Re: [PyMOL] Installation of Pymol ver 1.8

[Iain Kerr]

Hello Monu,


>From some limited googling, I think you are missing the GLEW package. If you 
>can tell us you what Linux distribution you are using (e.g. Ubuntu, Fedora) we 
>can help more. FYI, this is a better resource for PyMOL installation tips:


http://www.pymolwiki.org/index.php/Linux_Install


Assuming you are using one of the more popular Linux distributions, you could 
search for this package using Yum (Fedora, CentOS) or Synaptic (Ubuntu). They 
should install the required files in the correct paths without you having to 
link them to a bin or lib directory.


best,

Iain



From: bharat gupta 
Sent: Friday, March 4, 2016 5:34 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Installation of Pymol ver 1.8

Hi,

I am trying to install Pymol ver 1,8 downloaded from this link 
http://tubiana.me/how-to-install-and-compile-pymol-windows-linux-mac/. I am 
getting the following error while installing it:-

/usr/bin/ld: cannot find -lGLEW
collect2: ld returned 1 exit status
error: command 'g++' failed with exit status 1

I checked for the presence of lGLEW library in my system and it is already 
present,
[root@leelab02 lib64]# rpm -ql glew
/usr/bin/glewinfo
/usr/bin/visualinfo
/usr/lib64/libGLEW.so.1.5
/usr/lib64/libGLEW.so.1.5.5
/usr/share/doc/glew-1.5.5
/usr/share/doc/glew-1.5.5/LICENSE.txt

Do I have to provide a link for this file to /usr/bin ??

--
Best Regards
Monu

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Re: [PyMOL] Installation of Pymol ver 1.8

[bharat gupta]

Hi,

I am trying to install Pymol ver 1,8 downloaded from this link
http://tubiana.me/how-to-install-and-compile-pymol-windows-linux-mac/. I am
getting the following error while installing it:-

/usr/bin/ld: cannot find -lGLEW
collect2: ld returned 1 exit status
error: command 'g++' failed with exit status 1

I checked for the presence of lGLEW library in my system and it is already
present,
[root@leelab02 lib64]# rpm -ql glew
/usr/bin/glewinfo
/usr/bin/visualinfo
/usr/lib64/libGLEW.so.1.5
/usr/lib64/libGLEW.so.1.5.5
/usr/share/doc/glew-1.5.5
/usr/share/doc/glew-1.5.5/LICENSE.txt

Do I have to provide a link for this file to /usr/bin ??

-- 
*Best Regards*
Monu
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Re: [PyMOL] auto_show_cartoon or similar

[Thomas Holder]

Hi all,

The "auto_show_classified" feature is now available from the open-source SVN 
code repository. I've also uploaded pre-compiled builds to 
http://pymol.org/download (alpha release, not intended for production use).

The setting has 3 modes: 0 (off, default), 1 (like Adam suggested), 2 
(including the default lines), and 3 (simplified version with ribbon instead of 
cartoon).

See also:
http://pymolwiki.org/index.php/auto_show_classified

Any feedback will be appreciated.

Cheers,
  Thomas

On 08 Feb 2016, at 15:16, H. Adam Steinberg  wrote:

> Every application has to satisfy it's users.
> 
> Thinking out loud…
> If you show all lines the new users find it confusing and overwhelming but 
> they do get to see every atom. Experienced users generally know what atoms 
> are in a PDB or know how to find them if they are looking for them and 
> therefore do not need to see all lines.
> 
> The current proposal is to show more structure (cartoon, sticks, spheres) but 
> leave on all lines behind this structure. My first thought is what would that 
> look like. So I open a current structure and show both options (attached). If 
> I leave all lines on it’s still a bit of a mess. I think it looks better with 
> all lines off.
> 
> 
> 
>  PM.pdf>
> 
> 
> 
>> On Feb 8, 2016, at 1:29 PM, Thomas Holder  
>> wrote:
>> 
>> Adam, Abhinav, Dave,
>> thanks for the very useful feedback.
>> 
>> To keep it simple, I propose a "auto_show_classified" setting (will depend 
>> on "auto_classify_atoms", on by default) which will be equivalent to:
>> 
>> show cartoon, polymer
>> show sticks, organic
>> show spheres, inorganic
>> 
>> Question: should this automatically hide lines for classified atoms?
>> 
>> By the way, you may also like the "nice" preset (with "x" alias) from psico:
>> https://github.com/speleo3/pymol-psico/blob/master/psico/viewing.py
>> 
>> Cheers,
>> Thomas
>> 
>> On 08 Feb 2016, at 13:50, Bourgaize David  wrote:
>> 
>>> My thoughts exactly!
>>> 
>>> Dave Bourgaize
>>> 
>>> On 2/8/16, 9:54 AM, "H. Adam Steinberg"  wrote:
>>> 
 Every year I teach students PyMOL, and the look on their faces when they
 first open a pdb in PyMOL and get a cluster of green sticksŠ yikes!
 
 YES!!! to the default being secondary structure, ligands as sticks, and
 metal ions as spheres! Add - nucleic acids as cartoon.
 
> On Feb 8, 2016, at 10:57 AM, Kumar, Abhinav  wrote:
> 
> Showing metal ions  (and FES clusters etc) as spheres would also be
> useful.
> 
> Thanks,
> Abhinav
> 
> Abhinav Kumar, PhD
> Senior Scientist, Bioinformatics
> Intrexon, Inc.
> 329 Oyster Point Blvd., South San Francisco, CA 94080
> (650) 597-4072 | aku...@intrexon.com
> 
> 
> 
> From: Thomas Holder [thomas.hol...@schrodinger.com]
> Sent: Monday, February 08, 2016 8:51 AM
> To: Ivan Vulovic; Schubert, Carsten [JRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] auto_show_cartoon or similar
> 
> Hi Ivan and Carsten,
> 
> I can take "auto_show_cartoon" as a feature request. It's trivial to
> implement.
> 
> What also would be nice: automatically showing sticks for ligands. e.g.
> corresponding to the "not polymer" or the "organic" selection. Thoughts?
> 
> Cheers,
> Thomas
> 
> On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS]
>  wrote:
> 
>> Hi Ivan,
>> 
>> you could either try to overload the ³load² function in Pymol (not
>> sure this is supported) or write your own custom load function under a
>> different name, which loads the protein, assigns the name of the
>> object, hides lines and shows the cartoon.
>> 
>> Sorry, this is a rather generic answer but should point you in the
>> right direction.
>> 
>> Cheers,
>> 
>> Carsten
>> 
>> From: Ivan Vulovic [mailto:i...@uw.edu]
>> Sent: Saturday, February 06, 2016 8:18 PM
>> To: pymol-users@lists.sourceforge.net
>> Subject: [PyMOL] auto_show_cartoon or similar
>> 
>> Hello
>> 
>> Is there a way to make cartoon the default representation, something
>> akin to "auto_show_lines", but for cartoon? There was some dicussion of
>> this in 2010 (link below) but I haven't found anything more recent that
>> does what I'd like.
>> 
>> 
>> http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734
>> .html
>> 
>> Thanks
>> Ivan
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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