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[ccp4bb]: Summary: how to prepare images for submission? (1)
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Dear all,
I'm preparing some color images for structure paper submission. However, there is still not satisfactory solution for producing images of required resolution.
Any image croped by snapshot on the SGI work stations only has a resolution of 72 dpi, making it unrealistic for futher processing or direct submission. Trial-and-error photography of these images displayed on the screen using the best film-loaded or digital camaras suffers a lot from the over-saturation of local white regions and the white margines of imgview or imgworks, and terrible distorion of the image by the screen.
Could any person give me some tips about this issue?
Thanks in advance. I'm a new comer here and not sure whether this topic has been covered before.
Sincerely Yours,
Yong TANG
A doctorate student at:
Division of Structural Biology
National Lab of Biomacromolecules
Institute of Biophysics, Chinese Academy of Sciences
15# Datun Road, Chaoyang District
Beijing 100101, P.R. China
Tel: 0086-10-64888511
E-mail: tang@moon.ibp.ac.cn
~~~~
Hello,
I presume you want to generate images from pdb files etc.
To make ribbon diagrams and amino acid residues I use molscript, it can be
found at http://www.avatar.se/molscript/
This can generate raster3D files which can then be made into several file
formats include tiff. I usually increase the size of the file in raster3D
so that it can be resized without altering picture quality.
I also use Bobscript http://orval.rega.kuleuven.ac.be/~robert/BobScript/
to generate map files. Again output can be generated for raster3D. It runs
in a similar fashion to molscript.
I hope this can be of some help.
Mark Ellis
**********************************
Mr. Mark John Ellis
Molecular Biophysics Group
C29, CCLRC Daresbury Laboratory,
Warrington, Cheshire, WA4 4AD
Tel: +44 (0)1925 603590
E-mail: m.j.ellis@dl.ac.uk
~~~~
Yong,
You don't have to do snapshot to obtain high-quality picture for
publication. Usually many graphic programs will allow you to output
postscript format or other formats such as jpg, gif, etc. Then you could
use adobe illustrator to edit your picture further. Programs I found most
useful include Molscript, Grasp, Rasmol and Chime, Molmol, VMD. For
pictures with electron density, Bobscript and Setor produce very beautiful
pictures. Should you have any question please let me know. Good luck. Best
Regards, Shengfeng
Shengfeng Chen Phone: (732) 445-2200
Department of Chemistry e-mail: shengf@rutchem.rutgers.edu
Rutgers University
610 Taylor Road
Piscataway, NJ 08855
~~~~
On Mon, 18 Jun 2001, Yong TANG wrote:
> I'm preparing some color images for structure paper submission. However, there is still not satisfactory solution for producing images of required resolution.
two packages i would recommend for publication figures are Setor and
Molscript. Setor, which unfortunately only runs on SGIs, put out raster
screen images but also has an auxilliary program "Setorplot" which allows
Postscript output which looks good when rendered at any resolution.
Molscript also allows for Postscript output, and also will supply input
for Raster3D. Raster3D can output images of any specified resolution in
several formats, depending on what libraries are linked.
Setor can display electron density maps. Molscript itself won't but you
can display maps either by using the altrered version "Bobscript" or the
accesory program "Conscript".
cheers,
=======================================================================
"We are each of us responsible for the evil we may have prevented."
- James Martineau
=======================================================================
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
djs63@cornell.edu
~~~~
>XV has the pesky feature that it only outputs as many pixels as displayed.
In the XV box "save" dialog box, there is a checkbox labeled "use normal size"
or something like that. If you check this box the full size will be saved,
even if it is too large to fit on screen fullsize (I was alerted to this feature
by another reader after making the same complaint on this BB)
>
> Any image croped by snapshot on the SGI work stations only has a resolution
> of 72 dpi, making it unrealistic for futher processing or direct submission.
> Trial-and-error photography of these images displayed on the screen using
> the best film-loaded or digital camaras suffers a lot from the
> over-saturation of local white regions and the white margines of imgview or
> imgworks, and terrible distorion of the image by the screen.
>
Definitely do not photograph the screen- if only 72 DPI is displayed,
the photograph cannot have any higher quality even if the nominal
resolution is higher.
The resolution the publisher cares about (or should), is the final resolution
in the journal. If you make a figure with 900 x 900 pixels, which will easily
fit on any serious SGI screen, and it is to be printed as one column width,
say 3 inches, then you have your 300 DPI resolution, even if it is displayed
as 12x12 inches and 72 DPI on screen.
If the publisher's art person doesn't understand this and insists on 300 DPI,
load into photoshop, do image:image_size, uncheck the "resample inage" checkbox
(or check "constrain image size" in older versions), and enter 300 for
resolution. Then save in a format such as TIFF which preserves the image
size/resolution. This has not changed the actual pixels in any way,
just defined the pixel size to be smaller.
Instead of requiring a particular resolution, it would be more sensible if the
publisher would first decide on the final size of the image, then multiply
that by 300 dpi or whatever, and tell us how many pixels they want.
Ed
(From: "Edward A. Berry" EABerry@lbl.gov)
~~~~
I would just add to what David Schuller said and recommend SPOCK, which
outputs both MOLSCRIPT and RASTER3D formats; and MIDAS which allows you to
output an image to arbitrary resolution. For image manipulation tools once
you've created your image, try ImageMagick. It comes with RedHat Linux and
you can get precompiled binaries for SGI. XV has the pesky feature that it
only outputs as many pixels as displayed. ImageMagick will behave the way
you would expect. Unfortunately, each of these programs has a bit of a
learning curve. No away around that I'm afraid.
segelke1@llnl.gov
~~~~
Dear Yong
you should use programs such as RIBBONS (found at
http://www.cmc.uab.edu/ribbons/) which allows you to prepare very nice
images and save them as high resolution .TIFF files (which is the preferred
file form for papers).
Hope this helps
Giovanna
~~~~
If you can convert your maps to XPLOR format, then you may want to
consider using PyMOL, which can generate ray-traced renditions of
ribbons, surface, and electron density much more conveniently than
Molscript/Bobscript/Raster3d.
http://pymol.sourceforge.net
Furthermore, in command-line mode you can render figures with
arbitrarily large resolutions. For example, the command:
pymol -c < script.pml
where "script.pml" ends with something like
viewport 2000,1500 # expand the screen in memory
ray # ray-trace
png image.png # save png-format image file (2000x1500)
# end of script
These PNG files can be converted to whatever format you need using
ImageMagick.
-Warren
~~~~
NEVER - EVER even try to submit pictures to a journal from a snapshot.
(for the shake of respect to the readers)
Screen rendering uses 'light' pixels - printouts use 'dark' pixels -
if nothing else (i.e. resolution)
.... taking pictures is cute
There is a wealth of software for presentation graphics:
Molscript (and Bobscript) together with Raster3D are my presonal
preference. Ribbons is giving nice DNA pictures.
Look at a paper that you *like* the graphics and then look what these
people use !
A.
(From: Anastassis Perrakis perrakis@nki.nl)
~~~~
Dear Tang,
In case you have not got these already from someone else :
1. http://www.bmsc.washington.edu/raster3d/html/raster3d.html
2. http://flint.biochm.uottawa.ca/~setor_docs/
3. http://orval.rega.kuleuven.ac.be/~robert/BobScript/bob_doc_2_4.html
4. http://www.avatar.se/molscript/
All these programs are able to produce images at any required resolution
(possibly some minimal user intervention is required). This is not a
complete list.
Nicholas
~~~~
Dear Yong TANG,
Obviously it depends on what pictures you want to make, but for molecules MOLSCRIPT and RASTER3D are very good options. For density it think the program BOBSCRIPT is slightly better. For website please visit our website :www.xray.chem.rug.nl There are links to the different programs.
For the PC also Imageworks combined with showcase is suitable to make nice rendered pictures. Another alternative is the combination of XTALVIEW with RASTER3D.
For surfaces and some molecular representations you could get Weblab viewer lite from www.msi.com
All options are far superior to real photographs from the screen
I expect in the end everything has to be converted to EPS or TIFF, Imagemagick of GIMP are could programs for file conversion
Good luck,
best regards,
Arjan
~~~~
hiya
i wouldnt use snapshot -- have you tried using any of the nice picture
making programs such as molscript/bobscript, setor, grasp - can edit them
using gimp or image magik, render them using raster3d etc -- you should be
able to download these programs from the web if you dont already have them
installed! by the way - what sort of pictures are you trying to make?
good luck!
Valerie Pye
Dept of Biochemistry telephone: 0116 252 3365
University of Leicester fax: 0116 252 3473
Adrian Building
University Road
Leicester
LE1 7RH
~~~~
I realise this is a workaround, but why not have a look at Swiss-PdbViewer
(http://www.expasy.ch/spdbv/)? In combination with POV-Ray
(http://www.povray.org/) it can produce stunning pictures for publication
(including ones showing electron density maps).
Plus, both programs are free, and there are versions for all major
platforms...
Good luck, Luca
--------------------------------------------------------------------------------
Luca Jovine, Ph.D.
Department of Biochemistry and Molecular Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
One Gustave L. Levy Place, New York, NY 10029-6574, U.S.A.
Voice: +1.212.241-8620 FAX: +1.212.831-7126 eFAX: +1.509.356-2832
E-Mail: jovinl02@doc.mssm.edu W3: http://www.mssm.edu/students/jovinl02
--------------------------------------------------------------------------------
~~~~
Hi,
if you have the opportunity to use Photoshop or almost any other Image Processing Program, you should be able to import a postscript file as "generic eps" and then you're also able to increase the dpi's as you need it.
You might also try the following:
(have all your images in the directory snapshots)
#!/bin/tcsh -f
set files=`ls snapshots/*`
foreach image ($files)
makemovie -o ${image}_mod.rgb -c jpeg -f qt -r 1 -s 800,600 ${image}
@ counter ++
end
You can also increase the size (-s 800,600) to something what you might need, but remember the resolution is still 72 dpi, so in order to get more dpi's you'll have to shrink the modified image with eg. Photoshop, Gimp, Showcase
Good luck
Juergen
~~~~
First it would be more helpful if you specify what software you are
using to generate the images.
For most programs, It would be best to obtain postscript output. If
that is impossible, blow your image up to full-screen, then take the
snapshot, then import the snapshot into showcase and shrink it down.
That will give an effective resolution several fold better than 72 dpi
when printed out.
Wai
--
===================================================================
Yu Wai CHEN, Ph.D. .................. email:ywc@mrc-lmb.cam.ac.uk
Centre for Protein Engineering, tel:+44-(0)1223-402148
MRC Centre, Hills Rd, Cambridge CB2 2QH, UK fax:+44-(0)1223-402140
WWW homepage: http://www.mrc-cpe.cam.ac.uk/~ywc
~~~~
Hi,
If it's for publication, you should render your images with raster3d,
pov-ray, etc, depending on what software you are using to make the images,
so that you can make them as high-resolution as your computer can handle.
Molscript and Spock output raster3d input files, for example. O can use
molray to produce rendered images.
Here's the raster3d website:
http://www.bmsc.washington.edu/raster3d/raster3d.html
Ulug Unligil
unligil@crystal.harvard.edu
~~~~
Hi,
pictures are best made using molscript or bobscript (for electron
density display). Use the render option and use render3d afterwards
for best quality (the resolution can be set). I know this can be
a lot of work, but these kind of pictures look the best (anyway
better than taking snapshots from the screen).
Jeroen
--
Jeroen Raymundus Mesters, Ph.D. Alias Geronimo
Dept. of Structural Biology and Crystallography, Institute of Molecular
Biotechnology, P.O.Box 100 813, D-07708 Jena, Germany.
Tel: +49-3641-656063, Fax: +49-3641-656062, E-mail: jmesters@imb-jena.de
http://www.imb-jena.de/www_sbx/home.html
--
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me (Macbeth)
--