Re: [PyMOL] Problem launching PyMOL from macOS 13.7.1

Hello Dr. Saper, This does appear to be a bug and I was able to reproduce the same behavior on my Mac. Opening the same pdb repeatedly in the same window should result in states being added, but there's no reason why PyMOL should be doing this when double clicking on files. It seems like PyMOL is

[PyMOL] Problem launching PyMOL from macOS 13.7.1

I am running the latest PyMOL 3.1.3 on macOS 13.7,1. When I double click a .pse or .pdb file, PyMOL opens normally and displays the molecule of interest. If I think double click on another file, PyMOL opens a new window, the molecule displays, but now there is a seoncd state of the moleculeThe G

[PyMOL] problem on generating vacuum electrostatics in PyMol 2.5.4

Hi, I have just switched to the new PyMol version of 2.5.4, and am encountering a problem while trying to generate the vacuum electrostatics for a protein. However, I am getting an error message of "Pop-Error: invalid source selection name 'assign_tmp1'" I have never encountered this sor

[PyMOL] Problem to get RMSD between crystal ligand and docked ligand

Hello everyone, I am trying to obtain the RMSD value between a docked ligand I got with Autodock Vina (PDBQT file) and a crystal ligand structure i downloaded from rcsb.org (PDB file). The thing is when I open the crystal ligand file on PyMOL this error appears: Warning: Invalid characters in 'ML

[PyMOL] Problem with the legacy plugin CASTp pocket loader

Dear all, I encounter problems using the legacy plugin CASTp pocket loader on PyMOL Version 2.4.1. It fails to open poc files and terminates with "Error: unsupported file type poc". Any idea on how to solve this problem? Thanks a lot! With kind regards, Lionel -- logo-ipbs Lionel Mourey

Re: [PyMOL] problem with ray of PNG using pymol in non-gui mode

yep, it is not possible actually to switch off the Ray using no-gui mode in pymol ( i've just read another topic on this case). BTW I found that the problem of the disappearing of carton is mor related to the transparency, since it had already been set for the surface as well. In the case when I se

Re: [PyMOL] problem with ray of PNG using pymol in non-gui mode

Have you tried setting ray_trace_mode? Info here: https://pymolwiki.org/index.php/Ray -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* New Delhi, India [image: Mailtrack]

[PyMOL] problem with ray of PNG using pymol in non-gui mode

Dear Pymol Users! I've faced the problem of saving a PNG image without ray using the png command in non-gui mode. First if I do it in pymol gui #cmd.png('test.png',width=800,height=800,ray=0) .. it produces fine image (without ray) However if I execute the same command inside of my bash sript: $p

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 Ma

[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 exte

Re: [PyMOL] Problem with pymol

Hi Roger, Looks like Open3dQSAR tries to use a pipe to communicate with PyMOL. That is possible with "PyMOLWin.exe +2", with "PyMOLWinWithConsole.bat" and with "Scripts\pymol.exe". I suggest that you try this: env pymol="C:\Users...\PyMOLWinWithConsole.bat" Hope that helps. Cheers, Thomas

Re: [PyMOL] Problem In using Pymol 2.4 through IDLE -Python 3

Thank you, Dr. Christopher Gohlke I downloaded and installed Microsoft Visual C++ Redistributable for Visual Studio 2015, 2017 and 2019. This solved the problem. Now, PyMOL is running without any problem. In fact, I just successfully ran PyMOL from Portable Python 3.8 and also from IDLE. Cheers Wi

Re: [PyMOL] Problem In using Pymol 2.4 through IDLE -Python 3

Try installing the Microsoft Visual C++ Redistributable for Visual Studio 2015, 2017 and 2019 Christoph On 10/23/2020 8:11 PM, Dr. Vijay Masand wrote: Hello PyMOL users I installed open source PyMOL 2.

[PyMOL] Problem In using Pymol 2.4 through IDLE -Python 3

Hello PyMOL users I installed open source PyMOL 2.4 (Python 3.7) on Windows 10 (64 bit). It strated without any problem when the icon was double clicked.But when I tried to use it from IDLE (PYTHON 3.7- 64bit), it showed following error: "ImportError: DLL load failed: The specified module could no

[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 enab

[PyMOL] Problem With Dynamic_Gromacs Plugin

I just downloaded, compiled and installed gromacs-2020 without any warnings or errors. However when I attempt opening the Dynamic_Gromacs 2.2.1 plugin I get the error: 'module' object has no attribute 'showerror' and everything stops. Now, the plugin has been working with the Debian Stretch d

Re: [PyMOL] Problem with PDB file export

Hi Ezra, Good call, I knew it had to be foolish because it worked yesterday. Thanks!! Ofir ‫בתאריך יום ד׳, 22 בינו׳ 2020 ב-16:10 מאת ‪Ezra Peisach‬‏ <‪ ezra.peisach+py...@rcsb.org‬‏>:‬ > The dots and question marks are appropriate. You did not export a PDB > file, but instead an mmCIF/PDBx file.

Re: [PyMOL] Problem with PDB file export

The dots and question marks are appropriate. You did not export a PDB file, but instead an mmCIF/PDBx file. For an explanation of what the fields mean, you can look at http://mmcif.wwpdb.org/docs/tutorials/content/atomic-description.html On 1/21/20 9:46 PM, Ofir Shein Lumbroso wrote: Hi all

Re: [PyMOL] Problem with PDB file export

Hello, Can I ask which version of PyMOL you're using? I don't see anything wrong on my end. On Tue, Jan 21, 2020 at 9:48 PM Ofir Shein Lumbroso wrote: > Hi all, > I'm a new user of PyMOL and I'm trying to export a PDB file from a PyMOL > session and It seems to have some errors. I'm using the

Re: [PyMOL] Problem loading Amber trajectory

Hi Martin, Would it be possible to share those files with me? Thanks, Thomas > On Nov 28, 2019, at 6:00 PM, Rosellen, Martin > wrote: > > Dear all, > > I have issues loading Amber trajectories. First, I load the the topology > like this: > > load WT.prmtop, WT, 1, top > > output: > >

[PyMOL] Problem loading Amber trajectory

Dear all, I have issues loading Amber trajectories. First, I load the the topology like this: load WT.prmtop, WT, 1, top output:  ObjectMolecule: Attempting to read Amber7 topology file.  TOPStrToCoordSet: Warning: can't currently image a truncated octahedron... load_traj WT.trj, WT outp

[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 compatible

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 installed

[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 Open source Pymol 2.3.0 (missing external GUI)

Hi Heng-Keat, Getting CCTBX to work with PyMOL is quite a journey. Please read: https://pymolwiki.org/index.php/CCTBX#Open-Source_PyMOL Cheers, Thomas > On Feb 14, 2019, at 11:27 AM, t...@em.uni-frankfurt.de wrote: > > Dear all, > > After I reinstalled the pmw, it ran through and now it sai

Re: [PyMOL] Problem with Open source Pymol 2.3.0 (missing external GUI)

Dear all, After I reinstalled the pmw, it ran through and now it said 'no modules named _tkinter' as shown below: Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK Detected OpenGL version 3.0. Shaders available. Geometry shaders not available Detected GLSL version 1.30. OpenGL graphics engine:

[PyMOL] Problem with Open source Pymol 2.3.0 (missing external GUI)

To whom it may concern, I installed the pymol on my machine with Ubuntu 18.04.1 LTS I have a problem with 'Qt not available, using GLUT/Tk interface' when install pymol with: python setup.py install --prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no After I installed it wi

[PyMOL] Problem in slice plane visualization of protein

Dear Pymol users, I have a Delphi potential map for the protein. I would like to have a slice plane for this protein. When I use mesh command, it easily aligns with the atoms of the PDB and shows the positive and negative potential. However, there is a problem with the alignment of atoms by usi

[PyMOL] Problem with autodock_plugin.py

I'm running PyMOL v-2.2.0a0 on my Debian Stretch Platform and installed the current autodock plugin. Execution of the plugin on a test system 1ACL.pdb (I have run this system with MGL_Tools as the gui) did produce correct results. However the execution of the plugin differed from what I have

Re: [PyMOL] Problem installing KVFinder plugin

Hi Jenny, Try this fixed version of the plugin: http://pymol.org/tmp/kvfinder_pymolplugin_linux.py Cheers, Thomas > On Feb 8, 2018, at 11:27 AM, Jennifer Miles wrote: > > Hi all, > > I'm Jenny and I am new to this list. If anyone can help I would be very > thankful. > > I am trying to i

[PyMOL] Problem installing KVFinder plugin

Hi all, I'm Jenny and I am new to this list. If anyone can help I would be very thankful. I am trying to install the plugin KVFinder on the newest version of PyMOL with a Microsoft Surface running Windows 10. I have set up the environment variable is detailed in the installation guide shak

Re: [PyMOL] Problem with 'byring' selection

Hi Vijay, All "by" operators have a weak priority. This means the following two expressions are equivalent: elem S & byring all w. 4 of elem O elem S & byring (all w. 4 of elem O) This is a bit unfortunate, I agree that it is not very intuitive. I would actually expect the highest priority. Bu

Re: [PyMOL] Problem with 'byring' selection

Dear Tsjerk and Thomas For the following small molecule: ClC1[OH+]C(Cl)=CN=C1C(=O)N([NH+]1CCC(SC1)F)CCN As you advised to use following logic for selecting nitrogen atoms of rings exclusively. abc=cmd.select('elem N and byring not elem N') Likewise, to select Sulphur atoms which are part of rings o

Re: [PyMOL] Problem with 'byring' selection

Dear Tsjerk and Thomas Thanks for the information. This important information is not available on this page of PyMOLWiki: https://pymolwiki.org/index.php/Selection_Algebra I hope the page will be modified soon to include this important information. Cheers Vijay On 6/3/17, Tsjerk Wassenaar wrote:

Re: [PyMOL] Problem with 'byring' selection

Hi Vijay, It is logic. 'byring elem N' selects all nitrogens and then expands the selection to include the rings in which these participate. 'elem N and byring elem N' does the same, but then intersects (and) to extract only nitrogens. But that is the same as 'elem N'. If you want to have the nitr

[PyMOL] Problem with 'byring' selection

Dear PyMOL Users, I am using PyMOL 1.8.6 on Windows 10 (64 bit) with Python 2.7.12. I was working with small molecule (ClC1[OH+]C(Cl)=CN=C1C(=O)N([NH+]1CCC(SC1)F)CCN). When I tried to select all Nitrogen atoms which are exclusively in the ring only, I tried following command: abc=cmd.select('byring

Re: [PyMOL] problem with alter chain Id

clearing the "rank" property also works for me, then the script should not depend on retain_order anymore: currentName = "%s_%s" % (solutionPymolString, currentChain) cmd.alter(currentName, "chain='%s';rank=-1" % currentChain) However, I think there is also a problem with your script, yo

Re: [PyMOL] problem with alter chain Id

Hi Gregor, Looks like retain_order is on for her. This should fix it: PyMOL> set retain_order, off https://pymolwiki.org/index.php/Retain_order Cheers, Thomas On 01 Mar 2017, at 10:28, Gregor Hagelüken wrote: > Hi, > > I use a python script to copy an object, rotate it, alter its chain ID

[PyMOL] problem with alter chain Id

Hi, I use a python script to copy an object, rotate it, alter its chain ID and then merge it with the original object. Here is the relevant part of my script: angle = 360.0/monomers chains = ["A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K",

Re: [PyMOL] problem with symexp

You are absolutely right, Bernhard! I did indeed have another object in the session that contains a resi 131. I increased the cutoff until symmetry mates were indeed generated. Thanks! On Tue, Feb 7, 2017 at 4:54 PM, Bernhard Lechtenberg < blechtenb...@sbpdiscovery.org> wrote: > Hi Emilia > > I

Re: [PyMOL] problem with symexp

Hmm. I've stumbled on a clue. In case it's a bug in the code or a finding someone in the future might find useful when stumbling into the same problem, here is what I've just found: These two ways of executing symexp give different results - the first does not generate symmetry mates (again, there

[PyMOL] problem with symexp

Hello. I am trying to use symexp to inspect symmetry mates of several structures. I'm mystified about why some input structures lead to quick generation of symmetry mates, while others seem to lead to apparently never-ending symexp execution. All pdb files I've used as input contain a CRYST1 recor

Re: [PyMOL] a pymol problem: cannot transit smoothly between representations in animation

oth to the observer. Best regards Annemarie Honegger Message: 1 Date: Fri, 18 Nov 2016 02:37:50 + From: ? ? Subject: [PyMOL] a pymol problem: cannot transit smoothly between representations in animation To: "pymol-users@lists.sourceforge.net" Message-ID: Content-Type: text/plai

[PyMOL] a pymol problem: cannot transit smoothly between representations in animation

Dear all, I come across the same problem as the link below, which is that my movie made by pymol cannot transit between different representations smoothly. It cannot transit smoothly either when I click the scene buttons. It seems very simple in MovieSchool5 on pymolwiki website. I don't know w

Re: [PyMOL] problem saving the transformed coordinate after alignment

Thanks Gabriel and David for the useful suggestion. Best Regards, Subha On Wed, Oct 19, 2016 at 12:11 PM, David Hall wrote: > I think the answer is to just use save, not that save_transformed function. > > -David > > On Oct 19, 2016, at 1:47 PM, Subha K wrote: > > Hi there, > > I am trying to

Re: [PyMOL] problem saving the transformed coordinate after alignment

I think the answer is to just use save, not that save_transformed function. -David > On Oct 19, 2016, at 1:47 PM, Subha K wrote: > > Hi there, > > I am trying to save the transformed coordinates of an object after performing > an alignment. I came across the save_transformed.py > [https://py

Re: [PyMOL] problem saving the transformed coordinate after alignment

Subha K, You can just call cmd.save or save on the object name as so: fetch 1oky 1t46, async=0 align 1oky, 1t46 save /tmp/1oky_transformed.pdb, 1oky PyMOL will write out the transformed coordinates of 1oky into the pdb file. The structure of the alignment command is such that pymol transforms t

[PyMOL] problem saving the transformed coordinate after alignment

Hi there, I am trying to save the transformed coordinates of an object after performing an alignment. I came across the save_transformed.py [ https://pymolwiki.org/index.php/Modeling_and_Editing_Structures], but, this seems to give a completely different coordinate of the object and not the one th

Re: [PyMOL] problem of optirun in Pymol

Hello: I am using openSUSE 13.2 X64 OS. Pymol works fine without optirun in 1.8.4. Here is output from ./pymol -c PyMOL>python end PyMOL: normal program termination. However, when I type optirun ./pymol -c I didn't obtain any information. regards Albert On 10/10/2016 08:46 PM, Tho

Re: [PyMOL] problem of optirun in Pymol

Hi Albert, Which Linux OS and version (e.g. Ubuntu 12.04 64bit) is this? Does PyMOL work without optirun? Does it work in headless mode (pymol -c)? Thanks, Thomas On 10 Oct 2016, at 14:29, Albert wrote: > Hello: > > I've got 2 graphic card in my laptop: > > Intel® HD Graphics 4600+ Nvidia

[PyMOL] problem of optirun in Pymol

Hello: I've got 2 graphic card in my laptop: Intel® HD Graphics 4600+ Nvidia M1100M I have installed Bumblee optirun in my Linux OS. Currently, command line optirun pymol works fine for Pymol-1.8.2.3. However, I found that it doesn't work for Pymol-1.8.4. When I type optirun pymol Pymol doe

Re: [PyMOL] problem of internal_gui

I see. It works very well now. Thanks a lot On 10/06/2016 10:32 PM, Thomas Holder wrote: > Hi Albert, > > "internal_gui" is now a blacklisted setting not be stored or restored from > session files. > > You can launch PyMOL without internal gui like this from a Terminal: > > pymol -i session.ps

Re: [PyMOL] problem of internal_gui

Hi Albert, "internal_gui" is now a blacklisted setting not be stored or restored from session files. You can launch PyMOL without internal gui like this from a Terminal: pymol -i session.pse When inserting in AxPyMOL, please check the option [x] PyMOL Show (Hide controls) For older versions

[PyMOL] problem of internal_gui

Hello: I used commad line: set internal_gui, off to hide the internal gui. Then I save my pymol session as a .pse file. However, when I reopen this .pse file, the internal_gui is still there. When I insert .pse file to a PPT file, the internal_gui is also there. I am just wondering how to

Re: [PyMOL] Problem with ribbon

Hi Mark, Thanks for the bug report. Confirming that this is a picking bug with ribbon_as_cylinders=1, affecting 1.8.0.0 and later. Picking works correct for me with ribbon_as_cylinders=0 (default). Thomas On 05 Apr 2016, at 10:47, Mark A Saper wrote: > Hi All & Thomas > > There appears to b

[PyMOL] Problem with ribbon

Hi All & Thomas There appears to be a problem with ribbon representations. I am testing MacPyMOL on v 1.8.1.1 but the same behavior is seen with 1.8.0.4. Create a ribbon of a test protein, for example, show ribbon, test and (resi 10:20 or resi 25:35) Double click on the endp

Re: [PyMOL] Problem with isomesh without map

Hi Filip, This is a bug, we'll fix that (probably by next week, looks like an easy fix). Cheers, Thomas On 01 Apr 2016, at 16:16, Filip Leonarski wrote: > Hi, > >I'm struggling with making compact PSE files with Pymol state for ribosome > structures with electron density maps. In gene

[PyMOL] Problem with isomesh without map

Hi, I'm struggling with making compact PSE files with Pymol state for ribosome structures with electron density maps. In general these maps are huge in 200-500 MB range. In previous versions of PyMol (1.7.x) a following trick worked: a) make isomesh b) delete map c) save pse PSE was of a decent

Re: [PyMOL] Problem with pymol installation

Thanks for the help Christoph, it was my mistake, I had installed the 32bit version of python. Everything worked now and pymol is working properly. Best regards Sergio El 21/3/2016 18:34, "Christoph Gohlke" escribió: > Make sure you are using the 64-bit version of Python 2.7: > python-2.7.11.amd6

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 now

[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, numpy

Re: [PyMOL] Problem with feedback push

Thanks, Thomas. On Fri, Mar 11, 2016 at 6:21 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Spencer, > > Yes this is a bug in the feedback stack. As a workaround, you can enable > "cmd" and "parser" feedback manually before popping: > > _ feedback enable, cmd parser, warnings erro

Re: [PyMOL] Problem with feedback push

Hi Spencer, Yes this is a bug in the feedback stack. As a workaround, you can enable "cmd" and "parser" feedback manually before popping: _ feedback enable, cmd parser, warnings errors results _ feedback pop Hope that helps. Cheers, Thomas On 11 Mar 2016, at 04:48, Spencer Bliven wrote: >

Re: [PyMOL] Problem with feedback push

Here's a minimal .pymolrc to demonstrate the issue: #prints response, as expected get cartoon_power _ feedback push _ feedback disable,all,everything # Nothing prints here, as expected get cartoon_power_b _ feedback pop # Still nothing prints! get cartoon_use_shader P.S. The feedback

[PyMOL] Problem with feedback push

Since time immemorial my .pymolrc file has been wrapped by the construct _ feedback push_ feedback disable,all,everything ..._ feedback pop However, I've noticed that my `get` command doesn't print anything unless I specifically re-enable all feedback after starting pymol (or use the unwieldy `p

Re: [PyMOL] Problem aligning two structures: ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?)

Hi Max, If you send me the loop.pdb file then I'll have a look at the issue. Cheers, Thomas On 23 Feb 2016, at 09:03, Ebert Maximilian wrote: > Hi there, > > maybe the subject is a little bit misleading but i couldn’t find any better > description. Basically I am trying to align two PDB st

[PyMOL] Problem aligning two structures: ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?)

Hi there, maybe the subject is a little bit misleading but i couldn’t find any better description. Basically I am trying to align two PDB structures, one is from the PDB directly and the other one is a file containing conformation information about a specific loop of the protein from the PDB. S

[PyMOL] problem saving very large ray traced pngs

Dear all: I'm ray tracing images from a script with the png command, but am having problems saving images larger than ~ 6000x6000. While I get perfect images at 6000x6000, anything larger writes small, empty files (219kb instead of ~50Mb like expected). Is there some sort of buffer size that needs

[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 mailin

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 uniq

[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 Ma

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. Cheers,

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, an

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 source code version pymo

[PyMOL] problem of pymol 1.8

Hello: I've installed the open source code version pymol 1.8 in my Linux OS. 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 named wx Unable to initializ

Re: [PyMOL] Problem with loadBfact.py on windows

This is the problem. Pymol’s working directory is not where you have this file. So, the script never loads. > On Jul 10, 2015, at 12:20 PM, ABEL Stephane 175950 > wrote: > > No such file or directory: './loadB2Fact.py'

[PyMOL] Problem with loadBfact.py on windows (ABEL Stephane 175950

I have reinstall the program and removed an old version of Pymol. Now the script works Thanks -- Message: 2 Date: Fri, 10 Jul 2015 12:44:40 + From: ABEL Stephane 175950 Subject: [PyMOL] Problem with loadBfact.py on windows To: "pymol-

[PyMOL] Problem with loadBfact.py on windows

>> Stéphane, >>It looks like a slash/backslash issue between windows and linux: >>C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py Thanks Jed, How to change it, since I can not to modify it with text editor (it seems to be used by another pr

[PyMOL] Problem with loadBfact.py on windows

Hi Pymol users I use Pymol v1.3 on Windows and I would like to use the loadBfacts.py (http://www.pymolwiki.org/index.php/Load_new_B-factors) (renamed, here, loadB2Fact.py) to change the B factor value according to other values stored in an external txt file. On my linux machine, I use the follo

[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 name

Re: [PyMOL] Problem with How do I change the font in the Tck/Tk external GUI window?

Thanks, it works fine only for the font size of the label of the menu , for example File , but when I open File menu its items all have the original size and not the increased one and the same working there is for the PyMOL viewer window for ASHL , mouse mode etc. It is possible to modify your

Re: [PyMOL] Problem with How do I change the font in the Tck/Tk external GUI window?

te: > > ---- Original Message > > Subject: Re: [PyMOL] Problem with How do I change the font in the Tck/Tk > external GUI window? > Date: Wed, 22 Apr 2015 18:21:56 +0200 > From: s...@tiscali.it > To: Osvaldo Martin > Thanks , > I have made the ch

Re: [PyMOL] Problem with How do I change the font in the Tck/Tk external GUI window?

Hi Saverio, The file is the correct one. Inside the file ./python2.7/dist-packages/pmg_tk/PMGApp.py find the line def initializeTk_unix(self): pass and change it to make it look like def initializeTk_unix(self): self.root.option_add('*Font', 'Lucida 10') self

[PyMOL] Problem with How do I change the font in the Tck/Tk external GUI window?

Hi, I have installed pymol on Ubuntu 14.10 with sudo apt-get install pymol. Now I need to change the size of char in the gui menus. I have read the FAQ about this need. How do I change the font in the Tck/Tk external GUI window? * Open pymol/modules/pmg_tk/PMGApp.py in a text editor

Re: [PyMOL] Problem with h_add hydrogens in sequence viewer

e I want to add hydrogens to a structure or not having the autodock plugin loaded? I've cc'd the author of the plugin, Daniel Seeliger, hopefully he can shed some light on whether this setting is necessary for the functionality of the plugin. Matt *Re: [PyMOL] Problem with h_add hydrog

[PyMOL] problem with "Add Morph to eMovie"

I am having a problem with "Add Morph to eMovie" I have generating a morph and it shows up on the screen fine but when I try to "Add Morph to eMovie", It gives the following error: Error: 1 Exception in Tk callback Function: > (type: ) Args: () Traceback (innermost last): File "/chendata

Re: [PyMOL] Problem with MacPyMOL's linalg package

Thanks for the workaround. It works for me, although it will be a bit hard to incorporate into fully portable scripts. I think I'll avoid using scipy where possible. -Spencer On Wed, Nov 26, 2014 at 6:09 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Spencer, > > thanks for bring

Re: [PyMOL] Problem with MacPyMOL's linalg package

Hi Spencer, thanks for bringing this to our attention. Since OS X 10.9 ships with scipy preinstalled, you can try this workaround which imports scipy from the system python: import sys sys.path.insert(1, '/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python') import scipy

[PyMOL] Problem with MacPyMOL's linalg package

Importing scipy.linalg in MacPyMOL crashes the program for me. Probably the linalg module shipped with MacPyMOL is corrupt or incorrectly linked. I've reproduced it with MacPyMOL 1.6 and 1.7, with both X11 and aqua, and on Mac OS 10.9 and 10.10. I discovered this problem because importing the full

[PyMOL] Problem setting up Pymol with Autodock plugin

Hi Pymol users, currently I'm trying to set up the Autodock Plugin for pymol in Ubuntu 14.04 LTS, 64 bit with an Intel® Core™2 Duo CPU T9400 @ 2.53GHz × 2 and a GeForce 9650M GT/PCIe/SSE2. I installed Pymol, MGLtools and the plugin and I can start the plugin in Pymol. But when I get to the point

[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 so

[PyMOL] pymol, problem, openGL

I encounter the following error when starting pymol on a laptop, and as a result, pymol crashes. can anyone help me to resolve this issue? This Executable Build integrates and extends Open-Source PyMOL 1.7.2.1. Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version

[PyMOL] problem installing on CENTOS 7

Dear Pymol users, I have encountered a problem while trying to install pymol from the source code on Centos 7. I am running the following script for installation: * #!/bin/bash -e prefix=/home/christos/PROGRAMS/PYMOL/OPEN-SOURCE/pymol modules=$prefix/modules python setup.py build install

Re: [PyMOL] Problem with finding polar contacts

Hi Matt, I just double-checked, this was a major refactoring of the dynamic_measures setting which didn't make it into Open-Source PyMOL yet. So if you don't have access to Incentive PyMOL, then please use the workarounds. Cheers, Thomas On 27 Aug 2014, at 11:25, Matthew Baumgartner wrote:

Re: [PyMOL] Problem with finding polar contacts

Hi, I am running version 1.7.2.1 from the svn (revision 4088) and the bug with dynamic_measures persists. Unsetting it as in that link corrects that issue though. I can send you my files that find the error if you would like. Matt On 08/27/2014 11:19 AM, Thomas Holder wrote: > Hi Matt, > > thi

Re: [PyMOL] Problem with finding polar contacts

Hi Matt, this was a bug with the dynamic_measures setting. It was fixed in PyMOL 1.7.0. So please upgrade PyMOL or read this old post for workarounds: http://sourceforge.net/p/pymol/mailman/pymol-users/thread/501949e8.2080...@users.sourceforge.net/ Cheers, Thomas On 27 Aug 2014, at 10:30, Ma

[PyMOL] Problem with finding polar contacts

Hi, I ran into a bug with the find polar contacts function (distance with mode=2) today. The problem arises when I was trying to find the hydrogen bonds between a ligand and a receptor that had been processed with reduce (http://kinemage.biochem.duke.edu/software/reduce.php). A bug/feature of r

[PyMOL] Problem aligning small RNA structures

Hello, I want to make a lot of purely structural alignment of pairs of very short RNA structures, from a length varying from 3 to 12 nucleotides (in every alignments both RNA structures will have the same number of nucleotides), which are supposed to have similar geometry. I tried to use ceali

Re: [PyMOL] problem creating a 2D shape from pymol 3D structure using poseview.py

Hi Maryam, the get_viewport command was added in PyMOL 1.5, so I guess you are using an older version and upgrading will solve your problem. Cheers, Thomas On 06 Jun 2014, at 21:30, M. Faridounnia wrote: > Dear Pymolers, > > I was trying to run the posview.py downloaded from pymolwiki > (

[PyMOL] problem creating a 2D shape from pymol 3D structure using poseview.py

Dear Pymolers, I was trying to run the posview.py downloaded from pymolwiki ( http://www.pymolwiki.org:/index.php/PoseView) but when I try to run the script it gives this lines with the module error on get_viewport. I tried to File "/Volumes/Data/scm/vikki/bld/MacPyMOL.app/pymol/modules/pymol/

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