Re: [PyMOL] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

[hari jayaram]

Thanks All
Engin Ozkan wrote in saying that he could get schrodinger compiled Pymol
1.8.4 to work well with same setup as mine

I then tested a self compiled 1.8.4 and with an older version 1.7.6.0 ( and
1.7.4.5) on the same setup.

I could get smooth scrolling with  1.7 series versions on the same
 hardware .
My self compiled 1.8.2.1 and 1.8.4 are not behaving well and show the Jerky
scrolling.

I compiled using a simple pymol setup.py install

I will try and troubleshoot what in the compilation is giving the poor
response with newer pymol versions ( 1.8 series)  since I  can only use the
open-source pymol

Thanks
Hari


On Wed, Jan 11, 2017 at 5:55 PM hari jayaram  wrote:

> Sorry to post back in.
>
> As I posted yesterday ,  I have been trying to get pymol working on a
> Macbook Air ( and MacBook Pro since yesterday ) and am now convinced the
> X11 apps freezing problem is real and recurs frequently.
>
> While rotating a molecule the X session stops responding , the window
> close - window open-window minimize , red yellow green buttons gray out and
> then the whole session freezes
>
> I see this behavior on two machines I have tried using since my original
> machine where everything was working but with an earlier brew installed
> pymol ( 1.7.2 I think ) bit the dust.
>
> IS anyone else seeing this with 1.8.2.1 and OSX?
>
> Thanks
> hari
>
>
>
>
>
> I have used homebrew to install pymol version 1.8.2.1
>
> On Tue, Jan 10, 2017 at 7:02 AM hari jayaram  wrote:
>
> Hello All
> Sorry for that post. The problem got fixed by a restart.
> I failed to follow the unwritten rule of "non-Linux computers" :-) When in
> doubt---restart
>
> After a restart I tried pymol with a new user profile and it worked very
> smoothly
> I tried back with my migrated original account ...and the buttery smooth
> rotation returnedPhew :-)
>
> Sorry for the confusion
> Thanks
> Hari
>
>
>
>
> On Tue, Jan 10, 2017 at 6:49 AM hari jayaram  wrote:
>
> Hi ,
> I was happily using brew installed pymol 1.7.6  on my Macbook Pro (running
> OSX Sierra) and then had a hardware failure.
>
> I switched computers to MacBook Air running the same version of OSX
> (Sierra 10.12.2 ) and Xquartz (2.7.11) and now pymol ( and coot and other
> X11 using applications) refuses to function with smooth molecule rotation
> on even a 30kDa protein.
>
> I know the Macbook Airs are not that underpowered and am wondering how to
> troubleshoot the lack of smooth rotation.
>
> I have tried:
> Reinstalling pymol (now running 1.8)
> Reinstalling Xquartz ( still running 2.7.11)
> Using an external mouse
>
>
> ANd still have rotation that gets stuck. It starts rotating smoothly and
> then locks up. I can see the Mac red/yello/green circles go gray like X11
> is sleeping when this happens . It resumes after a second and rotation
> cotinues .
>
> Looking for others having the same issue does not pull up anything. I can
> get smooth rotation in Chimera and Cuemol2 on this new laptop so it seems
> to be a Pymol(Coot) X11/Xquartz issue that I dont know how to fix.
>
> Any ideas or help would be greatly appreciated since its two weeks till my
> faithful computer returns from a hardware fix.
>
> Thanks
> Hari
>
>
>
>
>
--
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Re: [PyMOL] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

[hari jayaram]

Sorry to post back in.

As I posted yesterday ,  I have been trying to get pymol working on a
Macbook Air ( and MacBook Pro since yesterday ) and am now convinced the
X11 apps freezing problem is real and recurs frequently.

While rotating a molecule the X session stops responding , the window close
- window open-window minimize , red yellow green buttons gray out and then
the whole session freezes

I see this behavior on two machines I have tried using since my original
machine where everything was working but with an earlier brew installed
pymol ( 1.7.2 I think ) bit the dust.

IS anyone else seeing this with 1.8.2.1 and OSX?

Thanks
hari





I have used homebrew to install pymol version 1.8.2.1

On Tue, Jan 10, 2017 at 7:02 AM hari jayaram  wrote:

Hello All
Sorry for that post. The problem got fixed by a restart.
I failed to follow the unwritten rule of "non-Linux computers" :-) When in
doubt---restart

After a restart I tried pymol with a new user profile and it worked very
smoothly
I tried back with my migrated original account ...and the buttery smooth
rotation returnedPhew :-)

Sorry for the confusion
Thanks
Hari




On Tue, Jan 10, 2017 at 6:49 AM hari jayaram  wrote:

Hi ,
I was happily using brew installed pymol 1.7.6  on my Macbook Pro (running
OSX Sierra) and then had a hardware failure.

I switched computers to MacBook Air running the same version of OSX (Sierra
10.12.2 ) and Xquartz (2.7.11) and now pymol ( and coot and other X11 using
applications) refuses to function with smooth molecule rotation on even a
30kDa protein.

I know the Macbook Airs are not that underpowered and am wondering how to
troubleshoot the lack of smooth rotation.

I have tried:
Reinstalling pymol (now running 1.8)
Reinstalling Xquartz ( still running 2.7.11)
Using an external mouse


ANd still have rotation that gets stuck. It starts rotating smoothly and
then locks up. I can see the Mac red/yello/green circles go gray like X11
is sleeping when this happens . It resumes after a second and rotation
cotinues .

Looking for others having the same issue does not pull up anything. I can
get smooth rotation in Chimera and Cuemol2 on this new laptop so it seems
to be a Pymol(Coot) X11/Xquartz issue that I dont know how to fix.

Any ideas or help would be greatly appreciated since its two weeks till my
faithful computer returns from a hardware fix.

Thanks
Hari
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

[hari jayaram]

Hello All
Sorry for that post. The problem got fixed by a restart.
I failed to follow the unwritten rule of "non-Linux computers" :-) When in
doubt---restart

After a restart I tried pymol with a new user profile and it worked very
smoothly
I tried back with my migrated original account ...and the buttery smooth
rotation returnedPhew :-)

Sorry for the confusion
Thanks
Hari




On Tue, Jan 10, 2017 at 6:49 AM hari jayaram  wrote:

> Hi ,
> I was happily using brew installed pymol 1.7.6  on my Macbook Pro (running
> OSX Sierra) and then had a hardware failure.
>
> I switched computers to MacBook Air running the same version of OSX
> (Sierra 10.12.2 ) and Xquartz (2.7.11) and now pymol ( and coot and other
> X11 using applications) refuses to function with smooth molecule rotation
> on even a 30kDa protein.
>
> I know the Macbook Airs are not that underpowered and am wondering how to
> troubleshoot the lack of smooth rotation.
>
> I have tried:
> Reinstalling pymol (now running 1.8)
> Reinstalling Xquartz ( still running 2.7.11)
> Using an external mouse
>
>
> ANd still have rotation that gets stuck. It starts rotating smoothly and
> then locks up. I can see the Mac red/yello/green circles go gray like X11
> is sleeping when this happens . It resumes after a second and rotation
> cotinues .
>
> Looking for others having the same issue does not pull up anything. I can
> get smooth rotation in Chimera and Cuemol2 on this new laptop so it seems
> to be a Pymol(Coot) X11/Xquartz issue that I dont know how to fix.
>
> Any ideas or help would be greatly appreciated since its two weeks till my
> faithful computer returns from a hardware fix.
>
> Thanks
> Hari
>
>
>
>
>
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

[hari jayaram]

Hi ,
I was happily using brew installed pymol 1.7.6  on my Macbook Pro (running
OSX Sierra) and then had a hardware failure.

I switched computers to MacBook Air running the same version of OSX (Sierra
10.12.2 ) and Xquartz (2.7.11) and now pymol ( and coot and other X11 using
applications) refuses to function with smooth molecule rotation on even a
30kDa protein.

I know the Macbook Airs are not that underpowered and am wondering how to
troubleshoot the lack of smooth rotation.

I have tried:
Reinstalling pymol (now running 1.8)
Reinstalling Xquartz ( still running 2.7.11)
Using an external mouse


ANd still have rotation that gets stuck. It starts rotating smoothly and
then locks up. I can see the Mac red/yello/green circles go gray like X11
is sleeping when this happens . It resumes after a second and rotation
cotinues .

Looking for others having the same issue does not pull up anything. I can
get smooth rotation in Chimera and Cuemol2 on this new laptop so it seems
to be a Pymol(Coot) X11/Xquartz issue that I dont know how to fix.

Any ideas or help would be greatly appreciated since its two weeks till my
faithful computer returns from a hardware fix.

Thanks
Hari
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net