Thank you everyone for the suggestions. I can now view and read the mtz files.
On Tue, May 10, 2022 at 8:54 PM Elke De Zitter <elke.de-zit...@ibs.fr> wrote: > 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" <mat...@itqb.unl.pt> > *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 <mat...@itqb.unl.pt> 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&A=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 > > > > > -- > 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&A=1 > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > -- -- ------------------------- 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&A=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/
