Re: [PyMOL] High Resolution Ray Tracing

[Stephen Kerry]

Thank you for all of the suggestions so far.

James, I have tried POV-Ray but am unable to emulate PyMOLs internal ray tracer 
to match my other images, which have smaller actual dimensions at the same dpi.

Harold, I agree 2400 dpi might be wasted, but the professional printer supports 
up to 9600 horizontal dpi x 4800 vertical dpi, so a source image with 1200 dpi 
would be a nice step up from 600 dpi. The lpi is 1200 as the four passes from 
each CMYK component apparently increases the vertical dpi by four.

Takanori, your idea of dividing a scene into sections and rendering them 
individually sounds ideal, but I have no idea how to go about that properly, in 
order to get the lighting and shadows to match up when the images are joined.

From: Takanori Nakane 
Sent: 10 May 2016 01:58:09
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] High Resolution Ray Tracing

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
>>
>> --
>> Find and fix application performance issues faster with Applications
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>
>
>
> 

Re: [PyMOL] High Resolution Ray Tracing

[harold steinberg]

The 9600 x 4800 is a very common poster printer spec. Most print shops use 180 
dpi images on their poster printers (for best print speed) and customers cannot 
tell the difference between that and a higher resolution.

As a test, render a small image (say 6” x 6”) in PyMOL at four different dpi, 
180 dpi (ray 1080), 300 dpi (ray 1800), 600 dpi (ray 3600) and 1200 dpi (ray 
7200). Then use Photoshop or GIMP to make them all 6” x 6”. 

Put them together side-by-side in a layout program and print them on one sheet 
to compare. I bet you will have an extremely difficult time telling them apart.


> On May 10, 2016, at 12:40 PM, Stephen Kerry  
> wrote:
> 
> Harold, I agree 2400 dpi might be wasted, but the professional printer 
> supports up to 9600 horizontal dpi x 4800 vertical dpi, so a source image 
> with 1200 dpi would be a nice step up from 600 dpi. The lpi is 1200 as the 
> four passes from each CMYK component apparently increases the vertical dpi by 
> four.

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] High Resolution Ray Tracing

[Thomas Holder]

Hi Adam et al.,

This is a super interesting and helpful discussion!

Just wanted to throw in the following shortcut for creating the 6" test images:

png image1.png, 6in, ray=1, dpi=180
png image2.png, 6in, ray=1, dpi=300
png image3.png, 6in, ray=1, dpi=600
png image4.png, 6in, ray=1, dpi=1200

Cheers,
  Thomas

On 10 May 2016, at 14:27, harold steinberg  wrote:

> The 9600 x 4800 is a very common poster printer spec. Most print shops use 
> 180 dpi images on their poster printers (for best print speed) and customers 
> cannot tell the difference between that and a higher resolution.
> 
> As a test, render a small image (say 6” x 6”) in PyMOL at four different dpi, 
> 180 dpi (ray 1080), 300 dpi (ray 1800), 600 dpi (ray 3600) and 1200 dpi (ray 
> 7200). Then use Photoshop or GIMP to make them all 6” x 6”. 
> 
> Put them together side-by-side in a layout program and print them on one 
> sheet to compare. I bet you will have an extremely difficult time telling 
> them apart.
> 
>> On May 10, 2016, at 12:40 PM, Stephen Kerry  
>> wrote:
>> 
>> Harold, I agree 2400 dpi might be wasted, but the professional printer 
>> supports up to 9600 horizontal dpi x 4800 vertical dpi, so a source image 
>> with 1200 dpi would be a nice step up from 600 dpi. The lpi is 1200 as the 
>> four passes from each CMYK component apparently increases the vertical dpi 
>> by four.
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] High Resolution Ray Tracing

[harold steinberg]

There is Sooo much I need to learn about PyMOL… :)


> On May 10, 2016, at 2:34 PM, Thomas Holder  
> wrote:
> 
> Hi Adam et al.,
> 
> This is a super interesting and helpful discussion!
> 
> Just wanted to throw in the following shortcut for creating the 6" test 
> images:
> 
> png image1.png, 6in, ray=1, dpi=180
> png image2.png, 6in, ray=1, dpi=300
> png image3.png, 6in, ray=1, dpi=600
> png image4.png, 6in, ray=1, dpi=1200
> 
> Cheers,
>  Thomas
> 
> On 10 May 2016, at 14:27, harold steinberg  wrote:
> 
>> The 9600 x 4800 is a very common poster printer spec. Most print shops use 
>> 180 dpi images on their poster printers (for best print speed) and customers 
>> cannot tell the difference between that and a higher resolution.
>> 
>> As a test, render a small image (say 6” x 6”) in PyMOL at four different 
>> dpi, 180 dpi (ray 1080), 300 dpi (ray 1800), 600 dpi (ray 3600) and 1200 dpi 
>> (ray 7200). Then use Photoshop or GIMP to make them all 6” x 6”. 
>> 
>> Put them together side-by-side in a layout program and print them on one 
>> sheet to compare. I bet you will have an extremely difficult time telling 
>> them apart.
>> 
>>> On May 10, 2016, at 12:40 PM, Stephen Kerry  
>>> wrote:
>>> 
>>> Harold, I agree 2400 dpi might be wasted, but the professional printer 
>>> supports up to 9600 horizontal dpi x 4800 vertical dpi, so a source image 
>>> with 1200 dpi would be a nice step up from 600 dpi. The lpi is 1200 as the 
>>> four passes from each CMYK component apparently increases the vertical dpi 
>>> by four.
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
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