Just to clarify, 1 and 2 is obsolete when using 3.
B
Hi All,
With Bernhard's help, I fixed this issue of render tool in Coot in Win7.
I summarize what I did here:
1.* - add C:\yourccp4installationdirectory\bin to PATH in the coot
startup script (runwincoot.bat in C:\yourwincootinstallationdirectory) *
I use Notepad to open the .bat file and do edit:
set
PATH=%COOT_PREFIX%\bin;%COOT_PREFIX%\libexec;%COOT_PREFIX%\python27;%PATH%;*C:\CCP4-7\7.**0\bin*).*
*My
CCP4 installation folder is C:\CCP4-7\7.0\bin. To locate files, I just
simply use Win7 search file from the start menu.
*2. - edit the raster3d.py file
(C:\yourwincootinstallationdrirectory\python27\lib\site-packages\coot\)
from (line 44 or so):
r3d_exe = find_exe("render", "PATH")
to
r3d_exe = find_exe("render", "CCP4_BIN", "PATH")*
*
*
After I did this, Coot can find Raster3D PATH, but I still have an error
of "Some errors in Raster3D" in terminal windows and fail to render.
*3. Download:*
*https://raw.githubusercontent.com/bernhardcl/coot/master/python/raster3d.py
<https://raw.githubusercontent.com/bernhardcl/coot/master/python/raster3d.py>
and replace the same file (maybe make a backup first) in
C:\yourwincootinstallationdrirectory\python27\lib\site-packages\coot\*
*4. Done. Works!*
*
*
Thanks Bernhard!
On Wed, Mar 29, 2017 at 11:58 AM, Xiao Lei <[email protected]
<mailto:[email protected]>> wrote:
Hello B.,
Works.Thank you very much!
On Wed, Mar 29, 2017 at 8:14 AM, B.Lohkamp <[email protected]
<mailto:[email protected]>> wrote:
Hello,
I see. Sorry. Now I remember this and I fixed this elsewhere
too. Please try the following. Download:
https://raw.githubusercontent.com/bernhardcl/coot/master/python/raster3d.py
<https://raw.githubusercontent.com/bernhardcl/coot/master/python/raster3d.py>
and replace the same file (maybe make a backup first) in
C:\yourwincootinstallationdrirectory\python27\lib\site-packages\coot\
This should work.
Bernhard
Hi B. ,
I followed your suggestions and now Wincoot can find
render.exe, but it
has a warning message of "this copy of render was not built
with tiff
support BL Warning: some error in rester3D" .
I attach the picture here. I'd appreciate if you have any
idea of how to
fix it.
Thanks a lot.
Inline image 1
On Tue, Mar 28, 2017 at 12:54 AM, B.Lohkamp
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>
wrote:
remove the % around the ccp4 path and you are set.
B
Hi Bernhard,
Thank you for your help. I attach my runwincoot.bat
below. My
render.exe
path is "C:\CCP4-7\7.0\bin". What should I do to add
to the PATH? I
could not understand the grammar well, should I add as :
set
PATH=%COOT_PREFIX%\bin;%COOT_PREFIX%\libexec;%COOT_PREFIX%\python27;%PATH%;%C:\CCP4-7\7.0\bin%
?
------------------------------------------------------------------------------------------------------------------------------------------
@set LANG=en
title WinCoot
set COOT_PREFIX=C:\WinCoot
set COOT_GUILE_PREFIX=C:/WinCoot
set COOT_HOME=%COOT_PREFIX%
set COOT_BACKUP_DIR=%COOT_PREFIX%\coot-backup
set COOT_SHARE=%COOT_PREFIX%\share
if not exist "%CLIBD_MON%" (
echo no $CLIBD_MON found setting COOT_REFMAC_LIB_DIR
set COOT_REFMAC_LIB_DIR=%COOT_SHARE%\coot\lib
)
set COOT_SCHEME_DIR=%COOT_SHARE%/coot/scheme
set
COOT_STANDARD_RESIDUES=%COOT_SHARE%\coot\standard-residues.pdb
set COOT_PIXMAPS_DIR=%COOT_SHARE%\coot\pixmaps
set COOT_RESOURCES_FILE=%COOT_SHARE%\coot\cootrc
set COOT_DATA_DIR=%COOT_SHARE%\coot
set
COOT_REF_STRUCTS=%COOT_SHARE%\coot\reference-structures
set
COOT_PYTHON_DIR=%COOT_PREFIX%\python27\lib\site-packages\coot
set
COOT_REF_SEC_STRUCTS=%COOT_SHARE%\coot\ss-reference-structures
set PYTHONHOME=%COOT_PREFIX%\python27
set
GUILE_LOAD_PATH=%COOT_GUILE_PREFIX%/share/guile/1.8;%COOT_GUILE_PREFIX%/share/guile;%COOT_GUILE_PREFIX%/share/guile/gtk-2.0;%COOT_GUILE_PREFIX%/share/guile/gui;%COOT_GUILE_PREFIX%/share/guile/www;%COOT_GUILE_PREFIX%/share/guile/site
set SYMINFO=%COOT_SHARE%\coot\syminfo.lib
set
PATH=%COOT_PREFIX%\bin;%COOT_PREFIX%\libexec;%COOT_PREFIX%\python27;%PATH%
start /affinity 1 coot-bin.exe %*
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
On Mon, Mar 27, 2017 at 10:24 PM, B.Lohkamp
<[email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>
<mailto:[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>> wrote:
Hi ...,
Hi Ethan,
Thank you for the information. I have ccp4i
installed on the
same PC,
the error from Coot is "Couldn't find render
in default
path and
PATH
Shall we search the whole disk?" If I click
"Yes", then
Coot freezes
forever and I need to force close it.
This can take a long time (depending on your
disk size) but
should
result in something. Anyway...
On Mon, Mar 27, 2017 at 2:18 PM, Ethan A Merritt
<[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>
<mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>>
<mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>
<mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>>>> wrote:
On Monday, 27 March, 2017 22:12:22 Paul
Emsley wrote:
> On 27/03/17 21:55, Xiao Lei wrote:
> >
> >
> > Because the picture quality from
Coot>>Draw>>Screenshot>>Simple is
> > very low, I tried
Coot>>Draw>>Screenshot>>Povray or
Raster3D to export
> > high quality picture, but I had an
error of
"render tool
missing" and
> > Coot tried automatically find the
render tool but
failed. I use
> > Wincoot 0.8 version in Win7. I do
know if any of you
have similar
> > experience.
This is for windows...
> The render program is part of Ethan
Merritt's Raster3D
package/suite.
> The build system in coot that attempts
to compile
it is a
bit fragile.
>
>
http://skuld.bmsc.washington.edu/raster3d/
<http://skuld.bmsc.washington.edu/raster3d/>
<http://skuld.bmsc.washington.edu/raster3d/
<http://skuld.bmsc.washington.edu/raster3d/>>
<http://skuld.bmsc.washington.edu/raster3d/
<http://skuld.bmsc.washington.edu/raster3d/>
<http://skuld.bmsc.washington.edu/raster3d/
<http://skuld.bmsc.washington.edu/raster3d/>>>
<http://skuld.bmsc.washington.edu/raster3d/
<http://skuld.bmsc.washington.edu/raster3d/>
<http://skuld.bmsc.washington.edu/raster3d/
<http://skuld.bmsc.washington.edu/raster3d/>>
<http://skuld.bmsc.washington.edu/raster3d/
<http://skuld.bmsc.washington.edu/raster3d/>
<http://skuld.bmsc.washington.edu/raster3d/
<http://skuld.bmsc.washington.edu/raster3d/>>>>
That is the source package, yes.
The Raster3D programs are now in the
CCP4 bundle also.
If render is not being found, you may
have a PATH error.
Is your Coot finding other CCP4 programs?
Indeed CCP4 has raster3d now, even on Windows. I
will adapt
for this
in Coot ASAP.
For now I suggest either of the following two
option:
- add C:\yourccp4installationdirectory\bin to
PATH in the coot
startup script (runwincoot.bat in
C:\yourwincootinstallationdirectory)
- edit the raster3d.py file
(C:\yourwincootinstallationdrirectory\python27\lib\site-packages\coot\)
from (line 44 or so):
r3d_exe = find_exe("render", "PATH")
to
r3d_exe = find_exe("render", "CCP4_BIN", "PATH")
If you need more help, please get in touch with
me directly.
Bernhard
>
> Paul.
>
> p.s. Draw -> Additional Representation
-> Ball & Stick
makes things a
> bit nicer, as does Extensions ->
Representation ->
Highlight
Interesting
> Site (still not as nice as a proper
molecular
graphics program
though).
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health
Sciences Bldg
MS 357742, University of Washington,
Seattle
98195-7742
