Improving picture quality of ED map in PYMOL
Dear Friends, Sorry, for the of topic question. Does anyone can tell how to improve the quality of a picture showing the electron density map of dna in a complex using PYMOL. I created the figure, but not happy with the quality as it is now. Might be there is a way to improve which I don't know. I want the lines in the mesh to be more sharp and fine. Any suggested program to prepare a publication quality figure to show the ED map would be of great help. Thanking you in advance... Raja
You can edit the width of the mesh lines within pymol; select "edit all" and
edit "mesh-width" (ie use smaller value). This will improve things.
On 9/1/09 2:16 PM, "Raja Dey"
Dear Friends, Sorry, for the of topic question. Does anyone can tell how to improve the quality of a picture showing the electron density map of dna in a complex using PYMOL. I created the figure, but not happy with the quality as it is now. Might be there is a way to improve which I don't know. I want the lines in the mesh to be more sharp and fine. Any suggested program to prepare a publication quality figure to show the ED map would be of great help. Thanking you in advance... Raja
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Raja There are a number of places on the interweb that have details about this. Some of the things you can do is change some of the settings before you do a ray trace and also output the view to a PNG that is larger than the screen and up the dpi. Nigel On 9/1/09 11:16 AM, Raja Dey wrote:
Dear Friends, Sorry, for the of topic question. Does anyone can tell how to improve the quality of a picture showing the electron density map of dna in a complex using PYMOL. I created the figure, but not happy with the quality as it is now. Might be there is a way to improve which I don't know. I want the lines in the mesh to be more sharp and fine. Any suggested program to prepare a publication quality figure to show the ED map would be of great help. Thanking you in advance... Raja
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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
Hi Raja, here is what I usually do to get a paper-quality picture out of PyMol: once I have model and maps displayed, I issues these commands: ray 500,500 png file_name You need to play with the above numbers to get the picture you like, and it will be saved under file name file_name.png. Since I use Pymol one a year or so, I can't remember what the above "magic" numbers/commands mean. Pavel. On 9/1/09 11:16 AM, Raja Dey wrote:
Dear Friends, Sorry, for the of topic question. Does anyone can tell how to improve the quality of a picture showing the electron density map of dna in a complex using PYMOL. I created the figure, but not happy with the quality as it is now. Might be there is a way to improve which I don't know. I want the lines in the mesh to be more sharp and fine. Any suggested program to prepare a publication quality figure to show the ED map would be of great help. Thanking you in advance... Raja
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Those commands represent the resolution of the image you're generating- you
can do "ray 1600,1200", for example, to get a 1600 X 1200 pixel image.
-Sam
On Tue, Sep 1, 2009 at 2:40 PM, Pavel Afonine
Hi Raja,
here is what I usually do to get a paper-quality picture out of PyMol:
once I have model and maps displayed, I issues these commands:
ray 500,500 png file_name
You need to play with the above numbers to get the picture you like, and it will be saved under file name file_name.png. Since I use Pymol one a year or so, I can't remember what the above "magic" numbers/commands mean.
Pavel.
On 9/1/09 11:16 AM, Raja Dey wrote:
Dear Friends, Sorry, for the of topic question. Does anyone can tell how to improve the quality of a picture showing the electron density map of dna in a complex using PYMOL. I created the figure, but not happy with the quality as it is now. Might be there is a way to improve which I don't know. I want the lines in the mesh to be more sharp and fine. Any suggested program to prepare a publication quality figure to show the ED map would be of great help. Thanking you in advance... Raja
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Hi, I do it like this: First just type
ray save junk.png
Read the resolution, multiply by 4 or 5 depending on the intended printed size. Should keep the geometry, which is nice if you have a stereo view.
ray 4*x,4*y save highresolution.png
You can also test different mesh settings like mesh_width
http://pymolwiki.org/index.php/Category:Settings
There is also a pymol mailing list, you could ask more detailed questions.
~L~
______________________________________________________
Lari Lehtiö
Pharmacy, Department of Biochemistry and Pharmacy
Åbo Akademi University,
BioCity, FIN-20520 Turku
Finland
+358 2 215 4270
______________________________________________________
Quoting Pavel Afonine
Hi Raja,
here is what I usually do to get a paper-quality picture out of PyMol:
once I have model and maps displayed, I issues these commands:
ray 500,500 png file_name
You need to play with the above numbers to get the picture you like, and it will be saved under file name file_name.png. Since I use Pymol one a year or so, I can't remember what the above "magic" numbers/commands mean.
Pavel.
On 9/1/09 11:16 AM, Raja Dey wrote:
Dear Friends, Sorry, for the of topic question. Does anyone can tell how to improve the quality of a picture showing the electron density map of dna in a complex using PYMOL. I created the figure, but not happy with the quality as it is now. Might be there is a way to improve which I don't know. I want the lines in the mesh to be more sharp and fine. Any suggested program to prepare a publication quality figure to show the ED map would be of great help. Thanking you in advance... Raja
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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participants (6)
-
Bert Van Den Berg -
Lari Lehtiö -
Nigel W Moriarty -
Pavel Afonine -
Raja Dey -
Sam Stampfer