examples/EMAN2_w_theano.md
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-## Using the Theano python module in EMAN2 for neural network particle picking
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-It is possible to use GPU-accelerated neural network particle picking in EMAN2 versions 2.2 and later in the SBGrid software installation.
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-*First you must configure your machine with the Nvidia CUDA Toolkit and a configuration file describing your GPUs*. Due to distribution restrictions we cannot install Nvidia nvcc compilers directly.
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+## GPU-accelerated Neural network particle picking in EMAN2
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+EMAN2 uses uses the Theano python module for GPU-accelerated neural network particle picking in versions 2.2 and later.
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+This is possible with the SBGrid installation but *you must first configure your machine with the Nvidia CUDA Toolkit and a configuration file describing your GPUs*. Due to distribution restrictions we cannot install Nvidia nvcc compilers directly.
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-### Download and install the Nvidia CUDA Toolkit for CUDA
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+### Download and install the Nvidia CUDA Toolkit
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Because the Theano module installed in EMAN2 requires the nvcc compiler and these are not re-distributable, you must first download the Nvidia CUDA Toolkit. You can find that [here](https://developer.nvidia.com/cuda-downloads?target_os=Linux&target_arch=x86_64&target_distro=CentOS). It is not necessary to have administrator privileges to install this, but you may want to ask your local administrator to assist to ensure you have the proper drivers for your GPU. Nvidia driver installation requires admin privileges.
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-### Set the CUDA_HOME variable with a path to your installed CUDA Toolkit.
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+### Set the CUDA_HOME variable
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For Theano to find the Nvidia nvcc compiler and the CUDA libraries required, the CUDA_HOME variable must be set in your shell with the correct path to the CUDA Toolkit.
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If your CUDA Toolkit installation is at : /usr/local/cuda
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setenv CUDA_HOME /usr/local/cuda
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```
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-### Configure your ~/.theanorc for your GPUs
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+### Configure your ~/.theanorc file
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-There are many options available for this and they are [described here](http://deeplearning.net/software/theano/library/config.html#envvar-THEANORC)
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+The ~/.theanorc file specifies the configuration attributes for theano. There are many options available for this and they are [described in detail here](http://deeplearning.net/software/theano/library/config.html#envvar-THEANORC)
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A simple configuration would be :
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