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")tor3d_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 <xiaolei...@gmail.com> wrote:
> Hello B.,
>
> Works.Thank you very much!
>
> On Wed, Mar 29, 2017 at 8:14 AM, B.Lohkamp <b.lohk...@gmail.com> 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/pyt
>> hon/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 <b.lohk...@gmail.com
>>> <mailto:b.lohk...@gmail.com>> 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%\p
>>> ython27;%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.p
>>> db
>>> 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\coo
>>> t
>>> set COOT_REF_SEC_STRUCTS=%COOT_SHARE%\coot\ss-reference-structur
>>> es
>>>
>>> set PYTHONHOME=%COOT_PREFIX%\python27
>>>
>>> set
>>> GUILE_LOAD_PATH=%COOT_GUILE_PREFIX%/share/guile/1.8;%COOT_GU
>>> ILE_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%\p
>>> ython27;%PATH%
>>>
>>> start /affinity 1 coot-bin.exe %*
>>> ------------------------------------------------------------
>>> ------------------------------------------------------------
>>> -----------------------------------------------------------
>>>
>>> On Mon, Mar 27, 2017 at 10:24 PM, B.Lohkamp <b.lohk...@gmail.com
>>> <mailto:b.lohk...@gmail.com>
>>> <mailto:b.lohk...@gmail.com <mailto:b.lohk...@gmail.com>>>
>>> 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
>>> <merr...@u.washington.edu
>>> <mailto:merr...@u.washington.edu>
>>> <mailto:merr...@u.washington.edu <mailto:merritt@u.washington.e
>>> du>>
>>> <mailto:merr...@u.washington.edu
>>> <mailto:merr...@u.washington.edu>
>>>
>>> <mailto:merr...@u.washington.edu
>>> <mailto:merr...@u.washington.edu>>>> 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/>>>
>>>
>>> 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-pack
>>> ages\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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
