detector on 'Crystalclear'. It gave me a .cif file as output.I am not able to read this file in ccp4 to carry out rest of the analysis in ccp4. I want to know how to convert this cif file to MTZ. Thanks Madhu
Re: [ccp4bb] Convert .cif to mtz
Hi Madhu, D*trek is what you processed your data with. In the ccp4i gui, select the program "Dtrek2mtz" and then in the field that says "convert scaled data output from ... ", select "d*trek" from the pull down menu. Go to http://www.ccp4.ac.uk/html/dtrek2mtz.html for more information. good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Fri, 24 Jun 2011, Madhu shankar Madhu shankar wrote: HI, I indexed and integrated data from RAXIS(Rigaku) detector on 'Crystalclear'. It gave me a .cif file as output.I am not able to read this file in ccp4 to carry out rest of the analysis in ccp4. I want to know how to convert this cif file to MTZ. Thanks Madhu
Re: [ccp4bb] Convert .cif to mtz
Easiest way: CCP4i Reflection Data Utilities Convert to MTZ -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Madhu shankar Madhu shankar Sent: Thursday, June 23, 2011 5:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Convert .cif to mtz HI, I indexed and integrated data from RAXIS(Rigaku) detector on 'Crystalclear'. It gave me a .cif file as output.I am not able to read this file in ccp4 to carry out rest of the analysis in ccp4. I want to know how to convert this cif file to MTZ. Thanks Madhu
[ccp4bb] Convert .cif to mtz
HI, I indexed and integrated data from RAXIS(Rigaku) detector on 'Crystalclear'. It gave me a .cif file as output.I am not able to read this file in ccp4 to carry out rest of the analysis in ccp4. I want to know how to convert this cif file to MTZ. Thanks Madhu
Re: [ccp4bb] convert .cif to .mtz
I'm looking for a convenient way of converting a .cif structure factor file (from PDB) to a map-file (e.g. .mtz) to open with COOT for example..? Already tried ccp4i with 'Convert to/modify/extend MTZ', but got a bunch of errors when opening with coot.. doesn't coot have an 'import from EDS' option (or somesuch)? why not use that? or if you really want to get the mtz or map file yourself, you can fetch them from EDS (http://eds.bmc.uu.se/) --dvd ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell & Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] convert .cif to .mtz
In recent coots, (This is 0.4.1, kendall, on a mac or linux) you no longer need to calculate fcalc and phases. If you choose auto open mtz and have at least one pdb file open, coot will ask you which pdb file to use to calculate fcalc and phases. (I guess it runs refmac then) and, voila, the maps are displayed. Sue On Jan 29, 2008, at 8:37 AM, Eleanor Dodson wrote: It has just worked for me? convert to mtz file type mmCIF then I had to put in my own cell and spacegroup. And I will have to calculate phases before I can use coot with it.. Eleanor Eleanor It looks like this.. # _audit.revision_id1_0 _audit.creation_date 2005-03-22 _audit.update_record 'Initial release' # loop_ _refln.wavelength_id _refln.crystal_id _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.status 1 100 -51 0.0 0.000 1 110 -51 0.0 0.000 1 140 -51 0.0 0.000 1 101 -51 0.0 0.000 1 111 -51 0.0 0.000 1 121 -51 0.0 0.000 Kristof Van Hecke wrote: Dear all, I'm looking for a convenient way of converting a .cif structure factor file (from PDB) to a map-file (e.g. .mtz) to open with COOT for example..? Already tried ccp4i with 'Convert to/modify/extend MTZ', but got a bunch of errors when opening with coot.. Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm Sue Roberts Biochemistry & Biophysics University of Arizona [EMAIL PROTECTED]
Re: [ccp4bb] convert .cif to .mtz
The underlying program cif2mtz will convert everything it can recognise, i.e. it will convert intensities or amplitudes or both, depending on what is there. But what is actually in a PDB cif structure factor file varies greatly. For a start, there's a high chance there are no phases, so no map without doing an extra step (simplest would be a couple of rounds of refinement in refmac and take the map coefficients produced into Coot). Hard to say more without details Martyn On Tue, 2008-01-29 at 16:35 +0100, Tim Gruene wrote: > The GUI actually is a quite convenient way. In my experience, however, the > GUI or the program called by the GUI does not check whether the cif > contains intensities or amplitudes. So you can use the GUI, look at the > script it generates and adjust it according to the header in your cif. > > Tim > > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > > On Tue, 29 Jan 2008, Kristof Van Hecke wrote: > > > Dear all, > > > > I'm looking for a convenient way of converting a .cif structure factor file > > (from PDB) to a map-file (e.g. .mtz) to open with COOT for example..? > > Already tried ccp4i with 'Convert to/modify/extend MTZ', but got a bunch of > > errors when opening with coot.. > > > > Many thanks > > > > Kristof > > -- > > Kristof Van Hecke, PhD > > Biomoleculaire Architectuur > > Celestijnenlaan 200 F > > B-3001 Heverlee (Leuven) > > Tel: +32(0)16327477 > > -- > > > > > > > > > > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] * * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] convert .cif to .mtz
It has just worked for me? convert to mtz file type mmCIF then I had to put in my own cell and spacegroup. And I will have to calculate phases before I can use coot with it.. Eleanor Eleanor It looks like this.. # _audit.revision_id1_0 _audit.creation_date 2005-03-22 _audit.update_record 'Initial release' # loop_ _refln.wavelength_id _refln.crystal_id _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.status 1 100 -51 0.0 0.000 1 110 -51 0.0 0.000 1 140 -51 0.0 0.000 1 101 -51 0.0 0.000 1 111 -51 0.0 0.000 1 121 -51 0.0 0.000 Kristof Van Hecke wrote: Dear all, I'm looking for a convenient way of converting a .cif structure factor file (from PDB) to a map-file (e.g. .mtz) to open with COOT for example..? Already tried ccp4i with 'Convert to/modify/extend MTZ', but got a bunch of errors when opening with coot.. Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
Re: [ccp4bb] convert .cif to .mtz
The GUI actually is a quite convenient way. In my experience, however, the GUI or the program called by the GUI does not check whether the cif contains intensities or amplitudes. So you can use the GUI, look at the script it generates and adjust it according to the header in your cif. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 29 Jan 2008, Kristof Van Hecke wrote: Dear all, I'm looking for a convenient way of converting a .cif structure factor file (from PDB) to a map-file (e.g. .mtz) to open with COOT for example..? Already tried ccp4i with 'Convert to/modify/extend MTZ', but got a bunch of errors when opening with coot.. Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] convert .cif to .mtz
Dear all, I'm looking for a convenient way of converting a .cif structure factor file (from PDB) to a map-file (e.g. .mtz) to open with COOT for example..? Already tried ccp4i with 'Convert to/modify/extend MTZ', but got a bunch of errors when opening with coot.. Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
