Hi Young-Jin,
The latest MacPyMOL works fine on El Capitan. XQuartz is not required, unless
you use the "MacPyMOLX11Hybrid" interface.
Which version do you have installed? In my tests, all MacPyMOL versions newer
than 1.4 work on El Capitan (not heavily tested, but they open and render
somethi
Hi,
By accident(!) I upgraded my Mac OS to El Captain. The problem is now I cannot
open my MacPymol that was fine up to previous or lion.
I downloaded XQuartz but still somehow doensn't open my old MacPymol. Has some
one experienced or solved this problem?
Thanks in advance.
Young-Jin
--
Hi CY and Jared,
Jared, CY is actually right that MacPyMOL won't run if you're not logged in to
the Mac desktop. I assume in your test, you were logged in on the imac
(WindowServer running for your user).
For this use case, we now provide the "Mac alternative X11-only build"
(current: "pymol-v
Hi CY -
If you're using the -c flag, you shouldn't need a windowing system at all. The
following works for me between a MacBook Air and an iMac, both running 10.9.5,
with MacPyMOL 1.7.6.0 installed on the iMac.
### begin shell ###
(macbook-air)~ › ssh jared@imac
Password:
Last login: Fri May 2
Hello,
I am trying to run MacPyMOL in command line mode with "-c -q" option. While
directly logged in to the computer, it works. But if I ssh into the
computer (even with X11 forwarding enabled), it fails with some errors
about connecting to WindowServer And I can tell it actually tried to
launch
Hi gg-kawa,
Is your question whether the "File > Open" dialog of the MacPyMOL interface can
start in the current directory? Right now this is not possible (hard coded to
use the home directory), but this is a reasonable feature request and I'm sure
we can change that for the next release.
Chee
Hi Luigi -
To get the right working directory, you can use the full path to the binary
followed by the `-d` flag to run a command (`cd $PWD`) once PyMOL opens.
Personally, I'd alias it in ~/.profile like this:
alias macpymol='/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -d "cd $PWD"'
Al
Hi,
I just started to use MacPyMol from standard unix like Pymol, and I would like
to start MacPyMol from a specific working directory, to have pdb and pse files
I am working on right at hand. However, I can’t understand how to get this
done. I can start by command line
open -a MacPyMol or
Hi everyone,
On 19 Jan 2015, at 03:30, Jordan Willis wrote:
> [...] If you really want a fresh install I would delete all the pymol
> directories in your computer with a find command like, and run a fresh
> install...
>
> sudo cd / ; find . -name “*pymol*" -exec rm -rf {} \;
>
> However, tha
(2) assuming you didn't change it when installing fink, fink will install
pymol in the /sw/bin directory.
(4) this is fink setting environment variables such as PATH. You can add a
line to your .bashrc to source it so it will be sourced every time you open
a terminal.
On Mon, Jan 19, 2015 at
Hi Lau,
If you install from command line, it will most likely install to
/usr/local/bin/. The problem is, your icons probably link to the app you
uninstalled. I would try to find the /usr/local/bin/pymol in your finder
window, then drag the binary to your desktop in you want an icon. If you rea
Hi,
Since my edu copy failed after I upgrade to yosemite. I have downloaded pymol
on my iMac 10.10.1 following the fink for 10.10 instructions on scottslab web:
http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Fink_for_10.10
After setting up fink, I ran sudo apt-get install pymol-py27. I am s
Hi Thomas,
Thank you very much, that was exactly it. After a while I lost track of
what I had installed..
Cheers,
João
2014-02-13 20:59 GMT+01:00 Thomas Holder :
> Hi João,
>
> I guess you had the "psico" module installed, which indeed adds an APBS
> option to the "A > generate" menu.
>
> htt
Hi João,
I guess you had the "psico" module installed, which indeed adds an APBS
option to the "A > generate" menu.
http://pymolwiki.org/index.php/psico
Cheers,
Thomas
João Rodrigues wrote, On 02/13/14 14:44:
> Dear all,
>
> I had the incentive version installed for a while (v1.7 beta2) and
Dear all,
I had the incentive version installed for a while (v1.7 beta2) and I was
surprised to see that in the [A] menu, under 'generate' there was an option
to generate an electrostatic map with apbs.
Unfortunately my laptop HD died, and when I reinstalled everything today
this option is missin
Thanks Thomas, that does work.
On Nov 23, 2012, at 6:31 AM, Thomas Holder wrote:
> Hi Adam,
>
> this seems to be not yet fully implemented with the new shader
> rendering. So you may turn shaders off for now:
>
> PyMOL> unset use_shaders
>
> Ray tracing is not affected, so you still can genera
Hi Adam,
this seems to be not yet fully implemented with the new shader
rendering. So you may turn shaders off for now:
PyMOL> unset use_shaders
Ray tracing is not affected, so you still can generate high quality
figures with correct colors:
PyMOL> ray
Hope that helps.
Cheers,
Thomas
H. Ad
Hi all,
If you run the script below to get a nice blob type surface (great for
illustrations) in 1.4 it all works perfectly, and you can color the new map
surface any color you want.
If you run the same script in 1.5 it all works perfectly too, but no matter
what you do you cannot change the co
to get around this, in the second window, I have to re-navigate to
> the right directory within MacPyMOL as the command line is not enough.
Glad you found a workaround for now. Please let me know about the above.
Cheers,
-- Jason
>> From: jason.vertr...@schrodinger.com
>> Da
econd window, I have to re-navigate to the
right directory within MacPyMOL as the command line is not enough.
Sean
> From: jason.vertr...@schrodinger.com
> Date: Wed, 1 Feb 2012 09:40:20 -0500
> Subject: Re: [PyMOL] MacPyMOL Knowledge of Opened Structures
> To: magic...@hotmail.com
>
Hi Sean,
Sorry to hear you're having problems.
> 1) Load A.pdb into MacPyMOL via "pymol A.pdb"
> 2) Load a CHARMM simulation trajectory into object "A" via "load A.dcd, A"
>
> 3) Load a completely different structure (must have different number of
> atoms than A.pdb), B.pdb, into a separate/new i
Hi PyMOLers,
I noticed some strange behaviour when I do the following:
1) Load A.pdb into MacPyMOL via "pymol A.pdb"2) Load a CHARMM simulation
trajectory into object "A" via "load A.dcd, A"
3) Load a completely different structure (must have different number of atoms
than A.pdb), B.pdb, into a
This depends on how you touch pad is configured and what mode you
selected froum the Mouse menu.
I would suggest a trial and error approach to your problem. Try doing
something and see what it does.
Also Google is your friend. http://www.google.fr/search?q=pymol+mouse
Marius
On Thu, Jun 23, 2011
Hi PyMol users,
How can be I friendly with PyMol using the touch pad (MacBook Pro). What are
the touch pad controls.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
Simplify data backup and recovery for your virtua
Hi Ben,
Thanks for finding this. A colleague looked into this and says it's
fixable. So, we'll have a fix out soon. This is a 10.5-specific
numpy issue. Our update release is planned to follow soon to clear up
a few small issues.
Cheers,
-- Jason
On Thu, Mar 24, 2011 at 3:42 PM, Ben Eisenbr
Hi Jason et al,
We just added PyMOL 1.4 to our software environment, and it looks like
Numpy doesn't want to run on 10.5.8 machines:
PyMOL>import numpy
Traceback (most recent call last):
File "/programs/m/pymol/1.4/MacPyMOL.app/pymol/modules/pymol/parser.py", line
260, in parse
exec(layer.
Great news Mac users:
The just-released Mac OS X 10.5.5 patch fixes the longstanding Stereo 3D
compositing problems under Leopard.
So, if MacPyMOL is the primary application for which you require Stereo 3D,
then as of today, you can safely buy a new Quadro-equipped Mac Pro or
upgrade your existin
Hi,
this is a good idea, and a fairly easy one to implement. do you mean
present all of the pdb files (or the like) from a chosen directory in a
list, and load each molecule via a double-click?
Yes. Exactly. Probably with the directory as a button/textelement at the top
of the list? Whateve
1) Header file display.
2) Filelist : show a directory as a list, to avoid repeated "load"
commands.
this is a good idea, and a fairly easy one to implement. do you mean
present all of the pdb files (or the like) from a chosen directory in a
list, and load each molecule via a double-click?
> 2) filelist:
>
> get a kind of temporary script which would be run on each file in the list
> when you opened it. A kind of frozen view (or a curried one?).
>
> Maybe I should just make it. Then I wouldn't have to explain the idea.
Ok, I was confused on what you meant before. I've been in s
2) filelist:
Yes. Yes it does. Although typing "load " works too...
What I should have said was that I often find myself (and others in our
group have in the past) looking at a whole bunch of structures, one after
the other. When you are looking at 100s of structures in a row it gets
tiring to k
Hi,
Some suggestions:
1) Header file display.
2) Filelist : show a directory as a list, to avoid repeated "load" commands.
3) Ramachandran plots : I keep meaning to try dynoplot on the hybrid
pymol, but never do.
4) Secondary structure display.
Oh the list is endless! But number one suggestion
Hi everyone:
A new plug-in architecture has been added to MacPyMol (available in
versions 1.00 beta 03 and later). This allows plug-ins to be developed
for MacPyMol using the native Mac development tools (Xcode) and
frameworks (Cocoa).
I have a couple of these plug-ins working, and so far they
Hi,
I've noticed this too, it can be quite frustrating. Oddly, the histories for
the two windows (main, and command) seem to be different.
I have never managed to work out what the problem is, but I sometimes wonder
if it is to do with whether a function returns a result or not? (Wild guess!
:)
Hi,
Happy Holidays everyone. This is actually a bug report for Warren.
If you have time, could you work on the implementation of the command
recall option (up and down arrow) in the command text input field in
the OS X-specific part of the window. It often forgets what the
previous com
Hi,
The link to the beta99:
http://delsci.com/beta/macpymol-0_99beta29.tar.gz
says "Page not found".
I wouldn't normally worry, but since using recent betas, my screen
goes odd when waking from sleep. Which isn't much to worry about
either (assuming it is caused by pymol, which I don't kno
nday, November 07, 2005 8:03 PM
> To: Warren DeLano
> Subject: Re: [PyMOL] MacPyMOL 0.99beta29
>
> Has anyone reported problems with these beta versions where
> they launch but when you click on the windows, the
> application seems to quit - using 10.4.3 but this problem
> stem
MacPyMOL Users,
For those experiencing performance and/or flicker issues under 10.4.3,
please update to 0.99Beta29 -- this should be the fastest, most stable
MacPyMOL to date (~2-4X faster than betas 26-28).
http://delsci.com/beta
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
P
I started using the new MacPyMOL beta and have discovered that it
does not support keyboard qualifiers to emulate a multibutton mouse.
This was very useful on my Powerbook as I could do most operations
without plugging in a 3-button mouse. Has anyone also noted this?
__
Hi,
just downloaded the new single window macpymol beta,
runs fine on imacG4
looks very nice, with the handle to minimise the tool bar and command
line etc.
just noticed the
find polar contacts
feature, very handy!
cheers
Dan
Dr. Daniel James White BSc. (Hons.) PhD
Bioimaging Coordinato
I find that MacPyMol 0.98 will not load certain pdb files which are
readily handled by other viewing programs. A common error message I
receive is:
File
"/users/warren/pymol/products/MacPyMOL.app/pymol/modules/pymol/
parser.py", line 356, in parse
exec(com2[nest]+"\n",pymol_names,pym
There are some weird things going on in MacPyMol 0.98beta 27. Are
these known bugs? Wizard Sculpting from menu doesn't work. In mouse
edit mode, control left button is behaving like control-shift left
button.
Suggestions?
_
Mark A. Saper, Ph.D.
sa...@umich.ed
Hi all,
Setup: (Mac OS X, 10.3.8, 1.33 GHz PowerPC G4, 256MB RAM,
PyMOLX11Hybrid v0.95, MaxPyMOL v0.95)
I've created a new plugin and I want it to load on startup.
Using PyMOLX11Hybrid or pymol under linux I would simply place the new
file in the following directory:
/Applications/PyMOLX
Thanks. The new beta is very good. Especially like the
side_chain_helper. Now I just wonder how I can get APBS plugin work
under MacPymol.
Jianghai
==
Jianghai Zhu
Molecular Biology & Biochemistry
Purdue University
==
On Dec 4, 2004, at 12:55 PM
d...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Jianghai Zhu
> Sent: Friday, December 03, 2004 6:00 PM
> To: pymol
> Subject: [PyMOL] macpymol beta bug
>
> Hi, all,
>
> I am using the MacPymol 0.98beta23. I found in the menu
>
Hi, all,
I am using the MacPymol 0.98beta23. I found in the menu "Setting -->
Cartoon" or "Setting --> Transparency" or "Setting --> Rendering" all
the submenus are grey and I can't select them. What command should I
use to do, for example, "use most memory in rendering"?
Jianghai
=
For those of you who prefer the MacPyMOL incentive version of PyMOL for the
Mac, there is a new beta at:
http://delsci.com/macbeta
This copy will enable you to use the sequence browser without having to use
X11 (via PyMOLX11Hybrid, Fink, etc.).
Cheers,
Warren
--
mailto:war...@delsci.com
Warren
Hi Warren,
There was already a similar posting on 2004-9-20
regarding MacPymol crashing during raytracing. I'm
experiencing the same problem. I'm running MacPymol on
a G4 powerbook with MacOS 10.3.6. A few months ago,
raytracing worked fine without any problems.
Now, Pymol crashes even when raytrac
I have my pdb files set to open up by default with MacPyMOL.
Is there a command I can put into .pymolrc or somewhere to
cd to the dirname of the file that I clicked on? Right now
the pwd is the /Applications folder, which means stuff saves to
the wrong place by default.
Did cd $PWD used to work,
hello all,
i am trying to use an external USB device (belkin's nostromo52) to map
keystrokes for use in MacPyMOL. However, it seems that MacPyMOL v.0.95
does not allow this while the "native" os x version 0.93 does.
any suggestions on how to get this to work would be greatly appreciated!
jam
Hi there Warren,
I have been using the v0.94 MacPyMOL that we got from you last december.
It has been very stable on my desktop system:
dual cpu G4867 MHz power PC (version 2.1)
OSX 10.2.8 (6R73)
v0.94
However, using the same version on my lap top has not been so reliable
G4 powerboo
MacPyMOL beta testers:
Are the latest beta builds of MacPyMOL still exhibiting a significant number
of spontaneous crashes in your hands?
http://delsci.com/macpymol
So far, I have been utterly unable to reproduce the reported instability on
my G4 and G5 test systems. Thus, I am wondering whe
Mac Users,
Development and testing on the MacPyMOL Incentive Product continues, but
parallel development on the open-source foundation has interfered a bit.
However, since I promised a public MacPyMOL announcement by late
January, I am hereby announcing that MacPyMOL Beta 2 can now be
downloaded
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