From mikewong at sfsu.edu  Wed Jan  5 16:09:07 2022
From: mikewong at sfsu.edu (Michael Wong)
Date: Thu, 6 Jan 2022 00:09:07 +0000
Subject: [Feature-users] Help for FEATURE Tool
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Message-ID: <BYAPR02MB5333A83410CCD769E8F0B95AA84B9@BYAPR02MB5333.namprd02.prod.outlook.com>

Hi Elif,

You'll need to download a copy of the latest PDB structures (in PDB format) to your PDB_DIR path.

The data are available here:
https://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/

PDB - FTP Archive over HTTP<https://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/>
For more information about PDB file downloads please see the wwPDB website.wwPDB website.
ftp.wwpdb.org




You will need to recursively download the directory. If you are on UNIX, you could use

wget -r https://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/

If you are on Mac OS, you can use homebrew (https://brew.sh/) to install wget (brew install wget).
[https://brew.sh/assets/img/homebrew-social-card.png]<https://brew.sh/>
The Missing Package Manager for macOS (or Linux)<https://brew.sh/>
The Missing Package Manager for macOS (or Linux). It’s all Git and Ruby underneath, so hack away with the knowledge that you can easily revert your modifications and merge upstream updates.
brew.sh


Similarly, you will need the DSSP data, available here:
http://www3.cmbi.umcn.nl/dssp/dssp.html

Please read their instructions on how to obtain their data. I suggest using rsync (instructions on the aforementioned link).

Best regards,

- Mike
________________________________
From: ELIF CANDAS <elifcandas at hacettepe.edu.tr>
Sent: Saturday, January 1, 2022 7:44 AM
To: feature-users at simtk.org <feature-users at simtk.org>; Michael Wong <mikewong at sfsu.edu>
Subject: Help for FEATURE Tool

Hello,

I installed FEATURE 3.1 from simktk.org. I followed feature-user-manual.pdf for installation. I am using Windows 10. I was able to install standard version of FEATURE. I tested and I didn't get any error. Then I set environment variables as follows.

FEATURE_DIR      C:\Users\elifc\Projects\feature\feature-3.1.0
PDB_DIR                C:\Users\elifc\Projects\feature\feature-3.1.0\data\pdb
DSSP_DIR              C:\Users\elifc\Projects\feature\feature-3.1.0\data\dssp
PYTHONPATH      %PYTHONPATH%C:\Users\elifc\Projects\feature\feature-3.1.0\tools\lib

I run the command written in the attached file. Then I got error about location of pdb file. Is the problem about environment variables? What else could be the reason? Could you please help me about it?

Thank you.

Yours sincerely,

--
Elif
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