Thank you for the reply. Like I pointed out please provide video tutorials organic and inorganic compounds. This will make the tutorials cover all materials and make it complete . Thank you.
Firstly, let me congratulate you for this excellent job. Profex is very flexible, with several unique features and easy to follow. I started learning Profex from downloaded tutorials last year. But these series of videos, all of which i have watched, are far more explanatory and easier to follow once you have read the manual. My questions , how do you obtain information on non XRDML/BRML files for instrument configuration? Also, can you provide a video on refinement of organic compounds and other synthetic materials, including inorganic?Most of the tutorials are on minerals.
Some other file formats are simple text files which may or may not contain hardware information. But it is almost impossible to find hardware information in binary raw files without having access to the file format specifications. They just set flags somewhere in the data, for example a "1" at byte position 256 may stand for "detector x". Reverse engineering these formats is very time consuming and not always completely possible. Most Profex import filters only read the measured data and sample description, that is all that is needed to display and convert the data.
Thank you for your informative response. I still ask for tutials on how to do structure refinement using profex on inorganic and organic materials; solid solutions and organic/,metal- organic complexes.
I am a mineralogist working with ceramics. With the materials you mention I have zero experience. It is unlikely that I will make such a tutorial, sorry.
When importing structure files, would it be possible to define my own radiation wavelengths as only lab based radiation sources are available on the menu? my data was measured from synchrotron, so I would like the simulated xrd also adjusted based on the radiation source.
Olá! Muito obrigado pelo excelente trabalho! 8:30, como você escolheu o grupo espacial? Hi! Thank you very much for the excellent work! 8:30, how did you choose the space group?
Most of what I'm demonstrating in this sequence should no longer be necessary because the automatic space group determination in Profex has been improved substancially. Only seriously corrupted CIF files that don't contain the space group number, HM symbol, nor Wyckoff symbols require manual selection. But to answer your question: At 07:00 the import dialog told me that it found space group No. 12 "C1 2/m 1" in the CIF file, but there were two different settings (setting 1 and 8) for the same Hermann-Mauguin symbol, and it couldn't determine the correct one. So I opened the "Browse BGMN space groups" dialog to display the differences between settings 1 and 8 of SG no. 12. A difference was found in Wyckoff=c, for which Setting=1 expects coordinates 0 0 1/2, but Setting=8 expects 1/2 0 1/2. Also Wyckoff=d was different, 1/2 1/2 1/2 in one setting, and 0 1/2 1/2 in the other (09:00). At time index 10:36 you can see that position Wat4 has coordinates 0 1/2 1/2, which corresponds to Wyckoff=d in Setting=8, whereas there is no Wyckoff position for 0 1/2 1/2 in Setting=1. So only Setting=8 can describe the coordinates 0 1/2 1/2 as a special Wyckoff position. That's why Setting=8 is the correct choice. All this is handled automatically and you wouldn't even notice that information is missing in the latest Profex releases. So make sure you are using the latest version (4.3.1 as I'm writing this).
@@profextutorials2325 Hi! Thank you very much for the reply, I had not seen the position of the Wat4 atom at 10:36, now it was possible to insert the cif file imported from the crystalography open database. I am working with the addition of residues in the cement, and I am mapping the phases by the XRD experimental method, the next step will be to verify degrees of polymerization with geopolymeric cements. The str file library you provide has given me a very good basis for phase quantification, if you need it, I can run tests and import experimental data to help with the library.
I added cif files following the same procedure as in the video but in the reference structures list, the files are not showing. i tried several times and tried various cif files of same compound,
Can you please check if the PHASE parameter on the first line in the converted STR file is empty? It can happen with some CIF files. You need to add the name manually in two lines of the STR file: Wrong: PHASE= // ... GOAL:=GEWICHT*ifthenelse(...) Fixed: PHASE=PhaseName // ... GOAL:PhaseName=GEWICHT*ifthenelse(...) Don't use special characters in the phase name, only a-z or 0-9. Then index the STR files again (Tools - index new structure files). This problem should no longer occur with Profex 5.2.1.
Hi, thank you for the great tutorial. When I installed version 4.2.2 of Profex, all (800+) reference structure files were indexed. However, afterwards the reference pattern list is empty. How could I fix this?
Hi, if you upgraded from an older version, you may have to purge the reference structure database. It is described in this video: th-cam.com/video/UqBtPYgMk8E/w-d-xo.html
whenever I verify my structure and want to save it on my mac, the application quits unexpectedly and so I never get to the step you're in at 5:50. Is there a way to fix this?
Sorry for the inconvenience. I can't reproduce the crash here. Can you send me the log file right after the crash occurred, before you start Profex again? You will find my e-mail address on the "Contact" page of the Profex website and the log file in the "Locations -> Log File" menu (if you are using the latest version of Profex).
Hello Profex! Congratulations on the video. After verifying the structures I am not able to select them afterward. My files are being saved in a roaming folder "File saved as C:/Users...../AppData/Roaming/doebelin.org/Profex5/Structures/. Do you think it can be the problem?
That is the correct place to store the files. You may just have to index the new structure files by running "tools -> Index new structure files" to generate the hkl lines.
Thank you for the reply. Like I pointed out please provide video tutorials organic and inorganic compounds. This will make the tutorials cover all materials and make it complete . Thank you.
Firstly, let me congratulate you for this excellent job. Profex is very flexible, with several unique features and easy to follow. I started learning Profex from downloaded tutorials last year. But these series of videos, all of which i have watched, are far more explanatory and easier to follow once you have read the manual. My questions , how do you obtain information on non XRDML/BRML files for instrument configuration? Also, can you provide a video on refinement of organic compounds and other synthetic materials, including inorganic?Most of the tutorials are on minerals.
Some other file formats are simple text files which may or may not contain hardware information. But it is almost impossible to find hardware information in binary raw files without having access to the file format specifications. They just set flags somewhere in the data, for example a "1" at byte position 256 may stand for "detector x". Reverse engineering these formats is very time consuming and not always completely possible. Most Profex import filters only read the measured data and sample description, that is all that is needed to display and convert the data.
Thank you for your informative response. I still ask for tutials on how to do structure refinement using profex on inorganic and organic materials; solid solutions and organic/,metal- organic complexes.
I am a mineralogist working with ceramics. With the materials you mention I have zero experience. It is unlikely that I will make such a tutorial, sorry.
When importing structure files, would it be possible to define my own radiation wavelengths as only lab based radiation sources are available on the menu? my data was measured from synchrotron, so I would like the simulated xrd also adjusted based on the radiation source.
You can replace the following line in the control file:
LAMBDA=CU
with
SYNCHROTRON=x.xxxxx
Where x.xxxx is the wavelength in nm.
Olá! Muito obrigado pelo excelente trabalho!
8:30, como você escolheu o grupo espacial?
Hi! Thank you very much for the excellent work!
8:30, how did you choose the space group?
Most of what I'm demonstrating in this sequence should no longer be necessary because the automatic space group determination in Profex has been improved substancially. Only seriously corrupted CIF files that don't contain the space group number, HM symbol, nor Wyckoff symbols require manual selection.
But to answer your question: At 07:00 the import dialog told me that it found space group No. 12 "C1 2/m 1" in the CIF file, but there were two different settings (setting 1 and 8) for the same Hermann-Mauguin symbol, and it couldn't determine the correct one. So I opened the "Browse BGMN space groups" dialog to display the differences between settings 1 and 8 of SG no. 12. A difference was found in Wyckoff=c, for which Setting=1 expects coordinates 0 0 1/2, but Setting=8 expects 1/2 0 1/2. Also Wyckoff=d was different, 1/2 1/2 1/2 in one setting, and 0 1/2 1/2 in the other (09:00). At time index 10:36 you can see that position Wat4 has coordinates 0 1/2 1/2, which corresponds to Wyckoff=d in Setting=8, whereas there is no Wyckoff position for 0 1/2 1/2 in Setting=1. So only Setting=8 can describe the coordinates 0 1/2 1/2 as a special Wyckoff position. That's why Setting=8 is the correct choice.
All this is handled automatically and you wouldn't even notice that information is missing in the latest Profex releases. So make sure you are using the latest version (4.3.1 as I'm writing this).
@@profextutorials2325 Hi! Thank you very much for the reply, I had not seen the position of the Wat4 atom at 10:36, now it was possible to insert the cif file imported from the crystalography open database.
I am working with the addition of residues in the cement, and I am mapping the phases by the XRD experimental method, the next step will be to verify degrees of polymerization with geopolymeric cements.
The str file library you provide has given me a very good basis for phase quantification, if you need it, I can run tests and import experimental data to help with the library.
@Marubozu If you want to provide structure files, I will be happy to add them to the default library. Much appreciated!
I added cif files following the same procedure as in the video but in the reference structures list, the files are not showing. i tried several times and tried various cif files of same compound,
Can you please check if the PHASE parameter on the first line in the converted STR file is empty? It can happen with some CIF files. You need to add the name manually in two lines of the STR file:
Wrong:
PHASE= //
...
GOAL:=GEWICHT*ifthenelse(...)
Fixed:
PHASE=PhaseName //
...
GOAL:PhaseName=GEWICHT*ifthenelse(...)
Don't use special characters in the phase name, only a-z or 0-9. Then index the STR files again (Tools - index new structure files).
This problem should no longer occur with Profex 5.2.1.
@@profextutorials2325 you are right. the phase parameter on the first line was empty. now my cif files are added in the database. thank you🙂
Hi, thank you for the great tutorial. When I installed version 4.2.2 of Profex, all (800+) reference structure files were indexed. However, afterwards the reference pattern list is empty. How could I fix this?
Hi, if you upgraded from an older version, you may have to purge the reference structure database. It is described in this video:
th-cam.com/video/UqBtPYgMk8E/w-d-xo.html
whenever I verify my structure and want to save it on my mac, the application quits unexpectedly and so I never get to the step you're in at 5:50. Is there a way to fix this?
Sorry for the inconvenience. I can't reproduce the crash here. Can you send me the log file right after the crash occurred, before you start Profex again? You will find my e-mail address on the "Contact" page of the Profex website and the log file in the "Locations -> Log File" menu (if you are using the latest version of Profex).
The str code opens but graph looks blank when I open an str file. How to deal with this?
There's probably an error in the STR file and verification fails. Check the messages tab for error messages.
Can anybody send me the CIF file of Sr2Al2SiO7 ?
Hello Profex! Congratulations on the video. After verifying the structures I am not able to select them afterward. My files are being saved in a roaming folder "File saved as C:/Users...../AppData/Roaming/doebelin.org/Profex5/Structures/. Do you think it can be the problem?
That is the correct place to store the files. You may just have to index the new structure files by running "tools -> Index new structure files" to generate the hkl lines.