Re: [PyMOL] MacPymol

[Thomas Holder]

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 
something). Some of them only open if you select "Allow apps downloaded from: 
Anywhere" in the Security & Privacy System Preferences. Some older versions 
also might have problems with multiple or external displays.

Cheers,
  Thomas

On 02 Dec 2015, at 18:01, Young-Jin Cho  wrote:

> 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

-- 
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PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] MacPymol

[Young-Jin Cho]

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
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[PyMOL] MacPyMOL in command line mode

[Yu Chen]

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 the GUI very briefly, then returned to the command line to process
the scripts. Is this right? Can I run it remotely on another computer just
from pure command line.

Thanks.

CY
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Re: [PyMOL] MacPyMOL in command line mode

[Sampson, Jared]

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 29 10:37:12 2015 from macbook-air
(imac)~ › /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -cqkd fetch 3opl, 
async=0; save tmp.png
PyMOLfetch 3opl, async=0; save tmp.png
HEADERHYDROLASE   01-SEP-10   3OPL
TITLE ESBL R164H MUTANT SHV-1 BETA-LACTAMASE
COMPNDMOL_ID: 1;
COMPND   2 MOLECULE: BETA-LACTAMASE SHV-1;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: PIT-2;
COMPND   5 EC: 3.5.2.6;
COMPND   6 ENGINEERED: YES;
COMPND   7 MUTATION: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 4 symmetry operators.
 CmdLoad: ./3opl.pdb loaded as 3opl.
 Ray: render time: 0.99 sec. = 3622.2 frames/hour (0.99 sec. accum.).
 ScenePNG: wrote 640x480 pixel image to file tmp.png.
(imac)~ › exit
logout
Connection to imac closed.
(macbook-air)~ ›
### end shell ###

The file ~/tmp.png is created on the iMac.  I also used -k to prevent PyMOL 
from reading my ~/.pymolrc; and -d to pass the string of PyMOL commands.  If 
you're running a .pml script, you don't need to include -d, just the path to 
the script (which must be on the remote machine).  As you noted, when it runs I 
see the MacPyMOL application icon pop into the Dock on the iMac and then 
disappear as soon as the script finishes.

Hope that helps.

Cheers,
Jared

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Xiangpeng Kong Lab
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http://kong.med.nyu.edu/






On May 28, 2015, at 11:28 AM, Yu Chen che...@umbc.edumailto:che...@umbc.edu 
wrote:

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 the GUI very 
briefly, then returned to the command line to process the scripts. Is this 
right? Can I run it remotely on another computer just from pure command line.

Thanks.

CY
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Re: [PyMOL] MacPyMOL in command line mode

[Thomas Holder]

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-v1.7.6.1-Darwin-x86_64.tar.gz) which is built like on a unix 
system, linked to X11 graphics (requires XQuartz) instead of OSX Cocoa. This 
version works without a WindowsServer in command line -c -q mode. CY, please 
give that version a try.

Cheers,
  Thomas

On 29 May 2015, at 12:35, Sampson, Jared jared.samp...@nyumc.org wrote:

 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 29 10:37:12 2015 from macbook-air
 (imac)~ › /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -cqkd fetch 
 3opl, async=0; save tmp.png
 PyMOLfetch 3opl, async=0; save tmp.png
 HEADERHYDROLASE   01-SEP-10   3OPL
 TITLE ESBL R164H MUTANT SHV-1 BETA-LACTAMASE
 COMPNDMOL_ID: 1;
 COMPND   2 MOLECULE: BETA-LACTAMASE SHV-1;
 COMPND   3 CHAIN: A;
 COMPND   4 SYNONYM: PIT-2;
 COMPND   5 EC: 3.5.2.6;
 COMPND   6 ENGINEERED: YES;
 COMPND   7 MUTATION: YES
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 4 symmetry operators.
  CmdLoad: ./3opl.pdb loaded as 3opl.
  Ray: render time: 0.99 sec. = 3622.2 frames/hour (0.99 sec. accum.).
  ScenePNG: wrote 640x480 pixel image to file tmp.png.
 (imac)~ › exit
 logout
 Connection to imac closed.
 (macbook-air)~ › 
 ### end shell ###
 
 The file ~/tmp.png is created on the iMac.  I also used -k to prevent PyMOL 
 from reading my ~/.pymolrc; and -d to pass the string of PyMOL commands.  If 
 you're running a .pml script, you don't need to include -d, just the path to 
 the script (which must be on the remote machine).  As you noted, when it runs 
 I see the MacPyMOL application icon pop into the Dock on the iMac and then 
 disappear as soon as the script finishes.
 
 Hope that helps.
 
 Cheers,
 Jared
 
 --
 Jared Sampson
 Xiangpeng Kong Lab
 NYU Langone Medical Center
 http://kong.med.nyu.edu/
 
 
 On May 28, 2015, at 11:28 AM, Yu Chen che...@umbc.edu wrote:
 
 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 the 
 GUI very briefly, then returned to the command line to process the scripts. 
 Is this right? Can I run it remotely on another computer just from pure 
 command line. 
 
 Thanks. 
 
 CY


-- 
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] MacPyMol working dir

[Thomas Holder]

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.

Cheers,
  Thomas

On 15 Apr 2015, at 16:20, Luigi Cavallo lcava...@unisa.it wrote:

 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
 /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL 
 
 and it works, but as I try the “open” option, it starts from my home 
 directory, so I have to go down the folders tree. Annoying.  I’ve seen that I 
 can start as
 
 /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -m
 
 I have a less fancy graphics, but if I try to “open” a file, it starts 
 looking in the directory I started from. Cool. However, according to the 
 manual I loose plugin control.
 Just wondering if there is a way to have the “open” file starting from the 
 working directory with the fancy interface of MacPyMol, rather than the basic 
 Unix interface.
 
 Thanks,
 gg-kawa

-- 
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PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] MacPyMol working dir

[Sampson, Jared]

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'

Alternatively, you could install the open source version, e.g. using 
Homebrewhttp://www.pymolwiki.org/index.php/MAC_Install#Installing_PyMOL_with_Homebrew,
 which opens properly in the working directory as well.

Cheers,
Jared

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Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Apr 15, 2015, at 4:20 PM, Luigi Cavallo 
lcava...@unisa.itmailto:lcava...@unisa.it wrote:

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
/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL

and it works, but as I try the “open” option, it starts from my home directory, 
so I have to go down the folders tree. Annoying.  I’ve seen that I can start as

/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -m

I have a less fancy graphics, but if I try to “open” a file, it starts looking 
in the directory I started from. Cool. However, according to the manual I loose 
plugin control.
Just wondering if there is a way to have the “open” file starting from the 
working directory with the fancy interface of MacPyMol, rather than the basic 
Unix interface.

Thanks,
gg-kawa


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[PyMOL] MacPyMol working dir

[Luigi Cavallo]

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
/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL 

and it works, but as I try the “open” option, it starts from my home directory, 
so I have to go down the folders tree. Annoying.  I’ve seen that I can start as

/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -m

I have a less fancy graphics, but if I try to “open” a file, it starts looking 
in the directory I started from. Cool. However, according to the manual I loose 
plugin control.
Just wondering if there is a way to have the “open” file starting from the 
working directory with the fancy interface of MacPyMol, rather than the basic 
Unix interface.

Thanks,
gg-kawa


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[PyMOL] MacPyMOL fink download

[Lau Sze Yi (SIgN)]

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 still quite 
new to unix,  and have a few questions that I need clarified:

 1.  I did not uninstall my old copy of MacPyMOL. I assume there is no 
interference between different versions?
 2.  Where exactly is the newly installed pymol stored?
 3.  I did not notice this before, but I have two copies of MacPyMOL buried in 
one of the folders of my PHENIX versions 1.8.3-1479 and 1.9-1692 respectively. 
I wasn’t sure if the pymol was already present when I downloaded my phenix or 
these are the ones I installed. I can open pymol using command line but not 
double clicking the icons in my finder window. Both these versions were shown 
to be last opened corresponding to the time I  used command line pymol on two 
separate time. I am confused now as to when I type pymol in my terminal, which 
MacPyMOL is supposed to be opened.
 4.  I need to do source /sw/bin/init.sh before I can start pymol. Is init.sh 
same as starting up fink to do its job? Is there a direct way to open pymol.

Appreciate your advice.

Regards,
Sze Yi


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Re: [PyMOL] MacPyMOL fink download

[Jordan Willis]

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 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, that will delete any files that have the word “pymol” in it. So if you 
have some sessions you need that have those words in it do not run that 
command. 



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Phone: 1-858-784-1000 ext: 43377

On Jan 18, 2015, at 11:29 PM, Lau Sze Yi (SIgN) 
lau_sze...@immunol.a-star.edu.sg wrote:

 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 still 
 quite new to unix,  and have a few questions that I need clarified:
 I did not uninstall my old copy of MacPyMOL. I assume there is no 
 interference between different versions? 
 Where exactly is the newly installed pymol stored? 
 I did not notice this before, but I have two copies of MacPyMOL buried in one 
 of the folders of my PHENIX versions 1.8.3-1479 and 1.9-1692 respectively. I 
 wasn’t sure if the pymol was already present when I downloaded my phenix or 
 these are the ones I installed. I can open pymol using command line but not 
 double clicking the icons in my finder window. Both these versions were shown 
 to be last opened corresponding to the time I  used command line pymol on two 
 separate time. I am confused now as to when I type pymol in my terminal, 
 which MacPyMOL is supposed to be opened. 
 I need to do source /sw/bin/init.sh before I can start pymol. Is init.sh same 
 as starting up fink to do its job? Is there a direct way to open pymol.
 Appreciate your advice.
 
 Regards,
 Sze Yi
 
 
 --
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Re: [PyMOL] MacPyMOL fink download

[David Hall]

(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 2:29 AM, Lau Sze Yi (SIgN) 
lau_sze...@immunol.a-star.edu.sg wrote:

 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 still
 quite new to unix,  and have a few questions that I need clarified:

1. I did not uninstall my old copy of MacPyMOL. I assume there is no
interference between different versions?
2. Where exactly is the newly installed pymol stored?
3. I did not notice this before, but I have two copies of MacPyMOL
buried in one of the folders of my PHENIX versions 1.8.3-1479 and 1.9-1692
respectively. I wasn’t sure if the pymol was already present when I
downloaded my phenix or these are the ones I installed. I can open pymol
using command line but not double clicking the icons in my finder window.
Both these versions were shown to be last opened corresponding to the time
I  used command line pymol on two separate time. I am confused now as
to when I type pymol in my terminal, which MacPyMOL is supposed to be
opened.
4. I need to do source /sw/bin/init.sh before I can start pymol. Is
init.sh same as starting up fink to do its job? Is there a direct way to
open pymol.

 Appreciate your advice.

 Regards,
 Sze Yi




 --
 New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
 GigeNET is offering a free month of service with a new server in Ashburn.
 Choose from 2 high performing configs, both with 100TB of bandwidth.
 Higher redundancy.Lower latency.Increased capacity.Completely compliant.
 http://p.sf.net/sfu/gigenet
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Re: [PyMOL] MacPyMOL fink download

[Thomas Holder]

Hi everyone,

On 19 Jan 2015, at 03:30, Jordan Willis jwillis0...@gmail.com 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, that will delete any files that have the word “pymol” in it. So if 
 you have some sessions you need that have those words in it do not run that 
 command. 

PLEASE DO NOT RUN THIS, this can screw up A LOT of things. Just to get an idea, 
here a couple of files that would have been deleted on my system:

/Users/thomas/.pymolrc.py
/sw/fink/10.7/stable/main/finkinfo/sci/pymol-py.info
/sw/fink/10.7/stable/main/finkinfo/sci/pymol-py.patch
/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/pymol
/Applications/ccp4-6.4.0/lib/python2.7/site-packages/iotbx/pymol.py
/Applications/Chimera.app/Contents/Resources/share/Molecule/copymolecule.py
/sw/lib/cctbx/cctbx_sources/iotbx/pymol.py
... and many more ...

-- 
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Schrödinger, Inc.


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[PyMOL] MacPymol + Missing Features (APBS?)

[João Rodrigues]

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 missing, although there is an apbs executable under
MacPyMOL.app/.../ext/bin. Is there something I'm missing or was this an
experimental feature that didn't make the cut?

Cheers,

João
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Re: [PyMOL] MacPymol + Missing Features (APBS?)

[Thomas Holder]

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 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 missing, although there is an apbs executable under
 MacPyMOL.app/.../ext/bin. Is there something I'm missing or was this an
 experimental feature that didn't make the cut?
 
 Cheers,
 
 João

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Re: [PyMOL] MacPymol + Missing Features (APBS?)

[João Rodrigues]

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 thomas.hol...@schrodinger.com:

 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 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 missing, although there is an apbs executable under
  MacPyMOL.app/.../ext/bin. Is there something I'm missing or was this an
  experimental feature that didn't make the cut?
 
  Cheers,
 
  João

 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor


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Re: [PyMOL] MacPyMOL 1.4 vs 1.5 problem with color

[Thomas Holder]

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. Adam Steinberg wrote, On 11/20/12 03:40:
 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 color of the new map surface from the 
 default white to any other color. Not via the settings, the command line, nor 
 the gui menus.
 
 Is there a command I can add to the script below that will allow me to change 
 the color of map surface (surfA)? or are there new commands that I should use 
 in this script to make this work in 1.5? or is this now broken in 1.5.0.4?
 
 ---
 set surface_quality, 1
 alter all, b=50
 alter all, q=1
 set gaussian_resolution,5
 map_new mapA, gaussian, 1, sele or pdb, 6
 isosurface surfA, mapA
 -
 
 Thanks in advance for the help!
 
 
 H. Adam Steinberg
 7904 Bowman Rd
 Lodi, WI 53555
 608/592-2366

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PyMOL Developer
Schrödinger Contractor

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Re: [PyMOL] MacPyMOL 1.4 vs 1.5 problem with color

[H. Adam Steinberg]

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 generate high quality
 figures with correct colors:
 
 PyMOL ray
 
 Hope that helps.
 
 Cheers,
  Thomas
 
 H. Adam Steinberg wrote, On 11/20/12 03:40:
 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 color of the new map surface from the 
 default white to any other color. Not via the settings, the command line, 
 nor the gui menus.
 
 Is there a command I can add to the script below that will allow me to 
 change the color of map surface (surfA)? or are there new commands that I 
 should use in this script to make this work in 1.5? or is this now broken in 
 1.5.0.4?
 
 ---
 set surface_quality, 1
 alter all, b=50
 alter all, q=1
 set gaussian_resolution,5
 map_new mapA, gaussian, 1, sele or pdb, 6
 isosurface surfA, mapA
 -
 
 Thanks in advance for the help!
 
 
 H. Adam Steinberg
 7904 Bowman Rd
 Lodi, WI 53555
 608/592-2366
 
 -- 
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor
 
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H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] MacPyMOL Knowledge of Opened Structures

[Jason Vertrees]

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 instance/window of MacPyMOL
 via pymol B.pdb
 4) Load a CHARMM simulation trajectory into object B via load B.dcd, B

 Loading of this second trajectory complains with the following error:

 ObjectMolecule: plugin 'dcd' cannot open file because the number of atoms in
 the object (4551) did not equal the number of atoms in the 'dcd' (5889)
 file.

I wrote this error message. PyMOL counts the atoms in the object and
makes sure each frame of the trajectory has an equivalent number. This
stops PyMOLers from accidentally working with incorrectly paired data
-- which happened quite a bit.

 I should mention that in the real example, A.pdb and B.pdb actually have
 the same name but are located in different directories (in case it matters).

Seeing this makes me think of two possibilities. First, you possibly
made a simple mistake on disk and B.pdb and B.dcd don't actually
match. Do these _exact_ files using the exact same commands work the
same in Linux? (Can you md5sum the files to check?) Second, if PyMOL
is sharing data then, because they have the same file name, you'll
have to rename one to something else, like A2.

Let us know.

Cheers,

-- Jason




 In this error, the number 5889 corresponds to the number of atoms in A.pdb
 while 4551 corresponds to the number of atoms in B.pdb.  Again, these are
 two separate windows of MacPyMOL (i.e. I did NOT load A.pdb and B.pdb into
 the same window).  Somehow, the first instance of PyMOL sees what is
 happening in the other.

 I should mention that in the real example, A.pdb and B.pdb actually have
 the same name but are located in different directories (in case it matters).

 On a non-Mac machine, these commands are fine.  As an experienced PyMOL
 user, it was quite embarrassing when a set of commands/steps that worked on
 a Linux workstation does not work on a Mac (especially when I was trying to
 show the simulations to a VMD user).  I'm fairly new to Macs so maybe
 there's something that I need to do?

 Also, when I load up B.pdb (the second structure), the MacPyMOL doesn't seem
 to run hide all and show cartoon from my .pymolrc.

 Any help/suggestions would be greatly appreciated!

 Sean

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Re: [PyMOL] MacPyMOL Knowledge of Opened Structures

[Sean Law]

Jason (and PyMOLers),
To clarify, B.dcd matches the number of atoms in B.pdb and A.dcd also matches 
the number of atoms in A.pdb.  In the previous example, if I perform steps 3 
and 4 first then it works in loading B.dcd into object B.  Then, if I try to 
open up A.pdb into a separate PyMOL window, loading of A.dcd into object A 
fails with the same error (obviously, with the atom numbers reversed).  Thus, 
somehow, the second PyMOL window is retaining/obtaining information from the 
first PyMOL window.
Okay, I've managed to make a little bit more progress on identifying this 
problem.  After navigating to the directory for A.pdb (/path/to/A/), I open 
A.pdb and load in A.dcd (the window is kept open).  No problem.  Then, on the 
command line (not in PyMOL), I navigate to the directory for B.pdb 
(/path/to/B/) and open B.pdb in a new PyMOL window (i.e. pymol B.pdb).  In 
this (B) window, if I do a pwd in the PyMOL GUI, instead of saying 
/path/to/B it returns /path/to/A!  For some reason, it doesn't recognize 
that I've changed directories.  This explains why it was throwing the atoms in 
object did not equal number of atoms error because it was indeed trying to 
load A.dcd into object B (which have different atom numbers).  I assumed that 
navigating to /path/to/B on the command line (outside of PyMOL) and then 
calling PyMOL from there was enough for PyMOL to know where it was.  However, 
it appears that having one instance of PyMOL already open will somehow affect 
the path of the second window.  Perhaps there's a workaround for this?  I've 
never encountered this behaviour on Linux before.  
For now, 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.
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
 CC: pymol-users@lists.sourceforge.net
 
 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 instance/window of MacPyMOL
  via pymol B.pdb
  4) Load a CHARMM simulation trajectory into object B via load B.dcd, B
 
  Loading of this second trajectory complains with the following error:
 
  ObjectMolecule: plugin 'dcd' cannot open file because the number of atoms in
  the object (4551) did not equal the number of atoms in the 'dcd' (5889)
  file.
 
 I wrote this error message. PyMOL counts the atoms in the object and
 makes sure each frame of the trajectory has an equivalent number. This
 stops PyMOLers from accidentally working with incorrectly paired data
 -- which happened quite a bit.
 
  I should mention that in the real example, A.pdb and B.pdb actually have
  the same name but are located in different directories (in case it matters).
 
 Seeing this makes me think of two possibilities. First, you possibly
 made a simple mistake on disk and B.pdb and B.dcd don't actually
 match. Do these _exact_ files using the exact same commands work the
 same in Linux? (Can you md5sum the files to check?) Second, if PyMOL
 is sharing data then, because they have the same file name, you'll
 have to rename one to something else, like A2.
 
 Let us know.
 
 Cheers,
 
 -- Jason
 
 
 
 
  In this error, the number 5889 corresponds to the number of atoms in A.pdb
  while 4551 corresponds to the number of atoms in B.pdb.  Again, these are
  two separate windows of MacPyMOL (i.e. I did NOT load A.pdb and B.pdb into
  the same window).  Somehow, the first instance of PyMOL sees what is
  happening in the other.
 
  I should mention that in the real example, A.pdb and B.pdb actually have
  the same name but are located in different directories (in case it matters).
 
  On a non-Mac machine, these commands are fine.  As an experienced PyMOL
  user, it was quite embarrassing when a set of commands/steps that worked on
  a Linux workstation does not work on a Mac (especially when I was trying to
  show the simulations to a VMD user).  I'm fairly new to Macs so maybe
  there's something that I need to do?
 
  Also, when I load up B.pdb (the second structure), the MacPyMOL doesn't seem
  to run hide all and show cartoon from my .pymolrc.
 
  Any help/suggestions would be greatly appreciated!
 
  Sean
 
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Re: [PyMOL] MacPyMOL Knowledge of Opened Structures

[Jason Vertrees]

Hi Sean,

 To clarify, B.dcd matches the number of atoms in B.pdb and A.dcd also
 matches the number of atoms in A.pdb.  In the previous example, if I perform
 steps 3 and 4 first then it works in loading B.dcd into object B.  Then,
 if I try to open up A.pdb into a separate PyMOL window, loading of A.dcd
 into object A fails with the same error (obviously, with the atom numbers
 reversed).  Thus, somehow, the second PyMOL window is retaining/obtaining
 information from the first PyMOL window.

Is this the open-source build or Incentive MacPyMOL? Also, what
command do you issue to start MacPyMOL from the command line?


 Okay, I've managed to make a little bit more progress on identifying this
 problem.  After navigating to the directory for A.pdb (/path/to/A/), I open
 A.pdb and load in A.dcd (the window is kept open).  No problem.  Then, on
 the command line (not in PyMOL), I navigate to the directory for B.pdb
 (/path/to/B/) and open B.pdb in a new PyMOL window (i.e. pymol B.pdb).  In
 this (B) window, if I do a pwd in the PyMOL GUI, instead of saying
 /path/to/B it returns /path/to/A!  For some reason, it doesn't recognize
 that I've changed directories.  This explains why it was throwing the atoms
 in object did not equal number of atoms error because it was indeed trying
 to load A.dcd into object B (which have different atom numbers).  I
 assumed that navigating to /path/to/B on the command line (outside of
 PyMOL) and then calling PyMOL from there was enough for PyMOL to know where
 it was.  However, it appears that having one instance of PyMOL already open
 will somehow affect the path of the second window.  Perhaps there's a
 workaround for this?  I've never encountered this behaviour on Linux before.

Interesting. I could see how this could get confusing, especially
since in reality your files are named the same thing.

 For now, 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
 Date: Wed, 1 Feb 2012 09:40:20 -0500
 Subject: Re: [PyMOL] MacPyMOL Knowledge of Opened Structures
 To: magic...@hotmail.com
 CC: pymol-users@lists.sourceforge.net


 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 instance/window of
  MacPyMOL
  via pymol B.pdb
  4) Load a CHARMM simulation trajectory into object B via load B.dcd,
  B
 
  Loading of this second trajectory complains with the following error:
 
  ObjectMolecule: plugin 'dcd' cannot open file because the number of
  atoms in
  the object (4551) did not equal the number of atoms in the 'dcd' (5889)
  file.

 I wrote this error message. PyMOL counts the atoms in the object and
 makes sure each frame of the trajectory has an equivalent number. This
 stops PyMOLers from accidentally working with incorrectly paired data
 -- which happened quite a bit.

  I should mention that in the real example, A.pdb and B.pdb actually
  have
  the same name but are located in different directories (in case it
  matters).

 Seeing this makes me think of two possibilities. First, you possibly
 made a simple mistake on disk and B.pdb and B.dcd don't actually
 match. Do these _exact_ files using the exact same commands work the
 same in Linux? (Can you md5sum the files to check?) Second, if PyMOL
 is sharing data then, because they have the same file name, you'll
 have to rename one to something else, like A2.

 Let us know.

 Cheers,

 -- Jason



 
  In this error, the number 5889 corresponds to the number of atoms in
  A.pdb
  while 4551 corresponds to the number of atoms in B.pdb.  Again, these
  are
  two separate windows of MacPyMOL (i.e. I did NOT load A.pdb and B.pdb
  into
  the same window).  Somehow, the first instance of PyMOL sees what is
  happening in the other.
 
  I should mention that in the real example, A.pdb and B.pdb actually
  have
  the same name but are located in different directories (in case it
  matters).
 
  On a non-Mac machine, these commands are fine.  As an experienced
  PyMOL
  user, it was quite embarrassing when a set of commands/steps that worked
  on
  a Linux workstation does not work on a Mac (especially when I was trying
  to
  show the simulations to a VMD user).  I'm fairly new to Macs so maybe
  there's something that I need to do?
 
  Also, when I load up B.pdb (the second structure), the MacPyMOL doesn't
  seem
  to run hide all and show cartoon from my .pymolrc.
 
  Any help/suggestions would be greatly appreciated!
 
  Sean
 
 
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[PyMOL] MacPyMOL Knowledge of Opened Structures

[Sean Law]

Hi PyMOLers,
I noticed some strange behaviour when I do the following:
1) Load A.pdb into MacPyMOL via pymol A.pdb2) 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 instance/window of MacPyMOL via pymol 
B.pdb4) Load a CHARMM simulation trajectory into object B via load B.dcd, B
Loading of this second trajectory complains with the following error:
ObjectMolecule: plugin 'dcd' cannot open file because the number of atoms in 
the object (4551) did not equal the number of atoms in the 'dcd' (5889) file.

In this error, the number 5889 corresponds to the number of atoms in A.pdb 
while 4551 corresponds to the number of atoms in B.pdb.  Again, these are two 
separate windows of MacPyMOL (i.e. I did NOT load A.pdb and B.pdb into the same 
window).  Somehow, the first instance of PyMOL sees what is happening in the 
other.
I should mention that in the real example, A.pdb and B.pdb actually have 
the same name but are located in different directories (in case it matters).
On a non-Mac machine, these commands are fine.  As an experienced PyMOL user, 
it was quite embarrassing when a set of commands/steps that worked on a Linux 
workstation does not work on a Mac (especially when I was trying to show the 
simulations to a VMD user).  I'm fairly new to Macs so maybe there's something 
that I need to do?
Also, when I load up B.pdb (the second structure), the MacPyMOL doesn't seem to 
run hide all and show cartoon from my .pymolrc.
Any help/suggestions would be greatly appreciated!
Sean  --
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[PyMOL] MacPyMOL touch pad control

[Chandan Choudhury]

Hi PyMol users,

How can be I friendly with PyMol using the touch pad (MacBook Pro). What are
the touch pad controls.

Chandan

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Re: [PyMOL] MacPyMOL touch pad control

[Marius Retegan]

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 at 4:25 PM, Chandan Choudhury iitd...@gmail.com wrote:

 Hi PyMol users,

 How can be I friendly with PyMol using the touch pad (MacBook Pro). What are
 the touch pad controls.

 Chandan

 --
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 INDIA

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[PyMOL] MacPyMOL 1.4 on OS X 10.5.8 load command error

[Ben Eisenbraun]

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:

PyMOLimport 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.com2+\n,self.pymol_names,self.pymol_names)
  File string, line 1, in module
  File 
/programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/__init__.py,
 line 136, in module
import add_newdocs
  File 
/programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/add_newdocs.py,
 line 9, in module
from numpy.lib import add_newdoc
  File 
/programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/lib/__init__.py,
 line 4, in module
from type_check import *
  File 
/programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/lib/type_check.py,
 line 8, in module
import numpy.core.numeric as _nx
  File 
/programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/core/__init__.py,
 line 5, in module
import multiarray
ImportError: 
dlopen(/programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/core/multiarray.so,
 2): no suitable image found.  Did find:
/programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/core/multiarray.so:
 unknown required load command 0x8022

There's some info about this error in this thread on Xcode-users:

http://lists.apple.com/archives/Xcode-users/2009/Oct/msg00514.html

And a page about the compressed linkedit loader commands which are the root
cause here:

http://networkpx.blogspot.com/2009/09/about-lcdyldinfoonly-command.html

The fix is not entirely clear to me by looking at those sources.  It looks
like you'll have to experiment a bit if you want to continue to support
10.5 users.

-ben

--
| Ben Eisenbraun
| SBGrid Consortium  | http://sbgrid.org   |
| Harvard Medical School | http://hms.harvard.edu  |

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Re: [PyMOL] MacPyMOL 1.4 on OS X 10.5.8 load command error

[Jason Vertrees]

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 Eisenbraun
b...@hkl.hms.harvard.edu wrote:
 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:

 PyMOLimport 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.com2+\n,self.pymol_names,self.pymol_names)
  File string, line 1, in module
  File 
 /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/__init__.py,
  line 136, in module
    import add_newdocs
  File 
 /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/add_newdocs.py,
  line 9, in module
    from numpy.lib import add_newdoc
  File 
 /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/lib/__init__.py,
  line 4, in module
    from type_check import *
  File 
 /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/lib/type_check.py,
  line 8, in module
    import numpy.core.numeric as _nx
  File 
 /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/core/__init__.py,
  line 5, in module
    import multiarray
 ImportError: 
 dlopen(/programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/core/multiarray.so,
  2): no suitable image found.  Did find:
 /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/core/multiarray.so:
  unknown required load command 0x8022

 There's some info about this error in this thread on Xcode-users:

 http://lists.apple.com/archives/Xcode-users/2009/Oct/msg00514.html

 And a page about the compressed linkedit loader commands which are the root
 cause here:

 http://networkpx.blogspot.com/2009/09/about-lcdyldinfoonly-command.html

 The fix is not entirely clear to me by looking at those sources.  It looks
 like you'll have to experiment a bit if you want to continue to support
 10.5 users.

 -ben

 --
 | Ben Eisenbraun
 | SBGrid Consortium                          | http://sbgrid.org       |
 | Harvard Medical School                     | http://hms.harvard.edu  |

 --
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[PyMOL] MacPyMOL Stereo 3D is back! (on Leopard)

[DeLano Scientific]

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 existing Mac system to Leopard without losing the ability to
work in Stereo 3D.  Hooray!

However, if you currently rely upon Stereo 3D in X11-based software which
presently works under Tiger's X11, then you should continue to hold off on
upgrading until Leopard's X11 (Xquartz) is updated to support stereo 3D
contexts as well.  I believe that this is something the Xquartz open-source
project can now accomplish independently of Apple, but to my knowledge, that
work has not yet been completed.  Capable volunteers are sought.  Refer to
http://xquartz.macosforge.org/trac/ticket/45 for info  progress.

On behalf of our entire user community, I would like to issue special thanks
to the folks in Apple developer relations  technical support for fixing
Stereo 3D in Leopard.  

PyMOL users, please do make a point of letting your Apple contacts know just
how much we appreciate their continued attention to the special needs of the
scientific, medical, and technical visualization markets.  If you don't have
any such contacts, then please send such feedback to me and I will happily
forward it along.

Cheers,
Warren
mailto:war...@delsci.com

Re: [PyMOL] MacPyMol plug-ins

[gilleain torrance]

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? Whatever.

if you have experience coding in Xcode, plug-in development is fairly

straightforward.



Not really. I've never invested the time in learning how to use xcode. I
hope there's also a way to do it from a vi/command line style...

In a nutshell, you use the pymol api to send pymol commands. The only

funky part i've seen so far involves bridging Python and Objective C



Used py-objC bridge before, and it was okay.

thanks

gilleain

Re: [PyMOL] MacPyMol plug-ins

[gilleain torrance]

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 (suggestion 0, in fact) is :

0) Tutorial on writing aqua plugins.

Then we can make the others ourselves...

gilleain

On 5/18/06, stephen rouse step...@fretlessmm.com wrote:

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 have proven
fairly useful. The first is a commands palette where you can save your
own pymol commands and execute them with a double-click.
The second gives you a table view of a molecule's PDB string, along
with the ability to make and save named pymol selections by interacting
with the contents of the table.

I'm in the process of creating a web page that explains these in more
detail, and figuring out an installer mechanism (the manual
installation method is decidedly non-mac-like) so anyone interested can
give them a try.

In the meantime, if any MacPyMol users have suggestions/requests for
plug-ins, i'd love to hear them.

-stephen



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Re: [PyMOL] MacPyMol plug-ins

[Peter Adrian Meyer]

 2) filelist:


snip

 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 similar
situations, if you are going to try something like this you might want to
take a look at the script I use (attached on the off chance you don't have
something similar).  It'll probably need some customization, seeing as I
use it for checking search results quickly (and don't deal w\ any gui
stuff).


 4) sec struc elem:

I'm two for two on misunderstanding you today apparently...Thanks for
clearing it up.

Pete


Pete Meyer
Fu Lab
BMCB grad student
Cornell Universityfrom pymol import cmd

class ModelHolder:
#loop over pdb files named base_##.pdb (from ##=0 to 99)
#to use: run ModelHolder.py ; m=ModelHolder('base')
def __init__(self,base):
self.base=base
self.pos=0
self.show()
def makefname(self):
fname=self.name()+'.pdb'
return fname
def name(self):
name=self.base+'_'+str(self.pos)
return name
def clear(self):
name=self.name()
cmd.delete(name)
def show(self):
n=self.name()
cmd.load(self.makefname(),n)
cmd.hide('everything',n)
cmd.show('ribbon',n)
#color red for even or cyan for odd pos
if self.pos%2==0: cmd.color('red',n)
else: cmd.color('cyan',n)
def next(self):
self.clear()
self.pos=self.pos+1
if self.pos99:
self.pos=0
cmd.bg_color('grey80')
self.show()
def last(self):
self.clear()
self.pos=self.pos-1
if self.pos0: 
self.pos=99
cmd.bg_color('grey80')
self.show()
def go(self,n):
pos=self.pos
self.clear()
if (n=0) and ( n=99):
self.pos=n
self.show()
else:
self.show()

Re: [PyMOL] MacPyMol plug-ins

[stephen rouse]

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?



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!


keep 'em comin'.


But number one suggestion (suggestion 0, in fact) is :
0) Tutorial on writing aqua plugins.


i'll work on a tutorial and post it on my website.

if you have experience coding in Xcode, plug-in development is fairly 
straightforward.
In a nutshell, you use the pymol api to send pymol commands. The only 
funky part i've seen so far involves bridging Python and Objective C 
data structures (e.g. when asking pymol for a response of some kind), 
but even this isn't that bad.


-stephen

[PyMOL] MacPyMol plug-ins

[stephen rouse]

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 have proven 
fairly useful. The first is a commands palette where you can save your 
own pymol commands and execute them with a double-click.
The second gives you a table view of a molecule's PDB string, along 
with the ability to make and save named pymol selections by interacting 
with the contents of the table.


I'm in the process of creating a web page that explains these in more 
detail, and figuring out an installer mechanism (the manual 
installation method is decidedly non-mac-like) so anyone interested can 
give them a try.


In the meantime, if any MacPyMol users have suggestions/requests for 
plug-ins, i'd love to hear them.


-stephen

[PyMOL] MacPyMOL command entry

[Mark A Saper]

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 commands are.


Many thanks,
Mark
_
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Associate Research Scientist in Biophysics

Biophysics Research Division, University of Michigan
Chemistry Building Room 3040
930 North University Ave
Ann Arbor MI 48109-1055 U.S.A.

sa...@umich.edu(734) 764-3353fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

Re: [PyMOL] MacPyMOL command entry

[gilleain torrance]

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!
:)

gilleain

On 12/22/05, Mark A Saper sa...@umich.edu wrote:

 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 commands are.

 Many thanks,
 Mark
 _
 Mark A. Saper, Ph.D.
 Associate Professor of Biological Chemistry
 Associate Research Scientist in Biophysics

 Biophysics Research Division, University of Michigan
 Chemistry Building Room 3040
 930 North University Ave
 Ann Arbor MI 48109-1055 U.S.A.

 sa...@umich.edu(734) 764-3353fax (734) 764-3323
 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html




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Re: [PyMOL] MacPyMOL 0.99beta29

[Gilleain Torrance]

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 know for sure  
anyway).


gilleain

On 8 Nov 2005, at 03:39, Warren DeLano wrote:


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

--
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Principal Scientist

. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942  Tech:(650)-872-0834
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com



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[PyMOL] MacPyMOL 0.99beta29

[Warren DeLano]

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. 
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213   
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834 
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com  

RE: [PyMOL] MacPyMOL 0.99beta29

[Warren DeLano]

Chris and Others,

Yes, there is at least one outstanding issue with the new MacPyMOL
that is unrelated to OpenGL.  If you experience a crash on startup, then
please email crash logs to me (copy and paste from the report error
window), along with a system profile.  

Apple Menu-About This Mac-More Info-File-Save.

Cheers,
Warren

PS./Aside  For max performance with 0.99beta29 (on machine where it
works):

set texture_fonts
set use_display_lists

--
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Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213   
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834 
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com  
 

 -Original Message-
 From: Christopher Yip [mailto:christopher_...@sympatico.ca] 
 Sent: Monday, 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 
 stemmed back to earlier 0.99 beta version...
 
 Thanks
 
 Chris
 
 
 On Nov 7, 2005, at 10:39 PM, Warren DeLano wrote:
 
 
   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. 
   Principal Scientist
 
   . DeLano Scientific LLC  
   . 400 Oyster Point Blvd., Suite 213   
   . South San Francisco, CA 94080 USA   
   . Biz:(650)-872-0942  Tech:(650)-872-0834 
   . Fax:(650)-872-0273  Cell:(650)-346-1154
   . mailto:war...@delsci.com  
 
 
 
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   https://lists.sourceforge.net/lists/listinfo/pymol-users
 
 
 Christopher M. Yip, Ph.D., P.Eng.
 
 Associate Professor - Canada Research Chair in Molecular Imaging
 
 Department of Chemical Engineering and Applied Chemistry
 
 Department of Biochemistry
 
 Institute of Biomaterials and Biomedical Engineering
 
 The Terrence Donnelly Centre for Cellular and Biomolecular Research
 
 University of Toronto
 
 Room 404 160 College St.
 Toronto, ON, CANADA M5S 3E1
 
 (416) 978-7853
 
 (416) 978-4317 (fax)
 
 christopher@utoronto.ca
 
 http://bigten.ibme.utoronto.ca
 
 
 
 

[PyMOL] MacPyMOL 0.99b19

[Mark A Saper]

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?

_
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
sa...@umich.edu(734) 764-3353fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

[PyMOL] macpymol beta

[Dan White]

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 Coordinator
Nanoscience Centre and Department of Biological and Environmental  
Sciences

Division of Molecular Recognition
Ambiotica C242
PO Box 35
University of Jyväskylä
Jyväskylä
FIN 40014
Finland

+358 14 260 4183 (work)
+358 468102840 (mobile)
http://www.bioimagexd.org
http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi

[PyMOL] MacPyMol won't load pdb files

[Paul Fitzpatrick]

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,pymol_names)
  File string, line 1, in ?
  File  
/users/warren/pymol/products/MacPyMOL.app/pymol/modules/pymol/ 
importing.py, line 549, in load

discrete,quiet,multiplex,zoom)
  File  
/users/warren/pymol/products/MacPyMOL.app/pymol/modules/pymol/cmd.py,  
line 771, in _load
finfo = tmp_file.read(tmp_file) # WARNING: will block and hang --  
thread instead?

AttributeError: addinfourl instance has no attribute '__int__'

Paul Fitzpatrick
Department of Biochemistry and Biophysics
Texas AM University
College Station, TX 77843-2128
ph: 979-845-5487
fax: 979-845-4946
email: fitz...@tamu.edu

RE: [PyMOL] macpymol beta bug

[Warren DeLano]

Hmm...

The problems are fixed in MacPyMOL beta24 (http://delsci.com/macbeta).

Also note that there is a new setting cartoon_side_chain_helper that
greatly simplifies figure preparation when you mix cartoons and side chains.
It takes care of making sure the cartoon goes through the CA position, and
it automatically hides main chain atoms when the cartoon representation is
visible for a residue.

You can activate it under the Display/Cartoon menu, or with set
cartoon_side_chain_helper

Cheers,
Warren

--
Warren L. DeLano, Ph.D. 
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213   
. South San Francisco, CA 94080
. Biz:(650)-872-0942  Tech:(650)-872-0834 
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com  
 

 -Original Message-
 From: pymol-users-ad...@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 
 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
 
 ==
 Jianghai Zhu
 Molecular Biology  Biochemistry
 Purdue University
 ==
 
 
 
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Re: [PyMOL] macpymol beta bug

[Jianghai Zhu]

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, Warren DeLano wrote:


Hmm...

The problems are fixed in MacPyMOL beta24 (http://delsci.com/macbeta).

Also note that there is a new setting cartoon_side_chain_helper that
greatly simplifies figure preparation when you mix cartoons and side 
chains.
It takes care of making sure the cartoon goes through the CA position, 
and
it automatically hides main chain atoms when the cartoon 
representation is

visible for a residue.

You can activate it under the Display/Cartoon menu, or with set
cartoon_side_chain_helper

Cheers,
Warren

[PyMOL] macpymol beta bug

[Jianghai Zhu]

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

==
Jianghai Zhu
Molecular Biology  Biochemistry
Purdue University
==

[PyMOL] MacPyMOL Beta

[Warren DeLano]

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 L. DeLano, Ph.D.
Principal Scientist, DeLano Scientific LLC,
400 Oyster Point Blvd., Suite 213,
South San Francisco, CA 94080
Biz:(650)-872-0942  Tech:(650)-872-0834
Fax:(650)-872-0273  Cell:(650)-346-1154 
 

[PyMOL] macPymol crashes during raytracing

[Holger Sondermann]

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 raytracing simple movies
(such as ribbons of a medium-size system) at different
states/frames during saving a movie. Re-installing
MacPymol didn't help.

Any idea what could be wrong? I appreciate your help.
Best wishes,
-Holger
-
Holger Sondermann, Ph.D.
UC Berkeley

[PyMOL] MacPyMOL and USB controllers

[James R. Graham]

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!

james

Re: [PyMOL] PyMOL/MacPyMOL Beta Feedback

[Nick Skelton]

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 powerbook 6.2 version 1.1
   OSX 10.2.8 (6R73)
   v0.94
Not sure about the graphics cards as they are not listed by the system 
profiler.


It may be purely circumstantial, but I most often see the crash on my 
lap top

after I have run dss to get secondary structure.  I will keep an eye on
this behaviour and let you know if I see any trends.

Nick

Warren DeLano wrote:


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 whether the problems might
be related to some sort of hardware or OS variability.  If you are still
experiencing consistent problems, then please provide specific details on
your system:

- Processor/Mac Model
- Graphics Card
- Specific MacOS version #.
- Latest beta version used.

For Windows  Linux users:

  I have also posted a couple of equivalent beta builds for Linux and
Windows.  If you would like to cautiously play around with and provide
feedback on the development versions, then you may do so via:
http://delsci.com/beta.  However, please do not treat these build as formal
releases.  They are not too stable and certain aspects of the user interface
remain fluid as old demons are exorcized and new demons understood.  


Cheers,
Warren


--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020






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Nick Skelton, Ph.D.
Department of Medicinal Chemistry
Genentech, Inc.
1 DNA Way,
South San Francisco, CA 94080

E-mail: ske...@gene.com
Tel.(650) 225 6402
FAX (650) 225 3734