Yeap, that fixed it. Thanks! FYI: I couldn't compile 0.5.1-pre without using the "--with-python" flag present. This was not the case with the 0.5 version. Here is the error output for those interested:
coot_wrap_python.cc:139:20: error: Python.h: No such file or directory coot_wrap_python.cc:2533:4: error: #error "This python version requires swig to be run with the '-classic' option" coot_wrap_python.cc:744: error: expected initializer before '*' token coot_wrap_python.cc:799: error: expected initializer before '*' token coot_wrap_python.cc:820: error: expected initializer before '*' token /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/excepti on:40: error: expected declaration before end of line make[1]: *** [coot_wrap_python.lo] Error 1 ==================================================== James M. Vergis, Ph.D. University of Virginia Molecular Physiology and Biological Physics MKWEINR 360A Snyder Building 480 Ray C. Hunt Drive PO Box 800886 Charlottesville, VA 22908-0886 phone: 434-243-2730 FAX: 434-243-8271 [EMAIL PROTECTED] ==================================================== -----Original Message----- From: Mailing list for users of COOT Crystallographic Software [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Lohkamp Sent: Tuesday, October 14, 2008 7:08 PM To: [email protected] Subject: Re: [COOT] Coot molprobity problem in Version 0.5? There is some problems with respect to the switch from 'old' molprobity programs to the new ones (which are hybrid36 enabled). Coot 0.5 works ONLY with hybrid36 enabled probe!! So you need to have the latest probe and reduce installed. However there is a bug in Coot 0.5 (fixed in 0.5.1-pre) as the "Clash" window buttons wont work (if they are empty your probe is too old). Hope this helps, Bernhard ----- Original Message ----- From: "James M. Vergis" <[EMAIL PROTECTED]> Date: Tuesday, October 14, 2008 4:33 pm Subject: [COOT] Coot molprobity problem in Version 0.5? To: [email protected] > I think there is a problem with the way coot parses the output from > coot-molprobity/probes-dots.out for displaying the probe clashes > and making > the "Molprobity Probe Clash Gaps" window. > > Using the reduce and probe versions in example #1 below, coot 0.5 will > display the packing/clashes on the molecule but the "Molprobity > Probe Clash > Gaps" window where you can click on each residue doesn't display the > information properly and will return a "not found error" and > therefore not > choose the residue. I think this is related to the extra space > between the > ":" and the "A" in the examples below. If I use the versions of > reduce/probe that work fine in coot 0.4.1 in 0.5, the "Molprobity > ProbeClash Gaps" window is empty and the clashes/packing are not > drawn on the > molecule. Running probe from the command line also results in > these gaps(I > hope all this makes sense). > > I have tried several combinations of reduce/probe (both compiled > from source > and downloaded binaries) and also tested this with a a pre-built > binary to > make sure my 64-bit version of coot 0.5 wasn't to blame. > > #1) PROBE-DOTS.OUT FROM VERSIONS OF > REDUCE(3.03.070307)/PROBE(2.12.071128)MOSTLY WORK WITH COOT 0.5: > ============================================================================ > ======================== > [EMAIL PROTECTED] coot-molprobity]$ more probe-dots.out > :1->1:wc: A 1 GLY C : A 2 ALA O > :0.364:0.443:-23.028:17.043:-10.447:0.000:0.0027:C:O:- > 23.028:17.043:-10.447: > 17.30:13.75 > :1->1:wc: A 1 GLY C : A 2 ALA O > :0.364:0.429:-22.911:17.044:-10.195:0.000:0.0033:C:O:- > 22.911:17.044:-10.195: > 17.30:13.75 > :1->1:wc: A 2 ALA C : A 1 GLY O > :-0.001:0.297:-22.934:16.874:-10.243:0.000:0.0152:C:O:- > 22.934:16.874:-10.243 > :12.50:19.32 > :1->1:wc: A 2 ALA C : A 1 GLY O > :-0.001:0.261:-22.605:16.482:-10.261:0.000:0.0211:C:O:- > 22.605:16.482:-10.261 > :12.50:19.32 > :1->1:wc: A 2 ALA C : A 1 GLY O > :-0.001:0.340:-22.339:16.228:-10.136:0.000:0.0098:C:O:- > 22.339:16.228:-10.136 > :12.50:19.32 > > #2) PROBE-DOTS.OUT FROM REDUCE(3.03.070307)/PROBE(2.12.070727) THAT > WORKWITH COOT 0.4.1 BUT NOT 0.5: > ============================================================================ > ======================= > [EMAIL PROTECTED] bin]$ more coot-molprobity/probe-dots.out > :1->1:wc:A 1 GLY C :A 2 ALA O > :0.364:0.443:-23.028:17.043:-10.447:0.000:0.0027:C:O:- > 23.028:17.043:-10.447: > 17.30:13.75 > :1->1:wc:A 1 GLY C :A 2 ALA O > :0.364:0.429:-22.911:17.044:-10.195:0.000:0.0033:C:O:- > 22.911:17.044:-10.195: > 17.30:13.75 > :1->1:wc:A 2 ALA C :A 1 GLY O > :-0.001:0.297:-22.934:16.874:-10.243:0.000:0.0152:C:O:- > 22.934:16.874:-10.243 > :12.50:19.32 > :1->1:wc:A 2 ALA C :A 1 GLY O > :-0.001:0.261:-22.605:16.482:-10.261:0.000:0.0211:C:O:- > 22.605:16.482:-10.261 > :12.50:19.32 > :1->1:wc:A 2 ALA C :A 1 GLY O > :-0.001:0.340:-22.339:16.228:-10.136:0.000:0.0098:C:O:- > 22.339:16.228:-10.136 > :12.50:19.32 > > ==================================================== > James M. Vergis, Ph.D. > University of Virginia Molecular Physiology and Biological Physics > MKWEINR 360A Snyder Building > 480 Ray C. Hunt Drive > PO Box 800886 > Charlottesville, VA 22908-0886 > phone: 434-243-2730 FAX: 434-243-8271 > [EMAIL PROTECTED] > ==================================================== > *************************************************** Dr. Bernhard Lohkamp now: University of York Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487698 fax: (+46) 08-327626 email: [EMAIL PROTECTED]
