Re: [PyMOL] Problem with Pymol following update to Mac Big Sur

Hi Marc, The latest versions of PyMOL (e.g. 2.4) work fine on macOS Big Sur. Old versions of MacPyMOL (until 1.8.6) are not compatible, unfortunately, and we're not aware of any workarounds to make it work. Upgrading PyMOL is your only option. Cheers, Thomas On Mon, Apr 19, 2021 at 8:16 AM

[PyMOL] Problem with Pymol following update to Mac Big Sur

Hello, I have recently updated the iOS of my MacBook Air to Big Sur (version 11.2.3) and since then, I cannot use Pymol anymore. This is very annoying as it is my favorite program to generate publication grade figures. Here is the error message I get : This Executable Build integrates and

Re: [PyMOL] Problem with pymol

ger\Pymol2\lib\site-packages\pymol\parser.py", > line 52, in stdin_reader > 1 = sys.stdin.readline() > AttributeError: 'NoneType' object has no attribute 'readline' > Screenshots are attached below. Do you have a solution to fix this problem? > Thanks, > Roger > >

[PyMOL] Problem installing PyMOL

Hello! I've been trying to download PyMOL for some time now and i just don't know what I'm doing wrong. I tried installing the Schrodinger version, but got the following error trying to install it: " Warning: QT_DEVICE_PIXEL_RATIO is deprecated. Instead use: QT_AUTO_SCREEN_SCALE_FACTOR to

[PyMOL] Problem with pymol in python 3.6

Hello I am going to work with pymol through python 3.6. When I type (from pymol import cmd) in the jupyter notebook, I get the following error: ModuleNotFoundError: No module named 'pymol' Could you please help me how can I fix the problem? How can I install a version of pymol that is

Re: [PyMOL] Problem with Pymol 2.3.0 with 'undefined symbol: MMTF_unpack_from_string'

Hi Heng-Keat, A "clean" build will probably fix this. It looks like you partially recompiled with --use-msgpackc=no? To do a clean build: Remove the "build" directory and try again. Cheers, Thomas > On Feb 14, 2019, at 8:00 PM, t...@em.uni-frankfurt.de wrote: > > Dear all, > > I

[PyMOL] Problem with Pymol 2.3.0 with 'undefined symbol: MMTF_unpack_from_string'

Dear all, I installed the pymol on my machine with Ubuntu 18.04.1 LTS. When I launch pymol and error appears: Traceback (most recent call last): File "/home/mauricetam/Documents/software/pymol-2.3.0//lib/python2.7/site-packages/pymol/__init__.py", line 64, in import pymol File

Re: [PyMOL] Problem with pymol installation

Make sure you are using the 64-bit version of Python 2.7: python-2.7.11.amd64.msi. If that does not help, please list the contents of %CD%: dir "%CD%"\*.whl Christoph On 3/21/2016 3:31 AM, Bondurant wrote: > Hi everybody, > I recently restored my laptop to factory settings and I am trying

[PyMOL] Problem with pymol installation

Hi everybody, I recently restored my laptop to factory settings and I am trying now to install latest precompiled pymol version following the instructions from http://www.pymolwiki.org/index.php/Windows_Install. I have installed python 2.7.11 and put in a Pymol_installation folder pip 8.0.3,

Re: [PyMOL] Problem using pymol

> Please let me know how can I renumber protein chains to avoid overlap and > give it a uniqu chain id. > You can manually modify chain IDs with the alter command. For instance, to rename chain A to X: alter chain A, chain = "X" To automatically select

[PyMOL] Problem with pymol

Respected Sir, Can I build a model using missing residues through Pymol ? If it is,Please tell me the way. With Regards, SoumiDas-- ___ PyMOL-users

[PyMOL] Problem using pymol

Respected Sir, Please let me know how can I renumber protein chains to avoid overlap and give it a uniqu chain id. How can I change .pse file to .pdb file? With regards, Soumi Das-- Go from Idea to

Re: [PyMOL] problem of pymol 1.8

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.

Re: [PyMOL] problem of pymol 1.8

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 On 18 Nov 2015, at 17:08, Albert wrote: > Hello: > > I've installed the open

Re: [PyMOL] problem of pymol 1.8

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,

[PyMOL] problem of Pymol git install

Hello: I've installed pymol git repo following steps: http://www.pymolwiki.org/index.php/Git_install However, when I start pymol, it always showed the following messages: No module named tkintertable.Tables Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui). No module

[PyMOL] problem running PyMol on fedora 16

Dear all, I installed PyMol 1.5 on my computer. The PyMol interface becomes non-responsive once I load a PDB (protein structure file) file in it. I uninstalled and re-installed PyMol, but the problem persists. Does Fedora have incompatibility issues with PyMol? Any help towards

Re: [PyMOL] problem installing pymol plugin

Hi Vaibhav, First: I assume you did NOT copy the PocketPickerScript to C:\Program Files\DeLano Scientific\PyMOL\modules\pmg_tk\startup, otherwise there would not be a No such file error. Second: The plugin does not use the best coding style, it has hard coded file paths. So I would not be

Re: [PyMOL] Problem installing PyMOL plugin contact map visualizer

Suhaila Haji Mohd Hussin wrote, On 03/05/12 00:22: So how do you do it on Windows then? But I already have PIL despite having that error import image is missing. I don't get it. for which python do you have PIL? Your PyMOL installation uses it's own python executable (built into the

[PyMOL] Problem installing PyMOL plugin contact map visualizer

Hello guys. I have a problem installing Contact Map Visualizer plugin. It's supposed to be on the plugin menu once installed and restarting the PyMOL but it was always not there. Please help me how to fix this anyone? I need to use it a.s.a.p please. File C:\Program Files\DeLano

Re: [PyMOL] Problem installing PyMOL plugin contact map visualizer

Suhaila, The image python module is missing. It looks like you should switch to an open-source version of PyMOL and try to install the visualizer that way. Cheers, -- Jason On Sun, Mar 4, 2012 at 12:58 PM, Suhaila Haji Mohd Hussin bell_beaut...@hotmail.com wrote: Hello guys. I have a

[PyMOL] problem with pymol installation

Dear all I try to run Pymol on windows vista I installed the 1.1 version, but when I launch pymol, I get a big error message I have no plugin installed (I first installed pymol and tried to install some plugin, but I got error messages, so I uninstalled everything and tried to reinstall pymol

Re: [PyMOL] Problem Compiling Pymol 1.2.x

On 11/20/2009 07:43 PM, Jason Vertrees wrote: Stephen, openSuse Linux does not come with Pmw installed by default. Please re-download and install Pmw. Let me know if it's something else. -- Jason Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Nov 20, 2009 at 4:54

[PyMOL] Problem Compiling Pymol 1.2.x

I had successfully compiled Plymol from the Subversion repository in OpenSuSE v103. Linux. I say successfully, because I have just upgraded my linux computer to OpenSuSE v11.2. Unfortunaltely, I have a bit of a problem compiling the source code in the new linux OS in that I can compile the PyMol

Re: [PyMOL] Problem Compiling Pymol 1.2.x

Hey Stephen, make sure you have Tkinter and freeglut-devel installed. These are the dependencies that make trouble in RHEL. Andreas Stephen P. Molnar wrote: I had successfully compiled Plymol from the Subversion repository in OpenSuSE v103. Linux. I say successfully, because I have

Re: [PyMOL] Problem Compiling Pymol 1.2.x

On 13:38 Fri 20 Nov , Stephen P. Molnar wrote: I had successfully compiled Plymol from the Subversion repository in OpenSuSE v103. Linux. I say successfully, because I have just upgraded my linux computer to OpenSuSE v11.2. Unfortunaltely, I have a bit of a problem compiling the source

Re: [PyMOL] Problem Compiling Pymol 1.2.x

On 11/20/2009 02:16 PM, Donnie Berkholz wrote: On 13:38 Fri 20 Nov , Stephen P. Molnar wrote: I had successfully compiled Plymol from the Subversion repository in OpenSuSE v103. Linux. I say successfully, because I have just upgraded my linux computer to OpenSuSE v11.2.

Re: [PyMOL] Problem Compiling Pymol 1.2.x

Stephen P. Molnar wrote: Here's teh end of the log file that I recorded. I really don't have anyplace to which to upload the entire 125 kb log file. Hi Stephen, as Donnie already mentioned, we cannot help if we could not see the _complete_ build.log. From the part you past, it looks

Re: [PyMOL] Problem Compiling Pymol 1.2.x

Stephen, openSuse Linux does not come with Pmw installed by default. Please re-download and install Pmw. Let me know if it's something else. -- Jason Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Nov 20, 2009 at 4:54 PM, Justin Lecher j.lec...@fz-juelich.de wrote:

[PyMOL] Problem with pymol installation in ubuntu 8.10

Dear All I am trying to install pymol as described in the pymol wiki. I am experiencing some problems. I am using Ubuntu 8.10 64 bits version in an AMD machine. The last part of the output after the sudo python setup.py install was layer0/os_gl.h:69: error: expected ‘)’ before ‘width’

Re: [PyMOL] problem with pymol on FC6

: Wednesday, August 20, 2008 7:45 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] problem with pymol on FC6 Hi all I have recently downloaded the pymol on my FC6. Normally when i install a program, i give a pathname of my program excutable in my .bashrc and then i could launch the program

[PyMOL] problem with pymol on FC6

Hi all I have recently downloaded the pymol on my FC6. Normally when i install a program, i give a pathname of my program excutable in my .bashrc and then i could launch the program by running pymol in a terminal application launcher. But, this time whta happened that after installation i have

[PyMOL] problem with pymol installation

Hi Pymol-users, I'm trying to install pymol from svn repository. After compiling ( python setup.py build, python setup.py install, python setup2.py install) when I'm running pymol I have such an error OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: GeForce4 MX 440

[PyMOL] problem running pymol on 64 bit ubuntu

Hi, Does anyone have any advice on this error? On a 64 bit ubuntu dapper installation, I get the following error whether I run the standalone executable or if I run the pymol that is installed with apt-get pymol install: freeglut (pymol): ERROR: Internal error Visual with necessary

Re: [PyMOL] Problem starting Pymol in a Python script

On Fri, Nov 07, 2003 at 01:52:42PM +, Tom Walsh wrote: Hi, I'm trying to start Pymol (version 0.93) in a Python script, using the first method described in __init__.py i.e.: import pymol pymol.finish_launching() I've set the PYTHONPATH and PYMOL_PATH variables as required but