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

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]

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

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.

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: > >

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

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:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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'

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

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

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

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

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 > (

Re: [PyMOL] problem in using delphi to color molecular surface

Hi Rongjin, does your map have the same name like your molecule (like test.pdb and test.phi)? If yes, load them with unique names: PyMOL> load test.pdb, molobj PyMOL> load test.phi, mapobj I used delphi successfully with PyMOL a while back. Cheers, Thomas On 23 May 2014, at 11:12, rjguan w

Re: [PyMOL] Problem Compiling v 1.6.0.0 in 64 bit Debian Testing

On Tue, 25 Jun 2013 09:47:19 -0400 Robert Campbell wrote: > Hi Stephen, > > On Tue, 2013-06-25 09:16 EDT, "Stephen P. Molnar" > wrote: > > > I have just installed the 64 bit Debian Testing distribution in an > > Oracle VM on my laptop as a test bed. > > > > I successfully compiled v 1.6.0.0

Re: [PyMOL] Problem Compiling v 1.6.0.0 in 64 bit Debian Testing

Hi Stephen, On Tue, 2013-06-25 09:16 EDT, "Stephen P. Molnar" wrote: > I have just installed the 64 bit Debian Testing distribution in an > Oracle VM on my laptop as a test bed. > > I successfully compiled v 1.6.0.0 in my 6 bit Debian Wheezy production > OS. > > I didn't get any error messag

Re: [PyMOL] problem with "distance"

Hi Vincent, we introduced dynamic_measures in PyMOL 1.4, which uses the atom ID and is not robust against duplicated IDs. So the workaround here is to switch dynamic_measures off: PyMOL> unset dynamic_measures Hope that helps. Cheers, Thomas vincent Chaptal wrote, On 06/20/13 17:09: > Hi, >

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

Hi Matt, use the "sort" command after adding atoms: PyMOL> h_add 1ycr PyMOL> sort See also: http://pymolwiki.org/index.php/Sort Cheers, Thomas Matthew Baumgartner wrote, On 03/26/13 13:59: > Hi, > When I fetch a new structure (1YCR, for example) then run 'h_add 1ycr' > the hydrogens are add

Re: [PyMOL] problem setting up morph under eMovie

Hi Michael, have you tried to use the command line for morphing? Have a look at the example section of http://pymolwiki.org/index.php/Morph Regarding the eMovie button, I'll forward the question to the eMovie author, he should know the answer. Cheers, Thomas Michael L Oldham wrote, On 02/04/1

Re: [PyMOL] Problem Opening Session File

Hi Pete, Versions of PyMOL before v1.5 will not be able to properly read maps in session files written by PyMOL v1.5 and later. We updated the map code to enable visualization of data beyond the unit cell, and added some new functions that allow you to copy symmetry and space group information fro

Re: [PyMOL] Problem Opening Session File

The handling of density maps changed with (I believe) version 1.5 - earlier versions would just load the map as given, later ones appear to try to do symmetry expansion (even if the map isn't covering the ASU). I've seen this result in a similar error message when loading session files (with el

Re: [PyMOL] problem installing/running mengine (freemol)

Hi Osvaldo, > Thanks for your answer. > I modified the lines you told me in the file freemol/src/mengine/field.h > (not field.c). Now the clean command works (altought there is no message > indicating the finalization of the minimization). Great, I'm glad that worked. And, yes, you're correct, I

Re: [PyMOL] problem installing/running mengine (freemol)

Hi Osvaldo, > when I run the clean command (I tried with different molecules and file > formats) I get > > Cleaning 176 atoms. Please wait... > *** buffer overflow detected ***: /opt/freemol/freemol/bin/mengine.exe > terminated Thanks for being patient on this, I just now had time to look at th

Re: [PyMOL] Problem with APBS Plugin

I have the same problems. If you use the pymol pqr grid instead of the pdb2pqr, you will find that it works. Sent from my iPhone On Aug 8, 2012, at 6:24 PM, Warren Gallin wrote: > Hi, > >I am trying to generate some electrostatic surfaces using the APB plugin, > but I am getting the foll

Re: [PyMOL] problem compiling latest svn on RHEL system

So, i took the solution to install CentOS 6.2 on one machine. Together with the EPEL repository, I could install all the necessary libraries. And then compile on CentOS. It now works fine for all our RHEL 6.2 computers in the group. Thanks! 2012/5/18 Jason Vertrees > Hi Troels, > > Sorry for

Re: [PyMOL] problem compiling latest svn on RHEL system

Hi Troels, Sorry for these delayed responses. For the last two weeks, I've been in training our PyMOL users across the "pond" in Europe. This seems like an RHEL problem. Have you checked their lists for answers? libpng-devel is important enough to be used by lots of people. Cheers, -- Jason On

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 b

Re: [PyMOL] problem with running py script in pymol

> But I get the following errors. Could anyone please help me in > overcoming this error? > > Traceback (most recent call last): >File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py", > line 338, in parse > parsing.run_file(path,self.pymol_names,self.pymol_names) >File "C:

Re: [PyMOL] problem in changing object names

Hi, Why can't you use set_name tun1, ..., etc? The attempt trying to change names is quite odd, and won't do what you want anyway. You could use basename="your_tag" cmd.set_name(cmd.get_object_list()[0], basename+"_subtag") ... and so on. Cheers, Tsjerk On Mar 21, 2012 6:56 AM, "Sajeewa Pemasi

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 PyM

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

Troels Emtekær Linnet wrote, On 03/04/12 21:28: > sudo apt-get install python-imaging genius, on a windows installation? :-/ -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Virtualizati

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

sudo apt-get install python-imaging Best Troels 2012/3/4 Jason Vertrees > 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 1

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 wrote: > Hello guys. > > I have a problem installing Contact

Re: [PyMOL] Problem with open source pymol

Thanks, Lina. It worked beautifully. On Wed, Dec 21, 2011 at 8:14 AM, lina wrote: > If you have fink, > > you can have an alternative way of installation. > > fink install pymol-py27 > > It works well. > > On Wed, Dec 21, 2011 at 4:19 AM, Lauren Porter > wrote: > > Pymol 1.3 is still available

Re: [PyMOL] Problem with open source pymol

If you have fink, you can have an alternative way of installation. fink install pymol-py27 It works well. On Wed, Dec 21, 2011 at 4:19 AM, Lauren Porter wrote: > Pymol 1.3 is still available online, but it doesn't work with any versions > of python greater than 2.5.  If I try to install Pymol

Re: [PyMOL] Problem with open source pymol

Pymol 1.3 is still available online, but it doesn't work with any versions of python greater than 2.5. If I try to install Pymol 1.4 doesn't work when I install it (problems with the GLEW library). I don't understand that problem either. It looks like it can't find GLEW, but I know that its path

Re: [PyMOL] Problem with open source pymol

Yes, I have GLUT installed (I'm using the framework), and I rerouted everything to make sure it was pointing to the right path. After doing that, I rebuilt and got a new error: Python 2.5.4 (r254:67916, Aug 1 2011, 15:52:49) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type "help", "copyright",

Re: [PyMOL] Problem with open source pymol

2011-12-19 12:32:21.901 Python[243:5d03] *** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason*: '-[GLUTApplication _setup:]:* unrecognized -- Do you have glut installed ? http://www.pymolwiki.org/index.php/Linux_Install#Requiremen

Re: [PyMOL] Problem with distance command(?)

Hi Jason, > This bug is now fixed in the open-source code (commit 3974) > and will be fixed in the next beta build of Incentive PyMOL. That was quick work - thanks! Kind regards James __ PLEASE READ: This email is confidenti

Re: [PyMOL] Problem with distance command(?)

James, This bug is now fixed in the open-source code (commit 3974) and will be fixed in the next beta build of Incentive PyMOL. Cheers, -- Jason On Wed, Dec 14, 2011 at 6:23 PM, James Davidson wrote: > Dear All, > > I am currently having a problem with the distance command when applied to > me

Re: [PyMOL] Problem with distance command(?)

James, > I am currently having a problem with the distance command when applied to > merged objects.  The real case is actually when I remove a ligand from a > binding site and merge in a new ligand.  But as a simple example, I think I > can demonstrate with the following: The problem is in the c

Re: [PyMOL] Problem with distance command(?)

Thanks for the reply Thomas, and thanks for the suggested work-around, Troels. I am presuming that the bug is in the distance command, rather than in 'create'. I previously tried to find where this might have crept in (but to be honest, didn't really know what I was looking for!). I did note th

Re: [PyMOL] Problem with distance command(?)

Hi James, I can confirm this, looks like a recently introduced bug. Correct result with pymol-1.4.1 Wrong result with pymol-1.5.0b1 Troels is right, if you alter the IDs you can work around the bug. alter ala2, ID=ID+100 But AFAIK only `index` is a unique atom property in PyMOL, so still I wo

Re: [PyMOL] Problem with distutils build 3951 on Ubuntu Lucid 10.04 : X Error of failed request: BadRequest

Hi Jason, Thanks for your reply. This was indeed a driver problem . Ubuntu had pushed a natty kernel headers to lucid users by mistake and that update broke my nvidia 195.36.24 x86_64 driver. To fix it , In desperation,

Re: [PyMOL] Problem with distutils build 3951 on Ubuntu Lucid 10.04 : X Error of failed request: BadRequest

Hari, >  Hit ESC anytime to toggle between text and graphics. >  Detected OpenGL version 2.0 or greater.  Shaders available. > X Error of failed request:  BadRequest (invalid request code or no such > operation) >   Major opcode of failed request:  128 (GLX) >   Minor opcode of failed request:  16

Re: [PyMOL] Problem reading multiframe pdb file for animation

Hi Peter, > When using Open-Source PyMOL 0.99rc6 I read in a pdb file which has > 40 coordinate sets (each is one frame in an animation) each beginning > with: > HEADER Output iset= n "_G=r_0_01" Please replace your HEADER stamps with REMARK in your PDB file. Then load with multiplex=0.

Re: [PyMOL] Problem reading multiframe pdb file for animation

Hi Peter, If you could send me the PDB (or one like it) I'd like to see it. The known flags for controlling how PyMOL loads multi-state files are: discrete= 0 or 1 If 0, then all states must have the same number of atoms and similar connectivity If 1, then all states are treated as differen

Re: [PyMOL] Problem when running APBS 1.1.0 in Pymol 1.3 - protein is misplaced

> Dear All, > > I am running APBS 1.1.0. via the "APBS Tools2" plugin on Pymol 1.3 (either on > Linux or Vista). > As usual i fetch a pdb structure and then do a "set grid" and then "run APBS". > This works fine for most of the proteins I am working on, however I found out > that in some of the p

Re: [PyMOL] Problem when running APBS 1.1.0 in Pymol 1.3 - protein is misplaced

It appears that PyMOL is writing out an improperly-formated PDB file here (the coordinate sections do not start at the correct columns). I'm looking into it. Thanks, -Michael On Tue, Sep 14, 2010 at 10:42 AM, Afonso Duarte wrote: > > Dear All, > > I am running APBS 1.1.0. via the "APBS Tools2"

Re: [PyMOL] Problem with coloring of sticks

Hi all, Before I go out an buy an ATI video card to test/debug this, can anyone else verify that this error occurs on the 965G or other desktop card? The 965GM, I think is a mobile-only card. If someone is experiencing issues on a desktop box, please provide me with the exact setup. Cheers, --

Re: [PyMOL] Problem with coloring of sticks

Hi Bernhard, After re-reading Timothy's original email, this very much sounds like a driver issue. Timothy reports proper functionality using the same laptop, but in Windows. Regardless, here's how I responded to Timothy's question (offline) about the coloring problems: """ Hi Tim, There are q

Re: [PyMOL] Problem with display on Intel graphics card

Hi Timothy, Can you please send me the screenshots. Adaptation to the vagaries of vendor-specific hardware is always an issue. I'm happy to look into the problem. Thanks, -- Jason On Tue, May 25, 2010 at 6:31 PM, Tim Travers wrote: > > Good afternoon, > > Sorry for posting twice, just in cas

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,

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 wrote: > Stephen P. Molnar wrote: >

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 succesfu

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. U

Re: [PyMOL] Problem Compiling Pymol 1.2.x

On 11/20/2009 01:57 PM, Andreas Förster wrote: > 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

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 > s

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 in showing the electron density map

Hi Peter, On Fri, 03 Apr 2009 02:38:03 +0530, peter hudson wrote: > Hello all > > I am trying to upload the ED map on pymol. but, it is not visible on the > screen. Although i checked at pymol wiki and i did as it is given on the > wiki. > For example. > > I took ccp4 format map and coverted i

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