Re: [PyMOL] Error aroused when install pymol from source

[David Hall]

I think if you install "msgpack-devel”, it will compile and install.

Generally, header files (which is what is included in C++ files) are in *-devel 
packages. The regular msgpack package just contains the shared library for use 
by programs already compiled against msgpack.

-David

> On Jun 7, 2017, at 10:18 PM, sunyeping via PyMOL-users 
>  > wrote:
> 
> Dear pymol users,
> 
> I am trying to intall pymol on my centos 7 system from source using the 
> mothed discribed at pymolwiki (https://pymolwiki.org/index.php/Linux_Install 
> )
> Everything was ok until I run install script: 
> 
> #!/bin/bash -e
> 
> prefix=/opt/pymol-svn
> modules=$prefix/modules
> 
> # If you want to install as root, then split this line up in "build"
> # and "install" and run the "install" with "sudo"
> python2.7 setup.py build install \
> --home=$prefix \
> --install-lib=$modules \
> --install-scripts=$prefix
> 
> I got a error message and the installation process was terminated:
> 
> In file included from contrib/mmtf-c/mmtf_parser.cpp:31:0:
> contrib/mmtf-c/mmtf_parser_private.h:38:23: fatal error: msgpack.hpp: No such 
> file or directory
>  #include 
>^
> compilation terminated.
> 
> I then installed msgpack by yum command and tried to run the pymol install 
> script again, but the same error still occurred.
> 
> I googled this problem but cannot find a answer. Could anyone help me here?
> 
> Best regards.
> 
> Yeping Sun
> --
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> 
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> )
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> 
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> 
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[PyMOL] find any contact between a ligand and the protein it binds into

[? ?]

Dear all:

I wonder how can I find all the interaction between a ligand and its receptor 
(a protein), including both polar and non-polar interaction (ie. Within 4A etc.)
I use the "action - find - any cotact - between chains within 4A", but it shows 
nothing. Why? Who can help me?

Thank you very much!
Best regards,
Lei Zhen
==
Name: Lei Zhen
Address:
Num.501, College of Chemistry,
Beijing Normal University
No. 19, XinJieKouWai St., HaiDian District,
Beijing 100875, P. R. China
Email: leiz...@mail.bnu.edu.cn / 
thunderqu...@outlook.com
Tel: (+86) 010-58806002
==

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Re: [PyMOL] Error aroused when install pymol from source

[Thomas Holder]

Hi Yeping,

3 options:

1) Get msgpack 2.x sources from https://github.com/msgpack/msgpack-c and tell 
the C++ compiler about the headers, e.g. with:

export CXXFLAGS="-I/tmp/msgpack-2.1.2/include"

2) If you have installed msgpack 1.x, which is a dynamic library, also install 
msgpack-devel and build pymol with --use-msgpackc=c

3) Build pymol with --use-msgpackc=no which disables MMTF load support

Note that msgpack version 0.x is not supported by PyMOL.

Hope that helps.

Cheers,
  Thomas

> On Jun 8, 2017, at 4:18 AM, sunyeping via PyMOL-users 
>  wrote:
> 
> Dear pymol users,
> 
> I am trying to intall pymol on my centos 7 system from source using the 
> mothed discribed at pymolwiki (https://pymolwiki.org/index.php/Linux_Install)
> Everything was ok until I run install script: 
> 
> #!/bin/bash -e
> 
> prefix=/opt/pymol-svn
> modules=$prefix/modules
> 
> # If you want to install as root, then split this line up in "build"
> # and "install" and run the "install" with "sudo"
> python2.7 setup.py build install \
> --home=$prefix \
> --install-lib=$modules \
> --install-scripts=$prefix
> 
> I got a error message and the installation process was terminated:
> 
> In file included from contrib/mmtf-c/mmtf_parser.cpp:31:0:
> contrib/mmtf-c/mmtf_parser_private.h:38:23: fatal error: msgpack.hpp: No such 
> file or directory
>  #include 
>^
> compilation terminated.
> 
> I then installed msgpack by yum command and tried to run the pymol install 
> script again, but the same error still occurred.
> 
> I googled this problem but cannot find a answer. Could anyone help me here?
> 
> Best regards.
> 
> Yeping Sun

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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