The CryoFold GUI has 4 sections, namely, MAINMAST, Targeted Molecular Dynamics, MDFF, and MELD. This keeps the default packages untouched.įor more information, refer to the ”Notes.txt” file. We recommend using the installation script as it creates a separate python environment called "CryoFold" where all the packages are installed in. The user can manually change this (to meld-cuda80, meld-cuda90 or meld-cuda92) to suit their CUDA compiler.
#Install meld in anaconda install#
The current script will install meld-cuda75 (line 10), which is for CUDA 7.5. Additionally, MELD is available for CUDA versions 7.5, 8.0, 9.0 and 9.2. Line 10 of the script specifies python version 3.5, which the user can change as per their choice.
#Install meld in anaconda manual#
Manual changes to installation script install_linux.sh or install_mac.sh might be necessary. The CryoFold GUI can then be launched by running gui.py by running python gui.py or by creating an executable. MAINMAST_GUI/MainmastThreadCA/ThreadCA.f -w -O3 -fbounds-check -o.
MAINMAST_GUI/MainmastThreadCA/MAINMAST -mcmodel=medium MAINMAST_GUI/MainmastThreadCA/MAINMAST.f -w -O3 -fbounds-check -o. Manual installationĪlternatively, the packages could be installed manually with the instructions on the following page:įor gfortran compilation of MAINMAST and ThreadCA, run the following commands from the command line: Finally, run start.sh to launch the CryoFold GUI. Run install_mac.sh script to install everything needed - GFortran compilation of Mainmast and ThreadCA, Anaconda environment creation, python packages (kivy, numpy, mdtraj and meld).
Run install_linux.sh script to install everything needed - GFortran compilation of Mainmast and ThreadCA, Anaconda environment creation, python packages (kivy, numpy, mdtraj and meld). NAMD installation (not required to run GUI): However, these two sections require VMD to be installed. For TMD and MDFF, CryoFold GUI generates NAMD input scripts that the user can submit manually (NAMD need not be installed to run the GUI). The GUI submits MAINMAST and MELD jobs, which requires these softwares to be installed as well. CryoFold has four sections, namely, MAINMAST, TMD, MDFF and MELD. The CryoFold GUI is optimized for LINUX/macOS distributions.Īnaconda and GFortran needs to be pre-installed in order to run the CryoFold GUI. MDFF requires less CPU-hours than ReMDFF. Note that the CryoFold GUI currently supports MDFF, not ReMDFF. ReMDFF requires 1-2 days on 11 CPUs, depending on system size. MELD currently performs synchronous REMD, so each GPU is a different replica. MELD requires 30 dedicated GPUs and a couple of days depending on the system size. This time could be reduced if the user manually checks the models of backbone trace by eye. MAINMAST requires 40-200 CPU hrs for the full-automated computation. This repository contains the scripts that run the GUI for cryofold, described in the following preprint: CryoFold: determining protein structures and ensembles from cryo-EM data