Activity for molmol
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Ivan posted a comment on discussion General Discussion
Hello, I was wondering if there was a way to assign a rainbow color to protein ribbons in MOLMOL? I want to color the N terminus blue and the C terminus red, and then have a smooth color gradient between the two residues. As an example, here is a Wikipedia page with such a figure: https://en.wikipedia.org/wiki/Coiled_coil I have tried looking at the manual for various coloring commands for primitives. I also tried looking at the standard macros but had no luck. Thank you in advance.
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Dave Wilson posted a comment on discussion General Discussion
Hi Alexander, Thank you for your question and comments. At the time this project was being "redeveloped" time and resource restrictions, together with low user numbers requirements, meant that installation binaries were not created for Unix systems. The folder was generated in case someone else decided to create the necessary installation binaries and wanted to make them available there. My understanding is that the source code is available under the code tab if you wish to download it. Thank you...
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Alexander Tee posted a comment on discussion General Discussion
Hi, please add some UNIX versions to the download section, the source code would also be great to have since since it would be possible to port it to even more platforms. Thanks.
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Changes in Apple's MacOS Catalina 10.15 from previous versions of MacOS have caused issues with running MOLMOL. To run MOLMOL in MacOS Catalina 10.15 please follow the instructions below. UPDATE: You can just reinstall XQuartz to get X11 back to where it needs to be. You can also open System Preferences and in the Security&Privacy>General tab click allow for each library as it tries to open MOLMOL. This requires trying to start MOLMOL about 10 times initially, but is fine after that. All the information...
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Hi Ivan, Thank you for your interest and encouraging words regarding MolMol. It is certainly possible to do what you wish with defining a specified secondary structure. It's not overly intuitive, but hopefully the hints below will help you achieve what you want. You need to calculate the secondary structure through Calc>Secondary. Then File>Write Secondary which writes the secondary structure information to a specific file. You can then use information in this file to add details to the ribbon.mac...
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Hello! I have recently been using MolMol and am finding it useful thus far. Its cartoon/ribbon display looks very nice. Given that I am rather new to the program, I still have to learn how to navigate the program and execute commands with proper syntax so I apologize in advance if I miss anything. Anyhow, I was wondering if there is a way to manually change the type of secondary structure of a residue in a protein. How would I approach changing it manually in MolMol to what I want instead of what...
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Hello! I have recently been using MolMol and am finding it useful thus far. Its cartoon/ribbon display looks very nice. Given that I am rather new to the program, I still have to learn how to navigate the program and execute commands with proper syntax so I apologize in advance if I miss anything. Anyhow, I was wondering if there is a way to manually change the type of secondary structure of a residue in a protein. How would I approach changing it manually in MolMol to what I want instead of what...
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Hello! I have recently been using MolMol and am finding it useful thus far. Its cartoon/ribbon display looks very nice. Given that I am rather new to the program, I still have to learn how to navigate the program and execute commands with proper syntax. Anyhow, I was wondering if there is a way to manually change the type of secondary structure of a residue in a protein. How would I approach changing it manually in MolMol to what I want instead of what is automatically determined? Another example:...
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Changes in Apple's MacOS Catalina 10.15 from previous versions of MacOS have caused issues with running MOLMOL. To run MOLMOL in MacOS Catalina 10.15 please follow the instructions below. Open a terminal window (Terminal can be found in the Applications/Utilities folder) Ignore the message stating that "The default interactive shell is now zsh. To update your account to use zsh, please run chsh -s /bin/zsh. For more details, please visit https://support.apple.com/kb/HT208050." and continue to use...
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Hi Siddartha, Thank you for your post and finding a solution to this issue. The issue is due to changes implemented in XQuartz 2.7.10 regading the Motif library. I haven't checked, however I suspect the solution you posted may only be temporary and have to be repeated each time XQuartz is upgraded. An alternative solution that may be more permanent (at least until XQuartz changes the reference of the Motif library again) is to add the following line to the user .profile file: export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace:${DYLD_LIBRARY_PATH}...
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Hi Siddartha, Thank you for your post and finding a solution to this issue. The issue is due to changes implemented in XQuartz 2.7.10 regading the Motif library. I haven't checked, however I suspect the solution you posted may only be temporary and have to be repeated each time XQuartz is upgraded. An alternative solution that may be more permanent (at least until XQuartz changes the reference of the Motif library again) is to add the following line to the user .bashrc file: export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace:${DYLD_LIBRARY_PATH}...
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Siddhartha P Sarma posted a comment on discussion General Discussion
Dear Colleagues, I had recenlty (last night) upgraded my Mac OS from 10.6.8 to El Capitan. I then tried installing the MOLMOL from this site. The Version I had installed was Macintosh-10.8.4-MolMol-V1.0.7.2. when running molmol, I got the following error message "attempt to add non-widget child "dsm" to parent "idl" which supports only vendor widgets" or something equivalent. The part in bold is verbatim, the rest I have filled in because I do not remembet the exact message. Nevertheless, the solution...
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