Bill: I have forwarded this to the OpenDX developer's list. Probably
someone there knows the cleanest way to do this. Glad the modules
are now working for you.
Richard
[EMAIL PROTECTED] wrote:
>
> Hi Richard:
>
> Thanks very much for the help. I manually edited config.status, stuck
> in an extra -I/usr/include and it all compiled without further
> complaint.
>
> Is there a way in the configuration file (or flag) to issue a flag that
> gives both include directories, i.e.,
>
> -I/usr/include and -/usr/local/include
> or
> -I/usr/include and -/sw/include
>
> ?
>
> I haven't yet had a chance to play with it but wanted to let you know
> your suggestion was all it needed to compile.
>
> Again, many thanks for your help.
>
> Bill
>
> On Thursday, November 14, 2002, at 06:03 AM, Richard Gillilan wrote:
>
> > I've had a bit of trouble compiling OpenDX/Jaguar under Jaguar, so
> > I haven't been able to test the modules since 10.1, however, this
> > sounds
> > familiar. There may be some confusion between /usr/include/string.h and
> > dx/include/string.h. Could be compounded by Darwin's inclusion of these
> > types of things in the system (was true for math.h I seem to recall ...
> > one did not actually need to include it .. perhaps same for string.h)
> > I think I had this problem during the actual OpenDX
> > compile at one point and was sable to fix it by changing the order of
> > includes
> > in a number of files. Hopefully that's now in the CVS version.
> > You sould just try changing the order of the includes in surf.h or
> > perhaps
> > specify an absolute path to /usr/include/string.h in the surf.h header.
> >
> > I notice the other modules usually have this kind of header:
> >
> > #include <dx/dx.h>
> > #include <stdio.h>
> > #include <string.h>
> > #include <math.h>
> >
> > I guess I should try the fink route for installing dx, maybe I'll have
> > better
> > luck.
> >
> > Richard
> >
> >> /sw/share/dx/include/string.h:19: undefined type, found `String'
> >> /sw/share/dx/include/string.h:26: undefined type, found `String'
> >> /sw/share/dx/include/string.h:33: undefined type, found `String'
> >> /sw/share/dx/include/dxconfig.h:65: warning: redefinition of macro
> >> byte
> >> dxsurf.c:4: warning: this is the location of the previous definition
> >> cpp-precomp: warning: errors during smart preprocessing, retrying in
> >> basic mode
> >> In file included from surf.h:4,
> >> from dxsurf.c:2:
> >> /sw/share/dx/include/string.h:19: parse error before "DXNewString"
> >> /sw/share/dx/include/string.h:26: parse error before "s"
> >> /sw/share/dx/include/string.h:33: parse error before "DXMakeString"
> >> make[3]: *** [dxsurf.o] Error 1
> >> make[2]: *** [all-recursive] Error 1
> >> make[1]: *** [all-recursive] Error 1
> >> make: *** [all-recursive-am] Error 2
> >> %
> >>
> >> Any ideas what to try?
> >>
> >> Thanks.
> >>
> >> Bill
> >>
> >> On Wednesday, November 13, 2002, at 04:06 AM, Richard Gillilan wrote:
> >>
> >> Bill: if you can't wait for a PyMol fix, this type of thing is
> >> done very well by OpenDX using
> >> my XTM crystallography module suite. I have a module which will
> >> read CNS-style
> >> density maps. You can slice and dice them, map density to any
> >> surface and color
> >> code smoothly or in steps with contour lines or both. An O-style
> >> Cover module exists,
> >> but is still a bit experimental. Surfaces can also be
> >> transparent etc.
> >> You can download OpenDX from www.opendx.org and then get my
> >> modules (add-ons) from
> >> anonymous ftp: bridgedec.chess.cornell.edu in directory pub.
> >> Look for XTM-src.tar.gz.
> >> The code runs on pretty much all platforms (though I have not
> >> verified the Windows port,
> >> David Thompson at Viz Inc. has it working and will supposedly
> >> offer on CD along with the
> >> whole OpenDX package as precompiled binaries).
> >>
> >> Richard Gillilan
> >> MacCHESS, Cornell
> >>
> >> On Tuesday, November 12, 2002, at 04:27 PM,
> >> [EMAIL PROTECTED] wrote:
> >>
> >> Hi Folks:
> >>
> >> Is there a way to display a cross-section of electron
> >> density (false)-color-coded for electron density? In other words, I
> >> would like to produce a 2-D plot that looks like a contour map (eg:
> >> output of CCP4 npo) but color-coded with respect to electron density.
> >> A continuum, if possible, would actually be better than a series of
> >> contour lines.
> >>
> >> Has this by any chance been implemented in pymol or
> >> anywhere?
> >>
> >> Many thanks,
> >>
> >> Bill Scott
> >>
> >> William G. Scott
> >>
> >> Associate Professor
> >> Department of Chemistry and Biochemistry
> >> and The Center for the Molecular Biology of RNA
> >> Sinsheimer Laboratories
> >> University of California at Santa Cruz
> >> Santa Cruz, California 95064
> >> USA
> >>
> >> phone: +1-831-459-5367 (office)
> >> +1-831-459-5292 (lab)
> >> fax: +1-831-4593139 (fax)
> >>
> >> -------------------------------------------------------
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> >> _______________________________________________
> >> PyMOL-users mailing list
> >> [EMAIL PROTECTED]
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>
> >> William G. Scott
> >>
> >> Associate Professor
> >> Department of Chemistry and Biochemistry
> >> and The Center for the Molecular Biology of RNA
> >> Sinsheimer Laboratories
> >> University of California at Santa Cruz
> >> Santa Cruz, California 95064
> >> USA
> >>
> >> phone: +1-831-459-5367 (office)
> >> +1-831-459-5292 (lab)
> >> fax: +1-831-4593139 (fax)
> >
> >
> >
> William G. Scott
>
> Associate Professor
> Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> Sinsheimer Laboratories
> University of California at Santa Cruz
> Santa Cruz, California 95064
> USA
>
> phone: +1-831-459-5367 (office)
> +1-831-459-5292 (lab)
> fax: +1-831-4593139 (fax)
