I have tried. it works. I can download all the files or download whole directory from the FTP.

1. Download files

   wget ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/08/e0/BCR-3-1-055.PMC13900.pdf ./
   

2. Download whole directory:

   wget -r ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/08/e0 ./
   

Hi,

I found a trick that make the process go a little bit faster.

1. Find the corresponding PMC ID (you can find it from PMC-ids.csv.gz)
2. Follow the format of this URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMCXXXXXX/pdf -> this URL will re-direct the browser to the download link if the pdf is available

I use an excel vba script to semi-automate the process by opening a browser and directing it to the generated URL. This process is not ideal but at least it will minimize the number of clicks you need to download the articles

I'd say, the easiest way to download all the documents is using FileZilla. Host: ftp.ncbi.nlm.nih.gov /pub/pmc

There you can download them (those from PMC, ie the articles from your list (1.1 million)), in various formats. The root of that directory include a couple of tar.gz files; articles-* has a list of all the 1 million articles in nxml (xml format), the articles.txt.* in plain text. The latter seemed great, at first, but I found some issues with outlining.

Other files 'file_list*' list the journal issues including PMC_id, and the location where more information can be downloaded (a link to ftp.ncbi.nlm.nih.gov/pub/pmc/{hex}/{hex}/{article}. This includes pdfs, nxmls and images...