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rlabduke / MolProbity

Protein and nucleic acid validation service
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PHP issue PHP Deprecated: Array and string offset access syntax with curly braces is deprecated #18

Closed mandar5335 closed 2 years ago

mandar5335 commented 2 years ago

Hi, I have installed molprobity on Ubuntu 20.04 LTS with php7.4. I need to use molprobity to get clashscore for RNA molecules. However, when I run molprobity/cmdline/clashscore command, I receive the following error: PHP Deprecated: Array and string offset access syntax with curly braces is deprecated in /home/mandar/softwares/molprobity/molprobity/lib/model.php on line 752

If this is a PHP version-related issue, which version is recommended?

Thanks, Mandar Kulkarni

rlabduke commented 2 years ago

Hi Mandar,

MolProbity has several incompatibilities with current PHP and requires a legacy version. You can try the following to install a compatible PHP:

sudo apt install software-properties-commo sudo add-apt-repository -y ppa:ondrej/php sudo apt update sudo apt list --upgradable sudo su - sudo aptitude install php5.6

Alternatively, you can skip the PHP layer and run the underlying clashscore code directly. Run this command to set up the cctbx environment: source path_to_MolProbity/build/setpaths.sh

Then run: molprobity.clashscore filename.pdb

You may also find useful "molprobity.rna_validate filename.pdb"

Good luck, -Christopher Williams ---Richardson Lab, Duke University

mandar5335 commented 2 years ago

Hi Christopher, Thanks for your reply and suggestions, I skipped the PHP layer and the molprobity.clashscore worked perfectly fine.

Best, Mandar Kulkarni