I am following this link http://www.pymolwiki.org/index.php/User:Tlinnet/Linux_Install to install pymol. I need libfreetype6-dev as a dependency, but it cannot be installed.

fmp@eva03:~/Bins$ sudo apt-get install libfreetype6-dev 
[sudo] password for fmp: 
Reading package lists... Done 
Building dependency tree Reading state information... Done 
The following packages were automatically installed and are no longer required:
 linux-headers-4.2.0-23 linux-headers-4.2.0-23-generic linux-image-4.2.0-23-generic linux-image-extra-4.2.0-23-generic 
Use 'apt-get autoremove' to remove them. 
The following NEW packages will be installed: libfreetype6-dev 
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 
Need to get 0 B/630 kB of archives. 
After this operation, 3 672 kB of additional disk space will be used. 
(Reading database ... 252267 files and directories currently installed.) 
Preparing to unpack .../libfreetype6-dev_2.5.2-4ubuntu2_amd64.deb ... 
Unpacking libfreetype6-dev:amd64 (2.5.2-4ubuntu2) ... 
dpkg: error processing archive /var/cache/apt/archives/libfreetype6-dev_2.5.2-4ubuntu2_amd64.deb (--unpack): 
trying to overwrite shared '/usr/share/man/man1/freetype-config.1.gz', which is different from other instances of package libfreetype6-dev:amd64 
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe) 
Processing triggers for man-db (2.7.4-1) ... 
Errors were encountered while processing: /var/cache/apt/archives/libfreetype6-dev_2.5.2-4ubuntu2_amd64.deb 
E: Sub-process /usr/bin/dpkg returned an error code (1)

Here are the final lines trying to install pymol

In file included from /usr/include/freetype2/ft2build.h:37:0,
                 from layer1/TypeFace.cpp:25:
/usr/include/freetype2/config/ftheader.h:3:58: fatal error: x86_64-linux-gnu/freetype2/config/ftheader.h: 
No such file or directory
     compilation terminated.
     c++ -pthread -std=c++0x -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_FREETYPE -DNO_MMLIBS -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python2.7 -c layer1/Character.cpp -o build/temp.linux-x86_64-2.7/layer1/Character.o -Wno-write-strings
 -Wno-unused-function -Wno-char-subscripts -ffast-math -funroll-loops -O3 -fcommon
     error: command 'c++' failed with exit status 1
  • Hi, welcome to Askubuntu. When you post code, please copy and paste the code directly from the terminal. Then, highlight the code and then press CTRL + K to automatically format it for your post; when you use > to post code, it loses it's proper formatting and makes it much harder to read and probably reduces your chances of getting people to take a look at it. Thanks! – mchid Jan 27 '16 at 6:14


If you don't need version 1.8 and if you are using Ubuntu 14.04 or newer, you can install version 1.7 through the official Ubuntu repositories. Just run the following commands to install pymol version and pymol dependencies:

sudo apt-get update
sudo apt-get install pymol

If it still complains about libfreetype6-dev, run the following commands to fix that and then run the above commands again.

sudo apt-get clean
sudo apt-get update
sudo apt-get purge libfreetype6-dev

To search for available packages through apt-get, run the following command like in this example:

apt-cache search pymol

To narrow the results to those containing a particular word, use grep like in this example:

apt-cache search pymol | grep pymol

To list the available version:

apt-cache show pymol | grep "Version:"

To list more info:

apt-cache show pymol


Alternatively, if you insist on installing the downloaded version, run the following commands to install libfreetype6-dev:

sudo apt-get clean
sudo apt-get update
sudo mv /usr/share/man/man1/freetype-config.1.gz ~/
sudo apt-get install libfreetype6-dev

This will move the manpage file to your home directory so you will have to view the file from there instead of using manpage.

| improve this answer | |
  • 1
    If I do option one, the dssp_stride plugin wont work, that's why I would like to try option two... Option two works. Thanks So.. is it safe to remove the *.gz file? – murpholinox Jan 27 '16 at 21:37
  • @murpholinox That depends. The *.gz file is the manpage file and this file contains the manpage so if you would like to view the manpage, you would need this file. If you do not care to ever view the manpage, I believe you would not need this file and so I believe it would be safe to remove this file if you do not wish to ever view the manpage. – mchid Jan 28 '16 at 21:32

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