Re: [Chimera-users] FW: eps image in publication quality
Dear Eric & Greg Thank you for the suggestions. The only available option to save the *sequence alignment image* is EPS format, actually I am looking a way to save the image in tif or png format. In the pop-up window of sequence alignment image , there are following options available under 'File' heading: Save as, save EPS, save Association info, Hide & quit. As Greg pointed out, I didn't find "Save Image dialog". Eric, when I copied the so generated EPS image in MS-Powerpoint for further editing, the quality of the image was not good. I have attached one of the EPS image ( in which I have aligned two structures: pdb id 4ICB & 3BCI.) Thank you for help, Mahendra Thapa University of Cincinnati,OH On Tue, Sep 15, 2015 at 8:42 PM, Thapa, Mahendra (thapamb) < thapamb@mail.uc.edu> wrote:
------------------------------ *From:* gregc@cgl.ucsf.edu *Sent:* Tuesday, September 15, 2015 6:42:06 PM (UTC-06:00) Central America *To:* Eric Pettersen; Thapa, Mahendra (thapamb) *Cc:* chimera-users@cgl.ucsf.edu *Subject:* Re: [Chimera-users] eps image in publication quality
Actually, chimera's EPS files are at a fixed resolution. To get a higher resolution, save the image with a higher resolution. An easy way to get a reasonable resolution is to switch to print units in the Save Image dialog, and choose a size in inches or cm. The default "Print resolution" of 100dpi is generally more than adequate since printers need many dots to represent a single pixel and most computer monitors are roughly 100dpi.
Also, note that EPS files are huge compared to PNG or TIFF files. Most, if not all, journals now accept TIFF or PNG images, so there is no need to generate an EPS file.
-- Greg
September 15 2015 5:18 PM, "Eric Pettersen" <pett@cgl.ucsf.edu <%22Eric%20Pettersen%22%20%3Cpett@cgl.ucsf.edu%3E>> wrote:
EPS (Encapsulated PostScript) is resolution independent — it essentially has infinite resolution. If it doesn’t look good in a viewer it’s because the viewer is doing a poor job of rendering it. What are you using to look at the EPS file? —Eric
Eric Pettersen UCSF Computer Graphics Lab
On Sep 15, 2015, at 9:04 AM, Mahendra B Thapa <thapamb@mail.uc.edu> wrote:
Dear Chimera Users, Using the following procedures in chimera window, I saved a sequence allignment image in eps format ( which looked like the first image of " file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html"). The image in the pop of window is nice but the saved image in the eps format is not so clear. Let me suggest how to save the image in the publication quality. (i) structure ---> matchmaker (ii) Tools ---> sequence ---> match ---> align (iii) file ---> save as ---> eps Thank you, Mahendra Thapa University of Cincinnati, OH _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Mahendra, Yeah, Greg’s response was appropriate for the main “Save Image” dialog, not the “Save EPS” from the sequence window. The latter is, as I said earlier, “infinite” resolution. Nonetheless, Microsoft products may not do a good job of rendering PostScript files, particularly on Windows machines (PostScript is better supported on Mac). Therefore you might want to use something like Photoshop if you have that available. Nonetheless, if you *print* from PowerPoint I think you will see that you get a good looking result. Also, zooming in in PowerPoint will give you a somewhat better looking image to look at / work with, but not as good as what gets printed. When I open your file on my Mac using Preview, it looks fine. I’ve attached a screenshot. I’ve also attached the PDF equivalent of your EPS files, in case PowerPoint can handle that better for whatever reason. One thing you might also possibly want to do is to change both your model’s colors to white, so you don’t get that garish magenta background on the second sequence name. Just go to the model panel, click on the small color well on that model’s line which will bring up a color editor and change the model color to white. —Eric
On Sep 16, 2015, at 6:36 AM, Mahendra B Thapa <thapamb@mail.uc.edu> wrote:
Dear Eric & Greg
Thank you for the suggestions. The only available option to save the sequence alignment image is EPS format, actually I am looking a way to save the image in tif or png format.
In the pop-up window of sequence alignment image , there are following options available under 'File' heading: Save as, save EPS, save Association info, Hide & quit.
As Greg pointed out, I didn't find "Save Image dialog".
Eric, when I copied the so generated EPS image in MS-Powerpoint for further editing, the quality of the image was not good. I have attached one of the EPS image ( in which I have aligned two structures: pdb id 4ICB & 3BCI.)
Thank you for help, Mahendra Thapa University of Cincinnati,OH
On Tue, Sep 15, 2015 at 8:42 PM, Thapa, Mahendra (thapamb) <thapamb@mail.uc.edu <mailto:thapamb@mail.uc.edu>> wrote:
From: gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu> Sent: Tuesday, September 15, 2015 6:42:06 PM (UTC-06:00) Central America To: Eric Pettersen; Thapa, Mahendra (thapamb) Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] eps image in publication quality
Actually, chimera's EPS files are at a fixed resolution. To get a higher resolution, save the image with a higher resolution. An easy way to get a reasonable resolution is to switch to print units in the Save Image dialog, and choose a size in inches or cm. The default "Print resolution" of 100dpi is generally more than adequate since printers need many dots to represent a single pixel and most computer monitors are roughly 100dpi.
Also, note that EPS files are huge compared to PNG or TIFF files. Most, if not all, journals now accept TIFF or PNG images, so there is no need to generate an EPS file.
-- Greg
September 15 2015 5:18 PM, "Eric Pettersen" <pett@cgl.ucsf.edu <mailto:%22Eric%20Pettersen%22%20%3Cpett@cgl.ucsf.edu%3E>> wrote: EPS (Encapsulated PostScript) is resolution independent — it essentially has infinite resolution. If it doesn’t look good in a viewer it’s because the viewer is doing a poor job of rendering it. What are you using to look at the EPS file? —Eric
Eric Pettersen UCSF Computer Graphics Lab
On Sep 15, 2015, at 9:04 AM, Mahendra B Thapa <thapamb@mail.uc.edu <mailto:thapamb@mail.uc.edu>> wrote:
Dear Chimera Users, Using the following procedures in chimera window, I saved a sequence allignment image in eps format ( which looked like the first image of "file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html <>"). The image in the pop of window is nice but the saved image in the eps format is not so clear. Let me suggest how to save the image in the publication quality. (i) structure ---> matchmaker (ii) Tools ---> sequence ---> match ---> align (iii) file ---> save as ---> eps Thank you, Mahendra Thapa University of Cincinnati, OH _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
<Match_3BCI_4ICB.eps>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Eric Pettersen -
Mahendra B Thapa