[PyMOL] on using pymol scripts

[Smith Liu]

Dear All,


If I want to use a pymol script, for example the script on centroid, will you 
please tell me how to download the corresponding script from the pymol website?


Smith--
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Re: [PyMOL] on using pymol scripts

[Andreas Forster]

Dear Smith,

right click on
https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/centroid.py,
select Save Link As.  This is a good skill to have because it allows you to
download all sorts of things from the internet.  You can use Google Chrome,
Mozilla Firefox and Microsoft Edge for that.

To download the script from the PyMOL website, you'll have to modify the
address above accordingly.

All best.


Andreas



On Thu, Nov 19, 2015 at 9:02 AM, Smith Liu  wrote:

> Dear All,
>
> If I want to use a pymol script, for example the script on centroid, will
> you please tell me how to download the corresponding script from the pymol
> website?
>
> Smith
>
>
>
>
>
> --
>
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>
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Re: [PyMOL] Help for saving movie in png

[Christian Becke]

Hi Pranab,

Am 13.11.2015 um 17:00 schrieb Pranab Jyoti Bhuyan:
> Can you please tell me how to save a movie as a series of *.png files
> from terminal in linux?
This can be done with the mpng command. See
http://pymolwiki.org/index.php/Mpng


Cheers,

Christian

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[PyMOL] what is wrong on my using centroid.py

[Smith Liu]

Dear All,


When I run the centroid.py, I have the following error message: "NameError: 
global name 'move' is not defined". My centroid.py script downloaded (have I 
misdone or miseddited something?) is as following. Will you please tell me how 
to solve the error message issue?


Smith




---
See more here: http://www.pymolwiki.org/index.php/centroid
 
DESCRIPTION
 get the centroid (geometric center) of a selection or move selection 
to the origin.
  
ARGUMENTS
 selection = string: a valid PyMOL selection {default: all}
 center = 0 or 1: if center=1 center the selection {default: 0}
 returns: centroid: [ x, y, z ]
  
 SEE ALSO
 get_extent, get_position, http://pymolwiki.org/index.php/Center_Of_Mass
 
 # @AUTHOR: Jason Vertrees
 # Copyright (c) 2008, Jason Vertrees
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without 
modification, are permitted provided that the following
 # conditions are met:
 #
 # * Redistributions of source code must retain the above copyright notice, 
this list of conditions and the following
 # * disclaimer.
 # * Redistributions in binary form must reproduce the above copyright 
notice, this list of conditions and the following
 # * disclaimer in the documentation and/or other materials provided with 
the distribution.
 # * Neither the name of the  nor the names of its 
contributors may be used to endorse or promote products derived
 # * from this software without specific prior written permission.
 #
 # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
 # NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
 # THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, 
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 # (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
 # OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF 
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # DATE  : 2008-09-26
 # REV   : 1
 
'''
from pymol import cmd
from pymol import stored
from chempy import cpv
 
 
 
 
def centroid(selection='all', center=0, quiet=1):
 
 
 model = cmd.get_model(selection)
 nAtom = len(model.atom)
 
 
 centroid = cpv.get_null()
 
 
 for a in model.atom:
 centroid = cpv.add(centroid, a.coord)
 centroid = cpv.scale(centroid, 1. / nAtom)
 
 
 if not int(quiet):
 print ' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid)
 
 
 if int(move):
 cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), centroid)",
 space={'centroid': centroid, 'sub': cpv.sub})
 
 
 return centroid
 
 
cmd.extend("centroid", centroid)








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[PyMOL] default fetch format

[Albert]

Hello:

I noticed that if we run command:

fetch 2ac1

to get PDB into pymol in Version 1.8.0, it downloaded .cif file by 
default. I am just wondering is it possible to change the default format 
as .pdb file?

thanks a lot

Albert

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Re: [PyMOL] what is wrong on my using centroid.py

[Osvaldo Martin]

Hi Smith,

There was an error in script, incidentally, I introduce the error, but now
is fixed. Please download again the centroid.py script.

Cheers,
Osvaldo.

On Fri, Nov 20, 2015 at 3:00 AM, Smith Liu  wrote:

> Dear All,
>
> When I run the centroid.py, I have the following error message:
> "NameError: global name 'move' is not defined". My centroid.py script
> downloaded (have I misdone or miseddited something?) is as following. Will
> you please tell me how to solve the error message issue?
>
> Smith
>
>
> ---
> See more here: http://www.pymolwiki.org/index.php/centroid
>
> DESCRIPTION
>  get the centroid (geometric center) of a selection or move
> selection to the origin.
>
> ARGUMENTS
>  selection = string: a valid PyMOL selection {default: all}
>  center = 0 or 1: if center=1 center the selection {default: 0}
>  returns: centroid: [ x, y, z ]
>
>  SEE ALSO
>  get_extent, get_position,
> http://pymolwiki.org/index.php/Center_Of_Mass
>
>  # @AUTHOR: Jason Vertrees
>  # Copyright (c) 2008, Jason Vertrees
>  # All rights reserved.
>  #
>  # Redistribution and use in source and binary forms, with or without
> modification, are permitted provided that the following
>  # conditions are met:
>  #
>  # * Redistributions of source code must retain the above copyright
> notice, this list of conditions and the following
>  # * disclaimer.
>  # * Redistributions in binary form must reproduce the above copyright
> notice, this list of conditions and the following
>  # * disclaimer in the documentation and/or other materials provided
> with the distribution.
>  # * Neither the name of the  nor the names of its
> contributors may be used to endorse or promote products derived
>  # * from this software without specific prior written permission.
>  #
>  # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
> IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
>  # NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
> FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
>  # THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
> INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
>  # (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
> SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
>  # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
> CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
>  # OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
> IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
>  #
>  # DATE  : 2008-09-26
>  # REV   : 1
>
> '''
> from pymol import cmd
> from pymol import stored
> from chempy import cpv
>
>
>
>
> def centroid(selection='all', center=0, quiet=1):
>
>
>  model = cmd.get_model(selection)
>  nAtom = len(model.atom)
>
>
>  centroid = cpv.get_null()
>
>
>  for a in model.atom:
>  centroid = cpv.add(centroid, a.coord)
>  centroid = cpv.scale(centroid, 1. / nAtom)
>
>
>  if not int(quiet):
>  print ' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid)
>
>
>  if int(move):
>  cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), centroid)",
>  space={'centroid': centroid, 'sub': cpv.sub})
>
>
>  return centroid
>
>
> cmd.extend("centroid", centroid)
>
>
>
>
>
>
>
>
>
> --
>
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[PyMOL] Pymol for inorganic chemists - dealing with bonds

[Henrique C. S. Junior]

Dear Pymol users,
As an inorganic chemist, to represent metallic centers and ligands in a
comprehensive way is very important. I've tried to select my metallic
centers and the atoms bonded directly to them, change this selection to
ball and stick and keep all the rest as wireframe. Some bonds changed to
sticks, some others not (and they are not changing, even if I try again).
What I want to do is this:
* Represent my metallic centers as spheres (maybe tweaking the radius a
little)
* Change bonds directly connected to my metallic centers to dashes or dots
(and change the colors of this dashes/dots if possible).
Any help is much appreciated.

-- 
*Henrique C. S. Junior*
Químico Industrial - UFRRJ
Mestrando em Química Inorgânica - UFRRJ
Centro de Processamento de Dados - PMP
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Re: [PyMOL] Pymol 1.8.0.0 requires ZLIB 1.2.3.5?

[Thomas Holder]

Hi Roger,

Please run ./setup.sh which will activate a more recent libz library which is 
bundled with the build. Please also see the INSTALL.txt for similar 
troubleshooting solutions.

Cheers,
  Thomas

On 19 Nov 2015, at 11:01, Roger Rowlett  wrote:

> Pymol 1.8.0.0 (64 bit linux) is throwing an error about a ZLIB 
> requirement (v 1.2.3.5). The latest Ubuntu 12.04 LTS version through 
> apt-get is 1.2.3.4. Is there supposed to be a local version of zlib.1.so 
> in the pymol install package?
> 
> ___
> Roger S. Rowlett
> Gordon & Dorothy Kline Professor
> Department of Chemistry
> Colgate University
> 13 Oak Drive
> Hamilton, NY 13346
> 
> tel: (315)-228-7245
> ofc: (315)-228-7395
> fax: (315)-228-7935
> email: rrowl...@colgate.edu
> 
> --

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] problem of pymol 1.8

[Thomas Holder]

Hi Albert,

It seems that you have a lot of plugins installed, you likely don't need them 
or maybe don't even know that they are installed. Please open the Plugin 
Manager from the "Plugin" menu and uncheck "Load on startup" for all plugins 
that you don't need or don't know what they do.

Cheers,
  Thomas

On 18 Nov 2015, at 17:29, Albert  wrote:

> Hi Thomas:
> 
> thanks a lot for helpful advice.
> 
> HOwever, I got something new warnings:
> 
> No module named cPluginManager
> Unable to initialize plugin 'xPyder' (pmg_tk.startup.xPyder).
> No module named backend_wxagg
> Unable to initialize plugin 'mtsslPlotter' (pmg_tk.startup.mtsslPlotter).
> 
> I google it, and cannot find any helpful information
> 
> 
> thanks again
> 
> ALbert
> 
> 
> On 11/18/2015 11:16 PM, Thomas Holder wrote:
>> Hi Albert,
>> 
>> These messages come from third-party plugins that you have installed, see:
>> http://pymolwiki.org/index.php/MtsslDock
>> http://pymolwiki.org/index.php/MtsslTrilaterate
>> 
>> Cheers,
>>   Thomas

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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