Just to clarify, 1 and 2 is obsolete when using 3.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 <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hello B.,
>
> Works.Thank you very much!
>
> On Wed, Mar 29, 2017 at 8:14 AM, B.Lohkamp <[log in to unmask]
> <mailto:[log in to unmask]>> 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
> <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> 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
> <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>>> 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
> <[log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>>>> 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
>
>
>
>
>
>
>
>
>
|
