Producing sexy ray-traced images - Revision history

import>Mp466: /* Making images for publication */

2010-05-20T05:13:33Z

Making images for publication

← Older revision		Revision as of 05:13, 20 May 2010
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	[[Image:Ray7.png\|thumb\|Met-enk after ray tracing with publication quality settings using mode 3\|200px\|right]]		[[Image:Ray7.png\|thumb\|Met-enk after ray tracing with publication quality settings using mode 3\|200px\|right]]

	These settings can of course be changed. You might find that you need to change the resolution if you have a wide-screen monitor (2000x1500 is for 4:3 aspect ratio monitors) as you might end up inadvertently chopping bits off the image. If in doubt, you can always just use the resolution your desktop is set to.		These settings can of course be changed. You might find that you need to change the resolution if you have a wide-screen monitor (2000x1500 is for 4:3 aspect ratio monitors) as you might end up inadvertently chopping bits off the image. If in doubt, you can always just use the resolution your desktop is set to. PyMOL's "ray X, Y" command means that a ray-traced image of size X-by-Y dots will be produced. So if you want a 300 dpi, 10" x 6" image, then you'd do "ray 3000,1800"

	Voila! you are now the proud owner of a rather good looking image! For more info, you should check out the [http://www.pymolwiki.org/index.php/Main_Page Pymol Wiki].		Voila! you are now the proud owner of a rather good looking image! For more info, you should check out the [http://www.pymolwiki.org/index.php/Main_Page Pymol Wiki].

import>Mp466: /* Making images for publication */

2010-05-19T22:25:38Z

Making images for publication

← Older revision		Revision as of 22:25, 19 May 2010
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	Voila! you are now the proud owner of a rather good looking image! For more info, you should check out the [http://www.pymolwiki.org/index.php/Main_Page Pymol Wiki].		Voila! you are now the proud owner of a rather good looking image! For more info, you should check out the [http://www.pymolwiki.org/index.php/Main_Page Pymol Wiki].

			Once you have a pretty png file you may need it in a compressed tiff format for a journal.
			This is easily done via the convert program which is a member of the ImageMagick suite.
			The compression is sometimes necessary.

			convert -compress lzw raytraced.png raytraced.tiff

import>Csw34: /* Recommended settings */

2009-10-06T15:31:06Z

Recommended settings

← Older revision		Revision as of 15:31, 6 October 2009
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	bg_color white		bg_color white
	set antialias,2		set antialias,2
	set hash_max, ~~400~~		set hash_max, 300

	You may actually want to have shadows in your image, but for anything larger than a small peptide, it can become very distracting. If you type ''ray'' again now, you can already see the improvement. 'hash_max' is very important as it defines the maximum amount of memory Pymol can use while ray tracing and defaults to a wimpy 100mb. Setting it to ~~400~~ seems to be around the point where further increases give no return. Make sure you have enough RAM though! But...there is more to come! Pymol supports a selection of ray tracing modes, four in fact. Which one you choose to use depends largely on which effect you require. Modes are selected with the command:		You may actually want to have shadows in your image, but for anything larger than a small peptide, it can become very distracting. If you type ''ray'' again now, you can already see the improvement. 'hash_max' is very important as it defines the maximum amount of memory Pymol can use while ray tracing and defaults to a wimpy 100mb. Setting it to 300 seems to be around the point where further increases give no return. Make sure you have enough RAM though! But...there is more to come! Pymol supports a selection of ray tracing modes, four in fact. Which one you choose to use depends largely on which effect you require. Modes are selected with the command:

	set ray_trace_mode, X		set ray_trace_mode, X

import>Csw34: /* Recommended settings */

2009-10-06T15:19:55Z

Recommended settings

← Older revision		Revision as of 15:19, 6 October 2009
Line 35:		Line 35:
	bg_color white		bg_color white
	set antialias,2		set antialias,2
			set hash_max, 400

	You may actually want to have shadows in your image, but for anything larger than a small peptide, it can become very distracting. If you type ''ray'' again now, you can already see the improvement. But...there is more to come! Pymol supports a selection of ray tracing modes, four in fact. Which one you choose to use depends largely on which effect you require. Modes are selected with the command:		You may actually want to have shadows in your image, but for anything larger than a small peptide, it can become very distracting. If you type ''ray'' again now, you can already see the improvement. 'hash_max' is very important as it defines the maximum amount of memory Pymol can use while ray tracing and defaults to a wimpy 100mb. Setting it to 400 seems to be around the point where further increases give no return. Make sure you have enough RAM though! But...there is more to come! Pymol supports a selection of ray tracing modes, four in fact. Which one you choose to use depends largely on which effect you require. Modes are selected with the command:

	set ray_trace_mode, X		set ray_trace_mode, X

import>Csw34 at 17:16, 9 July 2008

2008-07-09T17:16:45Z

← Older revision		Revision as of 17:16, 9 July 2008
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	=== Making images for publication ===		=== Making images for publication ===

	Once you've chosen your ray tracing options, you're ready to produce the final image. As you'll likely want it to be publication quality, I ~~reccomend~~ using the following		Once you've chosen your ray tracing options, you're ready to produce the final image. As you'll likely want it to be publication quality, I recommended using the following

	ray 2000,1500		ray 2000,1500
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	[[Image:Ray7.png\|thumb\|Met-enk after ray tracing with publication quality settings using mode 3\|200px\|right]]		[[Image:Ray7.png\|thumb\|Met-enk after ray tracing with publication quality settings using mode 3\|200px\|right]]

	These settings can of course be ~~changes~~. You might find that you need to change the resolution if you have a wide-screen monitor (2000x1500 is for 4:3 aspect ratio monitors) as you might end up inadvertently chopping bits off the image. If in doubt, you can always just use the resolution your desktop is set to.		These settings can of course be changed. You might find that you need to change the resolution if you have a wide-screen monitor (2000x1500 is for 4:3 aspect ratio monitors) as you might end up inadvertently chopping bits off the image. If in doubt, you can always just use the resolution your desktop is set to.

	Voila! you are now the proud owner of a rather good looking image! For more info, you should check out the [http://www.pymolwiki.org/index.php/Main_Page Pymol Wiki].		Voila! you are now the proud owner of a rather good looking image! For more info, you should check out the [http://www.pymolwiki.org/index.php/Main_Page Pymol Wiki].

import>Csw34 at 14:02, 16 June 2008

2008-06-16T14:02:32Z

← Older revision		Revision as of 14:02, 16 June 2008
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	png raytraced.png, dpi=300		png raytraced.png, dpi=300

	[[Image:Ray7.png\|thumb\|Met-enk after ray tracing with ~~production~~ quality settings using mode 3\|200px\|right]]		[[Image:Ray7.png\|thumb\|Met-enk after ray tracing with publication quality settings using mode 3\|200px\|right]]

	These settings can of course be changes. You might find that you need to change the resolution if you have a wide-screen monitor (2000x1500 is for 4:3 aspect ratio monitors) as you might end up inadvertently chopping bits off the image. If in doubt, you can always just use the resolution your desktop is set to.		These settings can of course be changes. You might find that you need to change the resolution if you have a wide-screen monitor (2000x1500 is for 4:3 aspect ratio monitors) as you might end up inadvertently chopping bits off the image. If in doubt, you can always just use the resolution your desktop is set to.

import>Csw34 at 14:01, 16 June 2008

2008-06-16T14:01:56Z

← Older revision		Revision as of 14:01, 16 June 2008
Line 2:		Line 2:

	=== Before you ray trace ===		=== Before you ray trace ===
	Before you start playing with ray tracing, you need to be sure that you're happy with the way your system is represented. There are LOADS of options in Pymol to change how things appear, and most of them are not ~~availiable~~ in the GUI. For a complete list, go to '''Settings>Edit All''' and have a play around!		Before you start playing with ray tracing, you need to be sure that you're happy with the way your system is represented. There are LOADS of options in Pymol to change how things appear, and most of them are not available in the GUI. For a complete list, go to '''Settings>Edit All''' and have a play around!

	So, you've got a PDB, loaded it into Pymol and arranged it so that it looks how you'd like - some bits as a cartoon, some as sticks etc. How do you go about making an image that you can then use for a poster, or a paper, or a CPGS/thesis? The answer lies in ray tracing. To get Pymol to actually produce a ray traced image is remarkably easy, just type		So, you've got a PDB, loaded it into Pymol and arranged it so that it looks how you'd like - some bits as a cartoon, some as sticks etc. How do you go about making an image that you can then use for a poster, or a paper, or a CPGS/thesis? The answer lies in ray tracing. To get Pymol to actually produce a ray traced image is remarkably easy, just type

import>Csw34 at 14:01, 16 June 2008

2008-06-16T14:01:28Z

← Older revision		Revision as of 14:01, 16 June 2008
Line 1:		Line 1:
	Pardon the title but you'll understand when you see the results!		Pardon the title but you'll understand when you see the results!

			=== Before you ray trace ===
			Before you start playing with ray tracing, you need to be sure that you're happy with the way your system is represented. There are LOADS of options in Pymol to change how things appear, and most of them are not availiable in the GUI. For a complete list, go to '''Settings>Edit All''' and have a play around!

	So, you've got a PDB, loaded it into Pymol and arranged it so that it looks how you'd like - some bits as a cartoon, some as sticks etc. How do you go about making an image that you can then use for a poster, or a paper, or a CPGS/thesis? The answer lies in ray tracing. To get Pymol to actually produce a ray traced image is remarkably easy, just type		So, you've got a PDB, loaded it into Pymol and arranged it so that it looks how you'd like - some bits as a cartoon, some as sticks etc. How do you go about making an image that you can then use for a poster, or a paper, or a CPGS/thesis? The answer lies in ray tracing. To get Pymol to actually produce a ray traced image is remarkably easy, just type
Line 19:		Line 22:

	To resolve these issues, I will now go through the key settings you should ALWAYS have set,		To resolve these issues, I will now go through the key settings you should ALWAYS have set,

			=== Recommended settings ===

	[[Image:Ray3.png\|thumb\|Met-enk after ray tracing with the recommended settings and using mode 0\|200px\|right]]		[[Image:Ray3.png\|thumb\|Met-enk after ray tracing with the recommended settings and using mode 0\|200px\|right]]
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	where X is 0,1,2 or 3. 0 is the default, 1 puts a black outline around the molecule, 2 gives you a black and white 'sketch' and 3 gives you a funky cartoon like image, with quantised colouring! All four are demonstrated in the images here. My personal favourite is mode 3 although you should bear in mind that it might not look as good when printed.		where X is 0,1,2 or 3. 0 is the default, 1 puts a black outline around the molecule, 2 gives you a black and white 'sketch' and 3 gives you a funky cartoon like image, with quantised colouring! All four are demonstrated in the images here. My personal favourite is mode 3 although you should bear in mind that it might not look as good when printed.

			=== Making images for publication ===

	Once you've chosen your ray tracing options, you're ready to produce the final image. As you'll likely want it to be publication quality, I reccomend using the following		Once you've chosen your ray tracing options, you're ready to produce the final image. As you'll likely want it to be publication quality, I reccomend using the following

import>Csw34 at 13:57, 16 June 2008

2008-06-16T13:57:44Z

← Older revision		Revision as of 13:57, 16 June 2008
Line 3:		Line 3:
	So, you've got a PDB, loaded it into Pymol and arranged it so that it looks how you'd like - some bits as a cartoon, some as sticks etc. How do you go about making an image that you can then use for a poster, or a paper, or a CPGS/thesis? The answer lies in ray tracing. To get Pymol to actually produce a ray traced image is remarkably easy, just type		So, you've got a PDB, loaded it into Pymol and arranged it so that it looks how you'd like - some bits as a cartoon, some as sticks etc. How do you go about making an image that you can then use for a poster, or a paper, or a CPGS/thesis? The answer lies in ray tracing. To get Pymol to actually produce a ray traced image is remarkably easy, just type

⚫	[[Image:Ray2.png\|thumb\|Met-enk after ray tracing with default settings\|200px\|right]]
	[[Image:Ray1.png\|thumb\|Met-enk before ray tracing\|200px\|right]]		[[Image:Ray1.png\|thumb\|Met-enk before ray tracing\|200px\|right]]
		⚫	[[Image:Ray2.png\|thumb\|Met-enk after ray tracing with default settings\|200px\|right]]

	ray		ray
Line 19:		Line 19:

	To resolve these issues, I will now go through the key settings you should ALWAYS have set,		To resolve these issues, I will now go through the key settings you should ALWAYS have set,

			[[Image:Ray3.png\|thumb\|Met-enk after ray tracing with the recommended settings and using mode 0\|200px\|right]]
			[[Image:Ray4.png\|thumb\|Met-enk after ray tracing with the recommended settings and using mode 1\|200px\|right]]
			[[Image:Ray5.png\|thumb\|Met-enk after ray tracing with the recommended settings and using mode 2\|200px\|right]]
			[[Image:Ray6.png\|thumb\|Met-enk after ray tracing with the recommended settings and using mode 3\|200px\|right]]

	set ray_trace_fog,0		set ray_trace_fog,0
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	png raytraced.png, dpi=300		png raytraced.png, dpi=300

	[[Image:~~Tamiflu~~.~~gif~~\|thumb\|~~Tamiflu~~\|200px\|right]]		[[Image:Ray7.png\|thumb\|Met-enk after ray tracing with production quality settings using mode 3\|200px\|right]]

	These settings can of course be changes. You might find that you need to change the resolution if you have a wide-screen monitor (2000x1500 is for 4:3 aspect ratio monitors) as you might end up inadvertently chopping bits off the image. If in doubt, you can always just use the resolution your desktop is set to.		These settings can of course be changes. You might find that you need to change the resolution if you have a wide-screen monitor (2000x1500 is for 4:3 aspect ratio monitors) as you might end up inadvertently chopping bits off the image. If in doubt, you can always just use the resolution your desktop is set to.

import>Csw34 at 13:55, 16 June 2008

2008-06-16T13:55:17Z

← Older revision		Revision as of 13:55, 16 June 2008
Line 2:		Line 2:

	So, you've got a PDB, loaded it into Pymol and arranged it so that it looks how you'd like - some bits as a cartoon, some as sticks etc. How do you go about making an image that you can then use for a poster, or a paper, or a CPGS/thesis? The answer lies in ray tracing. To get Pymol to actually produce a ray traced image is remarkably easy, just type		So, you've got a PDB, loaded it into Pymol and arranged it so that it looks how you'd like - some bits as a cartoon, some as sticks etc. How do you go about making an image that you can then use for a poster, or a paper, or a CPGS/thesis? The answer lies in ray tracing. To get Pymol to actually produce a ray traced image is remarkably easy, just type

		⚫	[[Image:Ray2.png\|thumb\|Met-enk after ray tracing with default settings\|200px\|right]]
		⚫	[[Image:Ray1.png\|thumb\|Met-enk before ray tracing\|200px\|right]]

	ray		ray
Line 8:		Line 11:

	png raytraced.png		png raytraced.png

⚫	[[Image:Ray2.png\|thumb\|Met-enk after ray tracing with default settings\|200px\|right]]
⚫	[[Image:Ray1.png\|thumb\|Met-enk before ray tracing\|200px\|right]]