Re: [PyMOL] Pymol in Linux

[Jason Vertrees]

On Sat, Feb 6, 2010 at 5:16 AM, Chandan Choudhury  wrote:
>
> I have been using pymol for sometime in Linux System (Suse 11.2). I notice
> that in Linux everything works fine but when I need to change some atom, in
> the edit mode, GUI doesnot select the desired atom. But in Windows OS, this
> problem doesnt erupt. Can  someone help me out, to efficiently use Pymol in
> Linux.
>
> Chandan


Chandan,

I cannot reproduce this bug, but I will keep an eye out for it.  Feel
free to send me a PyMOL session of your in which this bug takes place.

Thanks,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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Re: [PyMOL] pml script execution speed

[Jason Vertrees]

Michael,

I can also reproduce this effect.  I will look into it.

-- Jason

On Wed, Feb 10, 2010 at 11:15 AM, Michael Zimmermann
 wrote:
> Dear PyMOL users,
>
> I have noticed a few times now that when I run a .pml script from a
> function (i.e. MATLAB generates a .pml file and then does a system
> call for PyMOL to run it) or in batch mode (.bat file that just calls
> "PyMOL.exe -c -u file.pml") and if I am taking pictures with "png"
> then it runs considerably slower than if I open the GUI and run the
> script.  I'm doing this to automate frame generation for movie making.
>  Any idea why this would be and how to make the system call at least
> as fast as running the GUI?
>
> I use:
> Windows XP 64-bit SP2
> PyMOL v. 1.2r1
>
> --
> Michael Zimmermann
> Ph.D. student in Bioinformatics and Computational Biology
> Department of Biochemistry, Biophysics and Molecular Biology
> Iowa State University
>
> --
> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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Re: [PyMOL] New Ideas

[Jason Vertrees]

On Fri, Feb 5, 2010 at 1:36 PM, Sean Law  wrote:
> Is it possible to include a function that could easily add or delete states
> (from the beginning, middle, or end of a set of states)?
>
> Something with the following syntax:
>
> delete_states 14  #Deletes state 14
> delete_states 10-20  #Delete states 10-20
> delete_states 10-20,30-40  #Delete states 10-20 and 30-40
>
> That would be great.
>
> Sean


Sean,

That would be nice. Right now, I do:

# fetch 1nmr, a 20-state object
fetch 1nmr

# I want to only save 5 these states, not all 20
sought_states = [1, 2, 5, 17, 19 ]

# loop through sought_states, creating an object with just those states
for x in range(len(sought_states)):
cmd.create("1nmr.cut", "1nmr", sought_states[x], x )

# save the partial-state object
cmd.save( "1nmr_partial.pdb", "1nmr.cut", state=0 )

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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Re: [PyMOL] New Feature Ideas

[Michael Lerner]

Hi Sean,

On Fri, Feb 12, 2010 at 12:39 PM, Sean Law  wrote:

>  Hi all,
>
> Another feature that I find myself always wanting is a "kill script" button
> and/or command.  This comes in handy when I am testing a new python script
> and, accidentally, throw in an infinite loop.  It would be nice to have some
> sort of kill switch not only for python scripts but even for something as
> simple as ray-tracing.  There are times when I am ray-tracing a complicated
> scene and realize that half-way through the ray-tracing process that
> something was missing.  In that case, I normally have to kill PyMOL and
> start all over again (and hopefully, I'll have the scene/session saved).
> Having this function would greatly enhance my productivity.
>

You should see a button labeled "Abort" at the bottom right of the external
GUI window. You can click it to stop the ray tracer. It used to only work if
you started the ray tracer by clicking the "Ray" button in that same window,
but it appears to work no matter how you start the ray tracer now (1.2r2).

Cheers,

-Michael


>
> Thanks!
>
> Sean
>
> --
> Not using Hotmail on your phone? Why not? Get it 
> now.
>
>
> --
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-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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Re: [PyMOL] New Feature Ideas

[Sean Law]

Hi all,

Another feature that I find myself always wanting is a "kill script" button 
and/or command.  This comes in handy when I am testing a new python script and, 
accidentally, throw in an infinite loop.  It would be nice to have some sort of 
kill switch not only for python scripts but even for something as simple as 
ray-tracing.  There are times when I am ray-tracing a complicated scene and 
realize that half-way through the ray-tracing process that something was 
missing.  In that case, I normally have to kill PyMOL and start all over again 
(and hopefully, I'll have the scene/session saved).  Having this function would 
greatly enhance my productivity.

Thanks!

Sean
  
_

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