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[ccp4bb]: Summary: Image production (in detail) (2); thanks a lot
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Thanks for those who have responded to my problem.
~~~~
Dear all,
Thanks for those who have responded to my problem. Before I could report a summary about this issue here. I wish I could have a chance to go into some specific details about my problems.
GRASP: Grasp would produce nice .ps files. However, for purpose of further processing, such as for labeling charged residues, I have to outport it from SGI to Adobe Photoshop in PC. Since I don't know any img-format (from .ps to .tiff, for example) conversion programs in SGI, I have to use 'snapshot'. Suggestions of using gimp or imagemagick for format conversion have led us to download the programs. But the installation of gimp failed. It complained that 'the gtk-config script installed by GTK could not be found', although we've installed the glib-1.2.8.tar.gz (obtained from www.GTK.org) before hand. I attached the log file at the end of this mail and wish somebody could help me out with this. Imagemagick seems to need more other things.
Stereo-pair electron density map superimposed with structure model: O is exhaustedly used for model building, but for image production Turbo-Frodo seems to achieve more brilliant color and much better ball-and-stick model, and is able to produce stereo pairs (although they will crossover at the middle). Sometimes the feature of Van der Vaals surface presentation in Turbo could be a simple reason why using it. In such case, snapshot seems to be the only way of catching the images. I've been advised to use Bobscript and am lucky enough to obtain it from Dr. Esnouf today (I wish it will help soon). But still, is there any other program producing good VDW surface images?
Program Molscript and Raster3D have been running on our SGIs. Stereo-pairs production by Raster3d needs tiff library. However, we have real trouble in installing the tiff library. This make the production of stereo pairs with Raster3d impossible. We're using SGI O2 (Irix 6.5 operating system). We've downloaded the tiff software from www.libtiff.org (file: http://www.libtiff.org/tiff-v3.5.6-beta.tar.gz), but failed in compilation (there seems to be many errors, as attached below). Have I got the right thing, please?
It seems that if these two problem could be solved, I would be able to find my way out.
Best wishes,
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
~~~~
You can download image magick binaries for Irix and they can convert all
formats then.
For production of stereo images take the attachrd shell script (by
C. Vonrhein)
***************************************************
** Ulrich Baumann, Dpt. f. Chemie und Biochemie **
** Universitaet Bern, Freiestrasse 3 **
** CH-3012 Bern, Switzerland **
** phone +41-(0)31-631-4320/4324, fax -4887 **
***************************************************
~~~~
you can get prebuilt tiff libraries (tiffutils) from the sgi freeware site:
http://toolbox.sgi.com/TasteOfDT/public/freeware/
installable with swmgr
Yours,
Ashley
Ashley Buckle, PhD
Centre for Protein Engineering
Medical Research Council, Hills Road,
Cambridge, CB2 2QH, UK
Phone: (+44) (1223) 402131 Fax: +44 (1223) 402140 Mobile: 07866 434482
Email: ab@mrc-lmb.cam.ac.uk
Website: http://www.mrc-cpe.cam.ac.uk/~ab
~~~~
xv has already been mentioned - it can be used to convert images and is
available as a binary for SGI machines. As you may have seen on ccp4bb, some
people have problems using it.
Another SGI image conversion program is imgworks. This is part of the IRIX
distribution but I have a feeling that it may not be installed by default.
You may have to hunt around on the IRIX CDs for it. It can convert between
SGI-style RGB files, TIFFs, GIFs and JPEGs.
Hope this helps.
Chris
--
Dr Chris Richardson - sysadmin, Structural Biology Section, icr.ac.uk
~~~~
hiya,
try downloading gimp with GTK from
http://reality.sgi.com/winfred/gimp/
i managed to do it so it cant be that hard!
as for stereo pictures out of raster3d - i make them with the 'draw'
command in bobscript - its very good!
you dont need a tiff lib for raster3d (although it would be very nice i
don't know of anyone who's managed to get it to work!)
i use 'render -sgi' and get *.rgb files which can then be converted into
almost anything using 'xv'
hope this is of some help!
val
~~~~
Hi,
> GRASP: Grasp would produce nice .ps files.
>Since I don't know any img-format (from .ps to .tiff, for example)
>, although we've installed the glib-1.2.8.tar.gz (obtained from
>www.GTK.org)
>before hand. I attached the log file at the end of this mail and wish
>somebody could help me out with this.
>Imagemagick seems to need more other things.
GRASP surfaces can be exported into Pov4Grasp to produce very high
quality images with very high resolution. http://pov4grasp.free.fr//
Download a working / precompiled version of ImageMagick from
http://www.imagemagick.org/www/archives.html or say
ftp.imagemagick.org
Works great. Never could compile it that well myself.
For GTK libs checkout
http://freeware.sgi.com/index-by-alpha.html
You may need to install gtk+-1.2.9 or something. But before you do that
have you checked out gimp-1.2.1 on the same site ?
There (on the sgi freeware site) you can also find tiff libraries.
>
> Stereo-pair electron density map superimposed with structure model:
O is exhaustedly used for model building, but for image production
Turbo-Frodo seems to achieve more brilliant color and much better
ball-and-stick model, and is able to produce stereo pairs
(although they will crossover at the middle). Sometimes the feature
of Van der Vaals surface presentation in Turbo could be a simple
reason why using it. In such case, snapshot seems to be the only
way of catching the images.
I've been advised to use Bobscript and am lucky enough to obtain it
from Dr. Esnouf today (I wish it will help soon).
>But still, is there any other program producing good VDW surface images?
IMHO Bobscript is very good for e-density rendering but quite slow. But so
far I have been able to wait. For very large densities it is too slow and
may have to be recompiled with larger static arrays. In these case
I use the plot feature in o to write out o_plots and read them into my
program and convert it to Povray. Very straight forward. ( Sounds like
advertising :)
Bobscript is good at VDW surfaces as well if you mean simply converting
all your atoms into spheres with VDW radii. If you mean accessible
surfaces then there are programs like VMD, MSMS and SPOCK. I recommend
SPOCK but MSMS ( possibly in combination with VMD ) is good too.
VMD might answer most of your concerns includ. stereo. However in my mind
VMD's stick or ss models are poor quality.
>
> Program Molscript and Raster3D have been running on our SGIs.
Stereo-pairs production by Raster3d needs tiff library.
However, we have real trouble in installing the tiff library.
This make the production of stereo pairs with Raster3d impossible.
We're using SGI O2 (Irix 6.5 operating system).
We've downloaded the tiff software from www.libtiff.org (file:
http://www.libtiff.org/tiff-v3.5.6-beta.tar.gz),
but failed in compilation
(there seems to be many errors, as attached below). Have I got the right
>thing, please?
See above. Download it from the SGI site - no need to compile.
(BTW you need superuser privileges to install software from this site but
I guess you can get them from your admin or ask him/her to do it for you)
Also if ImageMagick works, there is no need to install Raster3d with tiff.
The new version uses display or convert as a delegate and whatever IM can
output, Raster3d can make use of it. So you don't need render with tiff
library - just compile it without.
If you would like to try glr ( frontend program to bobscript/render/povray
) let me know.
Hope this helps.
Lothar
~~~~
Hi,
Some suggestions are..
>GRASP: Grasp would produce nice .ps files. However, for purpose of
>further processing, such as for labeling charged residues, I have to
>outport it from SGI to Adobe Photoshop in PC.
(1) For adding text inside a .ps format file, you don't need to switch
from Unix platform to windows (for photoshop) in PC. You can use 'xfig' (a
freeware from ftp.x.org)
xfig
-Works fine with most Unix platforms (e.g. Linux Red-Hat).
-xfig can also convert .ps to .tiff (and many formats) for labeling.
-xfig is useful in preparing word processing documents using LaTeX.
Well, I am not advertising for xfig.. so, stopping here.
(2) ImageMagick is another good program. I think, most linux RedHat
versions has this program by default. However, for skipping the
installation troubles, use the binaries - available for various platforms.
Check these websites:
http://ftp.nluug.nl/graphics/ImageMagick/binaries/home.html
http://www.planetmirror.com/pub/imagemagick/binaries/
http://ftp.vim.org/graphics/ImageMagick/binaries/home.html
http://www.ccl.net/cca/software/X-WINDOW/ImageMagick/binaries/index.shtml
I am sure that there will be more suggestions from others.
Cheers,
Ravi
==============================================================
Dr. S. Ravichandran |
Postdoctoral Fellow | Home:
Prof. W.N. Lipscomb's group |
Dept of Chemistry & Chemical Biology | 47, Gardner street
Harvard University | Apartment No. 15,
12, Oxford Street, Cambridge | Allston, MA 02134
MA 02138 | USA
USA |
Phone: +1-617-4965-482 | Phone: +1-617-787-1499
FAX: +1-617-4963-330 |
E-mail: ravi@gibbs.harvard.edu |
sankaran@fas.harvard.edu |
==============================================================
~~~~
F.Y.I Re: Yong Tang's previous message about image manipulation ...
For all of you out there using sgi machines, many of the GNU applications
are provided as precompiled binary "inst" packages that can be downloaded
and directly installed from sgi's website (you need root privileges). The
GIMP program (a truly excellent application that's absolutely worth the time
invested in learning to use it) is one of the prebuilt packages offered by
sgi on their "freeware" list at:
http://freeware.sgi.com/index-by-alpha.html
Most of the core of the GNU suite is also offered on the sgi "Freeware"
CD-ROMs that come as a part of the OS distribution.
If you really want the latest bleeding edge, pre-alpha releases, then you
might want to consider setting up the GNU dvelopment environment on your sgi
if you don't have it already.
If you are planning to use the GNU programs for your work, it is well worth
while downloading and installing the "gcc" compiler and its associated
"build" environment (gmake etc.) as it makes the compilation of the GNU
sources much more straightforward. Use of the sgi default "cc" compiler
often entails some manual fiddling with compile time flags if you want to
produce working binaries rather than a few screens of compiler errors.
And while you're at it, why stop there? Consider running Linux on your PC.
All of the GNU environment (including GIMP) comes with it so you never need
to worry about converting your images for Photoshop again.
But for those of you whose work really requires that their OS and
applications to be poorly designed, unstable and overpriced, then GNU/Linux
is probably not for you, but I believe that there are alternative,
commercially available products that meet these needs ...
Gordon
~~~~
What ever it is GRASP or Molscript, always create RGB file not postscript
on SGI. then type "imgworks" or "imgview"(default in SGI, or
toolchest->find->mediatools) save as tiff file, transfer to PC.
GIMP will not read RGB file and not USEFUL. If you really want it works
for SGI. GOTO freeware.sgi.com download gimp and glib etc there what ever
conflicts.
If it is a postscript file( I doubt its quantity), it is easy to use adobe
ILLUSTRTOR
Wuyi Meng
Vertex Pharmaceuticals Inc.
(617)577-6471
Wuyi_Meng@vpharm.com
~~~~
Hi,
You could solve the problems with gimp and the tiff libraries for
your SGI machine by visiting the site freeware.sgi.com. Here you can find
the SGI port to most of the linux software. I feel you would be better of
with these rather than compiling the code. If you however insist of
compiling the code, then try to install the gcc compiler and then compile
them as most of these programs are tested with gcc. Hope this helps.
N.B: Regarding a program to draw a VDW surface, try the program from MSI
called weblab viewer. It runs on windows and doesnt not have a UNIX
version, but the surfaces are good and can be rendered using the program
povray. By the way you can also make good figures (i.e., tiff , jpeg , png
) files if you use molscript compiled with these libraries or you can use
a program called gl_render to write out povray input and use povray to
render the image. ALthough slow , the output is breathtaking.
krishna
*******************************************
Sri Krishna S.
Postdoctoral Researcher / Department of Biochemistry
U.T. Southwestern Medical Center at Dallas
5323 Harry Hines Blvd., Dallas, TX 75390-9038
Tel:(214)648-7119 (Office) (214)772-9439 (Home)
Fax:(214)648-9099
krishna@chop.swmed.edu
*******************************************
~~~~
Hi, there,
The grasp is a very nice programe to make image. You may try to write out the files use rgb format replace the ps format. The rgb format file you may open in SGI use IMGWORKS, then SAVE AS tiff or gif or jfif etc.. format files.
good luck.
wei shu
~~~~
Just two quick notes, you can use SPOCK in place of GRASP and output
RASTER3D format then you can generate very high resolution figures and you
can generate stereo pairs with RASTER3D without the tiff library. You can
generate two views rotated around y by 3-6 degrees and then paste the two
views together (ImageMagick montage or Photoshop). You will need to use
Normal3d to generate a raster3d file with an identity transformation matrix
in the orientation you want. Should look something like:
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
somewhere near the top. Use this raster3d file to generate the first image.
Then edit the file so that the transformation matrix looks like:
1 0 0.1 0
0 1 0 0
0.1 0 1 0
0 0 0 1
and render again (with different output name of course). Then crop both
images leaving about 5-10 pixels of background around the edges. Join the
two images along one of the vertical edges and whalla, you've got a stereo
image. Join them one way and you have wall-eye stereo, join them the other
way and you have cross-eye stereo.
Hope this helps.
~~~~
Regarding ImageMagick, did you download executables? I haven't used the SGI
version in some time but as I recall you can get a tar zipped file with all
executables and all libraries. You may have to set the LD_LIBRARY_PATH
variable to point at the .so files that come with the distribution. Do you
have a systems administrator? Perhaps they could help you with that.
Brent