[PyMOL] Color coded script

[mark . zierden]

Hi,

In the PyMolWiki under simple scripting parts of the command lines are color 
coded(red, blue and green). What does that mean?

cmd.extend(“doSimpleThing”,doSimpleThing)--
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Re: [PyMOL] Color coded script

[Julian Heinrich]

Hi,

are you referring to the code examples? I think the coloring scheme is just
a source code syntax highlighting, where all strings for example are in
red, comments are in green, and functions are blue.

Cheers,
Julian

On Tue, Nov 10, 2015 at 3:15 PM,  wrote:

> Hi,
>
> In the PyMolWiki under simple scripting parts of the command lines are
> color coded(red, blue and green). What does that mean?
>
> cmd.extend(“doSimpleThing”,doSimpleThing)
>
>
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[PyMOL] Iterate scenes smoothly

[Leandro Bortot]

Dear users,

 I'm trying to make a movie during which a surface changes its color. I
followed the tutorials from the wiki and successfully created two scenes
with the desired colors.
 However, I can't make them iterate smoothly. Instead, The first half
of the frames display the first scene and the second half the second scene.

 I'm using the following commands:

mset 1x 60
scene 001, store
scene 002, store
frame 1
mview store, scene=001
frame 60
mview store, scene=002
mview interpolate

Also, the scenes doesn't change smoothly when I press PgUp/Down.

 Am I doing something wrong?

Best regards,
Leandro
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Re: [PyMOL] Iterate scenes smoothly

[harold steinberg]

that’s the same result I always get…

> On May 9, 2016, at 12:23 PM, Leandro Bortot  wrote:
> 
> Dear users,
> 
>  I'm trying to make a movie during which a surface changes its color. I 
> followed the tutorials from the wiki and successfully created two scenes with 
> the desired colors. 
>  However, I can't make them iterate smoothly. Instead, The first half of 
> the frames display the first scene and the second half the second scene.
> 
>  I'm using the following commands:
> 
> mset 1x 60
> scene 001, store
> scene 002, store
> frame 1
> mview store, scene=001
> frame 60
> mview store, scene=002
> mview interpolate
> 
> Also, the scenes doesn't change smoothly when I press PgUp/Down.
> 
>  Am I doing something wrong?
> 
> Best regards,
> Leandro
> 
> --
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H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] Iterate scenes smoothly

[João M . Damas]

Not sure it works, but if the colors are related to some parameter, try
this:

http://www.pymolwiki.org/index.php/Morph

On Mon, May 9, 2016 at 7:26 PM, harold steinberg  wrote:

> that’s the same result I always get…
>
> On May 9, 2016, at 12:23 PM, Leandro Bortot  wrote:
>
> Dear users,
>
>  I'm trying to make a movie during which a surface changes its color.
> I followed the tutorials from the wiki and successfully created two scenes
> with the desired colors.
>  However, I can't make them iterate smoothly. Instead, The first half
> of the frames display the first scene and the second half the second scene.
>
>  I'm using the following commands:
>
> mset 1x 60
> scene 001, store
> scene 002, store
> frame 1
> mview store, scene=001
> frame 60
> mview store, scene=002
> mview interpolate
>
> Also, the scenes doesn't change smoothly when I press PgUp/Down.
>
>  Am I doing something wrong?
>
> Best regards,
> Leandro
>
>
> --
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> Manager
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> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
>
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
>
>
>
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> Manager
> Applications Manager provides deep performance insights into multiple
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>



-- 
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Tel:+351-214469613
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Re: [PyMOL] High Resolution Ray Tracing

[Stephen Kerry]

Thank you for trying this out on a workstation with 128 GB and then 256 GB of 
RAM. It is much appreciated as I do not have easy access to that kind of 
computational power. The fact that you also get these segfaults with all of 
your RAM, suggests that this might be a PyMOL limitation, rather than a 
hardware issue.



I have come to the conclusion that it is impossible to ray trace an image with 
an output resolution greater than 45 megapixels (7500 x 6000). Halving the dpi 
from 1200 to 600 gives a 11.25 megapixel (3750 x 3000) resolution.



I was wondering if the developers have come across this upper limit too? I have 
a 2400 dpi printer, so I want to go with the highest dpi possible for the best 
quality.


From: David Hall 
Sent: 06 May 2016 19:17:38
To: Stephen Kerry
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] High Resolution Ray Tracing

Feel free to send me the files off list.

-David Hall

On May 6, 2016, at 1:54 PM, Stephen Kerry 
mailto:stephen.kerr...@outlook.com>> wrote:


Dear All,

I have a protein complex scene that I need to create a large, high resolution 
(1200 dpi) ray traced image of, but am unable to do so as I always run out of 
memory at the end of the ray tracing process, with the following error:


python2.7(972,0x7fff7397f300) malloc: *** 
mach_vm_map(size=18446744068907188224) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

This is with PyMOL 1.81 from Fink on OSX 10.10 with an i7-4790K processor and 
32 GB of DDR3. Python2.7 expands up to 15 GB of RAM, with more than twice this 
reserved for virtual memory, but no swap is actually used.

Decreasing hash_max just increases the ray tracing time until the error at the 
end. Sometimes PyMOL will be terminated with this error, whilst at other times 
a transparent PNG is all that is produced.

Is there a way to force PyMOL to use virtual memory to avoid these 
errors/crashes at the expense of processing time?

If not, is there anyone who has PyMOL 1.8x installed on a system with 64 GB or 
more RAM, who would be able to render this ray traced image if I send the, the 
.pse file and .pml script off list? Takes about 10 mins to process.

Cheers,

Stephen


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Re: [PyMOL] High Resolution Ray Tracing

[Takanori Nakane]

Hi,

By tweaking the projection matrix, we can divide a big scene into
several sub-images and render them separately. Thus, we can reduce
the memory consumption. I think this is scriptable, although I
don't have time to implement myself.

 > I was wondering if the developers have come across this upper limit too?
 > I have a 2400 dpi printer, so I want to go with the highest dpi possible
 > for the best quality.

"2400 dpi" for a printer does not have the same meaning as 2400
dpi (or better, ppi, pixel per inch) for a screen.
Printers use many dots to represent an image pixel.
Did you take that into the account? Probably you don't need 2400 dpi
or 1200 dpi.

https://en.wikipedia.org/wiki/Dots_per_inch#/media/File:DPI_and_PPI.png

Best regards,

Takanori Nakane

Am 2016年05月10日 um 09:34 schrieb Stephen Kerry:
> Thank you for trying this out on a workstation with 128 GB and then 256
> GB of RAM. It is much appreciated as I do not have easy access to that
> kind of computational power. The fact that you also get these segfaults
> with all of your RAM, suggests that this might be a PyMOL limitation,
> rather than a hardware issue.
>
> I have come to the conclusion that it is impossible to ray trace an
> image with an output resolution greater than 45 megapixels (7500 x
> 6000). Halving the dpi from 1200 to 600 gives a 11.25 megapixel (3750 x
> 3000) resolution.
>
> I was wondering if the developers have come across this upper limit too?
> I have a 2400 dpi printer, so I want to go with the highest dpi possible
> for the best quality.
>
> 
> *From:* David Hall 
> *Sent:* 06 May 2016 19:17:38
> *To:* Stephen Kerry
> *Cc:* pymol-users@lists.sourceforge.net
> *Subject:* Re: [PyMOL] High Resolution Ray Tracing
> Feel free to send me the files off list.
>
> -David Hall
>
>> On May 6, 2016, at 1:54 PM, Stephen Kerry > > wrote:
>>
>> Dear All,
>>
>> I have a protein complex scene that I need to create a large, high
>> resolution (1200 dpi) ray traced image of, but am unable to do so as I
>> always run out of memory at the end of the ray tracing process, with
>> the following error:
>>
>> python2.7(972,0x7fff7397f300) malloc: ***
>> mach_vm_map(size=18446744068907188224) failed (error code=3)
>> *** error: can't allocate region
>> *** set a breakpoint in malloc_error_break to debug
>>
>> This is with PyMOL 1.81 from Fink on OSX 10.10 with
>> ani7-4790Kprocessor and 32 GB of DDR3. Python2.7 expands up to 15 GB
>> of RAM, with more than twice this reserved for virtual memory, but no
>> swap is actually used.
>>
>> Decreasing hash_max just increases the ray tracing time until the
>> error at the end. Sometimes PyMOL will be terminated with this error,
>> whilst at other times a transparent PNG is all that is produced.
>>
>> Is there a way to force PyMOL to use virtual memory to avoid these
>> errors/crashes at the expense of processing time?
>>
>> If not, is there anyone who has PyMOL 1.8x installed on a system with
>> 64 GB or more RAM, who would be able to render this ray traced image
>> if I send the, the .pse file and .pml script off list? Takes about 10
>> mins to process.
>>
>> Cheers,
>>
>> Stephen
>>
>> --
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>> Manager
>> Applications Manager provides deep performance insights into multiple
>> tiers of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free trial!
>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___
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>> )
>> Info Page:https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives:http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
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ap

Re: [PyMOL] High Resolution Ray Tracing

[harold steinberg]

I can try to address the 2400 dpi printer resolution.

Printer manufactures specify their printer's resolution in the number of pixels 
per inch (ppi) in the horizontal plane because it’s higher, and looks better in 
advertising. But all printers also have a vertical printing resolution that is 
much lower, and therefore is the true limit on the resolution that a printer 
can print high quality images.

Printed magazines are screened at 133 lines per inch in the vertical dimension 
and so twice that resolution is all you need in ppi to get the best possible 
print. Magazines typically print at 2400 dpi in the horizontal plane. 266 dpi 
is all you’d really need, but people generally use 300 dpi because they don’t 
understand how offset printing presses work. Coffee table books (high end) 
print at 200 lines per inch.

Poster printers, which can print extremely high resolution in the horizontal 
plane generally only need 180 dpi in files because of the lower resolution in 
the vertical plane. And the fact that throwing a huge 2400 dpi file at a poster 
printer will generally slow it’s print speed to a crawl… and that make printing 
multiple posters in a limited amount of time hard to do.

All printers are pretty similar but you should check yours for it’s specific 
details. All printers have multiple settings and options that will effect print 
speed and quality but check yours for the lpi (lines per inch) and then double 
that number to figure out how much dpi you need.

Most people do not understand how this all works, I can try and give a primer 
on it. Using the information above as the example, if you want to have a final 
image size of four inches in a magazine, then you’d need to ray trace your file 
at 4" x 300 dpi = 1200 dpi in width.

So once you figure out the size of the image you want the final image to be, 
multiple that by twice your printer's vertical printing limitation, to get the 
ray trace image width.



> On May 9, 2016, at 7:34 PM, Stephen Kerry  wrote:
> 
> Thank you for trying this out on a workstation with 128 GB and then 256 GB of 
> RAM. It is much appreciated as I do not have easy access to that kind of 
> computational power. The fact that you also get these segfaults with all of 
> your RAM, suggests that this might be a PyMOL limitation, rather than a 
> hardware issue.
>  
> I have come to the conclusion that it is impossible to ray trace an image 
> with an output resolution greater than 45 megapixels (7500 x 6000). Halving 
> the dpi from 1200 to 600 gives a 11.25 megapixel (3750 x 3000) resolution.
>  
> I was wondering if the developers have come across this upper limit too? I 
> have a 2400 dpi printer, so I want to go with the highest dpi possible for 
> the best quality.
> From: David Hall mailto:li...@cowsandmilk.net>>
> Sent: 06 May 2016 19:17:38
> To: Stephen Kerry
> Cc: pymol-users@lists.sourceforge.net 
> 
> Subject: Re: [PyMOL] High Resolution Ray Tracing
>  
> Feel free to send me the files off list.
> 
> -David Hall
> 
>> On May 6, 2016, at 1:54 PM, Stephen Kerry > > wrote:
>> 
>> Dear All,
>> 
>> I have a protein complex scene that I need to create a large, high 
>> resolution (1200 dpi) ray traced image of, but am unable to do so as I 
>> always run out of memory at the end of the ray tracing process, with the 
>> following error:
>> 
>> python2.7(972,0x7fff7397f300) malloc: *** 
>> mach_vm_map(size=18446744068907188224) failed (error code=3)
>> *** error: can't allocate region
>> *** set a breakpoint in malloc_error_break to debug
>> 
>> This is with PyMOL 1.81 from Fink on OSX 10.10 with an i7-4790K processor 
>> and 32 GB of DDR3. Python2.7 expands up to 15 GB of RAM, with more than 
>> twice this reserved for virtual memory, but no swap is actually used.
>> 
>> Decreasing hash_max just increases the ray tracing time until the error at 
>> the end. Sometimes PyMOL will be terminated with this error, whilst at other 
>> times a transparent PNG is all that is produced.
>> 
>> Is there a way to force PyMOL to use virtual memory to avoid these 
>> errors/crashes at the expense of processing time?
>> 
>> If not, is there anyone who has PyMOL 1.8x installed on a system with 64 GB 
>> or more RAM, who would be able to render this ray traced image if I send 
>> the, the .pse file and .pml script off list? Takes about 10 mins to process.
>> 
>> Cheers,
>> 
>> Stephen
>> 
>> --
>> Find and fix application performance issues faster with Applications Manager
>> Applications Manager provides deep performance insights into multiple tiers 
>> of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free trial!
>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___
>>  
>> 

Re: [PyMOL] High Resolution Ray Tracing

[James Kress]

Did you try using POV-Ray with PyMOL to do the ray tracing?

renderer = 1 uses PovRay's renderer. This is Unix-only and you must have
"povray" in your path. It utilizes two temporary files: "tmp_pymol.pov" and
"tmp_pymol.png". Also works on Mac via Povray37UnofficialMacCmd but it needs
to be in your path as "povray".

 

Jim

 

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The KressWorksR Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

"Engineering The Cure" C

(248) 573-5499

 

Learn More and Donate At:

Website:   http://www.kressworks.org

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Confidentiality Notice | This e-mail message, including any attachments, is
for the sole use of the intended recipient(s) and may contain confidential
or proprietary information. Any unauthorized review, use, disclosure or
distribution is prohibited. If you are not the intended recipient,
immediately contact the sender by reply e-mail and destroy all copies of the
original message.

 

From: Stephen Kerry [mailto:stephen.kerr...@outlook.com] 
Sent: Monday, May 09, 2016 8:35 PM
To: David Hall 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] High Resolution Ray Tracing

 

Thank you for trying this out on a workstation with 128 GB and then 256 GB
of RAM. It is much appreciated as I do not have easy access to that kind of
computational power. The fact that you also get these segfaults with all of
your RAM, suggests that this might be a PyMOL limitation, rather than a
hardware issue. 

 

I have come to the conclusion that it is impossible to ray trace an image
with an output resolution greater than 45 megapixels (7500 x 6000). Halving
the dpi from 1200 to 600 gives a 11.25 megapixel (3750 x 3000) resolution. 

 

I was wondering if the developers have come across this upper limit too? I
have a 2400 dpi printer, so I want to go with the highest dpi possible for
the best quality. 

  _  

From: David Hall mailto:li...@cowsandmilk.net> >
Sent: 06 May 2016 19:17:38
To: Stephen Kerry
Cc: pymol-users@lists.sourceforge.net
 
Subject: Re: [PyMOL] High Resolution Ray Tracing 

 

Feel free to send me the files off list.

 

-David Hall

 

On May 6, 2016, at 1:54 PM, Stephen Kerry mailto:stephen.kerr...@outlook.com> > wrote:

 

Dear All,

 

I have a protein complex scene that I need to create a large, high
resolution (1200 dpi) ray traced image of, but am unable to do so as I
always run out of memory at the end of the ray tracing process, with the
following error:

 

python2.7(972,0x7fff7397f300) malloc: ***
mach_vm_map(size=18446744068907188224) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

This is with PyMOL 1.81 from Fink on OSX 10.10 with an i7-4790K processor
and 32 GB of DDR3. Python2.7 expands up to 15 GB of RAM, with more than
twice this reserved for virtual memory, but no swap is actually used.

Decreasing hash_max just increases the ray tracing time until the error at
the end. Sometimes PyMOL will be terminated with this error, whilst at other
times a transparent PNG is all that is produced.

Is there a way to force PyMOL to use virtual memory to avoid these
errors/crashes at the expense of processing time?

If not, is there anyone who has PyMOL 1.8x installed on a system with 64 GB
or more RAM, who would be able to render this ray traced image if I send
the, the .pse file and .pml script off list? Takes about 10 mins to process.

Cheers,

Stephen

 


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Applications Manager provides deep performance insights into multiple tiers
of
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