Question: Problem Creating Pdb Mirror
2
gravatar for Andrea_Bio
9.9 years ago by
Andrea_Bio2.6k
Andrea_Bio2.6k wrote:

Hi

I'm having trouble creating a pdb mirror. I can't connecto to the pdb rsynch server. If I enter this:

rsync  rsync.wwpdb.org::

or

rsync -rlptv --delete-after --port=334444 rsync.wwpdb.org::ftp/data/structures/divided/pdb/ ~/wwpdb/divided/pdb/

I get:

rsync: failed to connect to rsync.wwpdb.org: Connection timed out (110)
rsync error: error in socket IO (code 10) at clientserver.c(122) [Receiver=3.0.7]

I don't know if its because the server is actually down or because I'm doing something wrong.

I'm not that confident with the structure of the pdb. If i download these files from the ftp site

ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/

I think thats the same as the structures in the rsync path: ftp/data/structures/divided/pdb/

as the rsync top level ftp directory = /pub/pdb according to this site: http://www.wwpdb.org/downloads.html

So if the rsync server is down I could ftp.

Any help much appreciated

thanks

pdb • 2.8k views
ADD COMMENTlink modified 6.3 years ago by Biostar ♦♦ 20 • written 9.9 years ago by Andrea_Bio2.6k
2

If you are behind a firewall, you may need a HTTP_PROXY environment variable to bypass the firewall.

ADD REPLYlink written 9.9 years ago by Khader Shameer18k
2
gravatar for Suk211
9.9 years ago by
Suk2111.0k
state college
Suk2111.0k wrote:

I tried this command and I can download the PDB files using rsync.

rsync -rlpt -v -z --delete --port=33444 rsync.wwpdb.org::ftp_data/structures/divided/pdb/ ./pdb

 

[suk211@statmech7 test]$ rsync -rlpt -v -z --delete --port=33444 \
> rsync.wwpdb.org::ftp_data/structures/divided/pdb/ ./pdb
receiving file list ... done
created directory ./pdb
./
00/
00/pdb100d.ent.gz
00/pdb200d.ent.gz
00/pdb200l.ent.gz
00/pdb300d.ent.gz
00/pdb400d.ent.gz

For more information refer this link http://www.wwpdb.org/downloads.html

Hope this helps.

ADD COMMENTlink modified 12 months ago by RamRS30k • written 9.9 years ago by Suk2111.0k

thanks for looking. the instructions that I am following specifically say i have to download from the path I have given in my query. Can you download from that path?

rsync.wwpdb.org::ftp/data/structures/divided/pdb/

My instructions also so the trailing slash at the end of the path is important.

ADD REPLYlink written 9.9 years ago by Andrea_Bio2.6k

thanks for looking. the instructions that I am following specifically say i have to download from the path I have given in my query. Can you download from this path: rsync.wwpdb.org::ftp/data/structures/divided/pdb/

My instructions also say the trailing slash at the end of the path is important.

ADD REPLYlink written 9.9 years ago by Andrea_Bio2.6k

This just worked for me: rsync -rlpt -v -z --delete --port=33444 rsync.wwpdb.org::ftp/data/structures/divided/pdb/ ~/wwpdb/divided/pdb/ and my original command still doesn't work. I don't really see why one should work and not the other.

ADD REPLYlink written 9.9 years ago by Andrea_Bio2.6k

If the answer solves your question, please mark it as such.

ADD REPLYlink written 9.9 years ago by Egon Willighagen5.2k

Isn't the answer the fact I had a typing error in my original command which I didn't spot. I had a port number 334444. I'd typed an extra 4.

ADD REPLYlink written 9.9 years ago by Andrea_Bio2.6k
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