[COOT] Zinc-density
Hi everybody, i just installed coot and played around a bit with my structure and the Fit Protein command. Now to my question, i have a zinc atom in my structure coordinated by 3 cysteines. it refines pretty well, but when i do Fit Protein Coot always links the 3 cys directly in the zinc density, so it seems it doesn't know that a zinc is there. it is displayed as zinc and everything but it doesn't assign density to it. Has someone any suggestions? best regards Moritz Metlitzky
[COOT] Coot problem on mac
Hi,
I'm trying to install Bill Scott's standalone coot version on a
colleague's brand new MacBook Pro (I'm very jealous) however seem to
have a gtk problem as whenever I invoke coot it doesn't recognise any
of the .png image files that make the buttons etc. (Error log in
attachment). When I had this problem on my machine a few months back
the advice was to include the following in my .bashrc, however this
isn't working on his machine - any ideas?
alias setcoot="source /usr/local/xtal/coot/bin/init.sh"
function coot { COOT_REFMAC_LIB_DIR='/usr/local/xtal/coot/share/coot/
lib' PATH=/usr/local/xtal/coot/bin:$PATH /usr/local/xtal/coot/bin/
coot "$@" ; }
defaults write com.apple.x11 wm_ffm true
Thanks,
Simon
Last login: Wed May 13 12:03:54 on ttys001
[~]setcoot
[~]coot
Acquiring application resources from /usr/local/xtal/coot/share/coot/cootrc
INFO:: splash_screen_pixmap_dir /usr/local/xtal/coot/share/coot/pixmaps
** (coot-real:6467): WARNING **: Error loading pixmap file:
/usr/local/xtal/coot/share/coot/pixmaps/coot-0.5.2.xpm
INFO:: Colours file: /usr/local/xtal/coot/share/coot/colours.def loaded
There are 118 data in
/usr/local/xtal/coot/share/coot/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/a/ALA.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/a/ASP.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/a/ASN.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/c/CYS.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GLN.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GLY.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GLU.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/p/PHE.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/h/HIS.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/i/ILE.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/l/LYS.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/l/LEU.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/m/MET.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/m/MSE.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/p/PRO.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/a/ARG.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/s/SER.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/t/THR.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/v/VAL.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/t/TRP.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/t/TYR.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/p/PO4.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/s/SO4.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GOL.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/e/ETH.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/c/CIT.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/a/AR.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/a/AD.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/c/CR.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/c/CD.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GR.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GD.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/t/TD.cif
There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/u/UR.cif
Reading coordinate file: /usr/local/xtal/coot/share/coot/standard-residues.pdb
PDB file /usr/local/xtal/coot/share/coot/standard-residues.pdb has been read.
Spacegroup: P 1
Cell: 40.631 109.18 93.243 90 90 90
** (coot-real:6467): WARNING **: Error loading pixmap file:
/usr/local/xtal/coot/share/coot/pixmaps/display-manager.png
Error loading icon: Couldn't recognize the image file format for file
'/usr/local/xtal/coot/share/coot/pixmaps/add-alt-conf.svg'
Error loading icon: Couldn't recognize the image file format for file
'/usr/local/xtal/coot/share/coot/pixmaps/add-peptide-1.svg'
Error loading icon: Couldn't recognize the image file format for file
'/usr/local/xtal/coot/share/coot/pixmaps/add-water.svg'
Error loading icon: Couldn't recognize the image file format for file
'/usr/local/xtal/coot/share/coot/pixmaps/anchor.svg'
Error loading icon: Couldn't recognize the image file format for file
'/usr/local/xtal/coot/share/coot/pixmaps/aniso-atom.svg'
Error loading icon: Couldn't recognize the image file format for file
'/usr/local/x
[COOT] mouse buttons and arrow keys [was Re: problems of version 0.6]
Dear Maia,
Maia Cherney wrote:
> I would like to use only one-button keys, so that I could use only
> one hand when fitting.
Why!? Because the other one is needed to prop up your head, maybe? :-)
http://linuxoutlaws.com/files/dan-jaunty-party-thumb.jpg
I find using my left hand for keyboarding makes things way faster than
clicking on icons with the right hand on the mouse.
Well, now help me with key-bindings, please. I need one or two buttons
on the mouse for map dragging. Pymol and x-fit use the middle button
for translation. It confuses me all the time, when I work in coot after
working in pymol. Do you have any unused two-button combinations on the
mouse? If it's not possible to touch the mouse buttons in the
key-bindings, please help me to program arrow key for translation. Could
you give me a script for that, I can't write it myself.
There are no two-button combinations ("chording") on the mouse. I have
avoided them so far - it seems an esoteric interface and there have been
better ways of providing the necessary functionality.
Middle mouse drag for translate could be enabled as an option, I suppose.
As for the arrow keys for translate, add the following to your ~/.coot
file. You might need to tweak zsc. Be slightly careful not to overly
dwell with you finger on the button if you do not have a fast
processor/graphics card and have a fast key repeat.
Paul.
(let* ((zsc 0.02)
(screen-coords-nudge
(lambda (tvm nudge ori)
(map (lambda (e) (* nudge (apply + (map * e ori tvm)))
(f (lambda (axes)
(let ((nudge (* (zoom-factor) zsc))
(rc (rotation-centre))
(tvm (transpose-simple-matrix (view-matrix
(apply set-rotation-centre
(map + rc (screen-coords-nudge tvm nudge axes)))
(add-key-binding "Translate Up""Up"(lambda () (f '(0 1 0
(add-key-binding "Translate Down" "Down" (lambda () (f '(0 -1 0
(add-key-binding "Translate Left" "Left" (lambda () (f '(-1 0 0
(add-key-binding "Translate Right" "Right" (lambda () (f '( 1 0 0)
Re: [COOT] mouse buttons and arrow keys [was Re: problems of version 0.6]
Dear Paul,
thank you for your reply. I thought for several days that you ignored my
wishes, but you have not. Actually, a lot of people would be happy with
the middle button translation. Your guess is right. I do prop up my
head (as many others), or I hold a cup of coffee (as many others). So,
how to enable the middle mouse drag for translate? (Chording on the
mouse is fine with me, too).
Thanks for the arrow keys for translate.
Maia
Paul Emsley wrote:
Dear Maia,
Maia Cherney wrote:
> I would like to use only one-button keys, so that I could use only
> one hand when fitting.
Why!? Because the other one is needed to prop up your head, maybe? :-)
http://linuxoutlaws.com/files/dan-jaunty-party-thumb.jpg
I find using my left hand for keyboarding makes things way faster than
clicking on icons with the right hand on the mouse.
Well, now help me with key-bindings, please. I need one or two
buttons on the mouse for map dragging. Pymol and x-fit use the
middle button for translation. It confuses me all the time, when I
work in coot after working in pymol. Do you have any unused
two-button combinations on the mouse? If it's not possible to touch
the mouse buttons in the key-bindings, please help me to program
arrow key for translation. Could you give me a script for that, I
can't write it myself.
There are no two-button combinations ("chording") on the mouse. I
have avoided them so far - it seems an esoteric interface and there
have been better ways of providing the necessary functionality.
Middle mouse drag for translate could be enabled as an option, I suppose.
As for the arrow keys for translate, add the following to your ~/.coot
file. You might need to tweak zsc. Be slightly careful not to overly
dwell with you finger on the button if you do not have a fast
processor/graphics card and have a fast key repeat.
Paul.
(let* ((zsc 0.02)
(screen-coords-nudge
(lambda (tvm nudge ori)
(map (lambda (e) (* nudge (apply + (map * e ori tvm)))
(f (lambda (axes)
(let ((nudge (* (zoom-factor) zsc))
(rc (rotation-centre))
(tvm (transpose-simple-matrix (view-matrix
(apply set-rotation-centre
(map + rc (screen-coords-nudge tvm nudge axes)))
(add-key-binding "Translate Up""Up"(lambda () (f '(0 1 0
(add-key-binding "Translate Down" "Down" (lambda () (f '(0 -1 0
(add-key-binding "Translate Left" "Left" (lambda () (f '(-1 0 0
(add-key-binding "Translate Right" "Right" (lambda () (f '( 1 0 0)
[COOT] Troubles with torsion rotations in NAD
I have an NAD cofactor. Coordinates attached; they were generated by running libcheck on the CCP4 dictionary file NAD.cif (standard file taken from CCP4 6.1.0). I am trying to rotate various torsional angles. I am using the "Edit Chi Angles" feature of Coot 0.6-pre-1. Is this the best way? Behaviour seems a bit irregular. I frequently see this message (such as when attempting to rotate about var_2 NN1 <--> NC1*): first atom : NN1: not found in residue WARNING:: failure to find all atom pair in residue atoms! Atom NN1 is in my file (attached). So is every other atom which appears in a torsion line with NN1 in the .cif file. If I choose the top listed bond (var_1 NC7 <--> NC3), the nicotinamide ring rotates, but the rest of the dinucleotide doesn't. Attempting var_8 gives a CHI readout, but I can't see anything moving. Same for var_9. Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu ATOM 1 NO7 NAD A 1 0.000 0.000 0.000 1.00 20.00 O ATOM 2 NC7 NAD A 1 0.986 1.010 0.066 1.00 20.00 C ATOM 3 NN7 NAD A 1 2.264 0.661 0.123 1.00 20.00 N ATOM 6 NC3 NAD A 1 0.588 2.438 0.051 1.00 20.00 C ATOM 7 NC4 NAD A 1 -0.737 2.770 0.244 1.00 20.00 C ATOM 9 NC5 NAD A 1 -1.049 4.111 0.230 1.00 20.00 C ATOM 11 NC6 NAD A 1 -0.094 5.090 0.042 1.00 20.00 C ATOM 13 NC2 NAD A 1 1.527 3.446 -0.147 1.00 20.00 C ATOM 15 NN1 NAD A 1 1.195 4.766 -0.150 1.00 20.00 N ATOM 16 NC1* NAD A 1 2.221 5.786 -0.370 1.00 20.00 C ATOM 18 NC2* NAD A 1 1.763 6.840 -1.365 1.00 20.00 C ATOM 20 NO2* NAD A 1 2.558 6.768 -2.519 1.00 20.00 O ATOM 22 NC3* NAD A 1 1.875 8.201 -0.658 1.00 20.00 C ATOM 24 NO3* NAD A 1 2.789 9.047 -1.317 1.00 20.00 O ATOM 26 NO4* NAD A 1 2.550 6.464 0.832 1.00 20.00 O ATOM 27 NC4* NAD A 1 2.438 7.884 0.733 1.00 20.00 C ATOM 29 NC5* NAD A 1 1.589 8.323 1.928 1.00 20.00 C ATOM 32 NO5* NAD A 1 0.283 7.838 1.811 1.00 20.00 O ATOM 33 NP NAD A 1 -0.861 7.976 2.917 1.00 20.00 P ATOM 34 NO1 NAD A 1 -2.086 7.327 2.393 1.00 20.00 O ATOM 35 NO2 NAD A 1 -0.343 7.583 4.244 1.00 20.00 O ATOM 36 O3 NAD A 1 -1.143 9.553 2.862 1.00 20.00 O ATOM 37 AP NAD A 1 -2.060 10.247 3.976 1.00 20.00 P ATOM 38 AO1 NAD A 1 -2.821 11.380 3.407 1.00 20.00 O ATOM 39 AO2 NAD A 1 -2.959 9.251 4.599 1.00 20.00 O ATOM 40 AO5* NAD A 1 -0.988 10.748 5.044 1.00 20.00 O ATOM 41 AC5* NAD A 1 0.055 11.614 4.702 1.00 20.00 C ATOM 44 AC4* NAD A 1 0.566 12.256 5.988 1.00 20.00 C ATOM 46 AO4* NAD A 1 1.597 13.153 5.579 1.00 20.00 O ATOM 47 AC1* NAD A 1 1.502 14.414 6.212 1.00 20.00 C ATOM 49 AC2* NAD A 1 0.221 14.422 7.029 1.00 20.00 C ATOM 51 AO2* NAD A 1 0.520 14.729 8.366 1.00 20.00 O ATOM 53 AC3* NAD A 1 -0.412 13.032 6.866 1.00 20.00 C ATOM 55 AO3* NAD A 1 -0.587 12.391 8.108 1.00 20.00 O ATOM 57 AN9 NAD A 1 1.512 15.495 5.237 1.00 20.00 N ATOM 58 AC8 NAD A 1 0.492 15.869 4.414 1.00 20.00 C ATOM 60 AN7 NAD A 1 0.920 16.921 3.701 1.00 20.00 N ATOM 61 AC5 NAD A 1 2.181 17.233 4.029 1.00 20.00 C ATOM 62 AC6 NAD A 1 3.036 18.216 3.566 1.00 20.00 C ATOM 63 AN6 NAD A 1 2.658 19.073 2.623 1.00 20.00 N ATOM 66 AC4 NAD A 1 2.580 16.341 5.009 1.00 20.00 C ATOM 67 AN3 NAD A 1 3.831 16.437 5.520 1.00 20.00 N ATOM 68 AC2 NAD A 1 4.702 17.412 5.081 1.00 20.00 C ATOM 70 AN1 NAD A 1 4.308 18.303 4.103 1.00 20.00 N # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level NAD .
Re: [COOT] Scheme on WinCoot (Win XP)
Hi Bernhard, Thanks for the clarification. >commenting on this. Maybe there should be some low level implementation >without the use of fancy (scheme) widgets, so that at least scripts can >be run.. (on my - long - list now). Ok, I think that would be a good idea. Given the fact that almost all scripting examples on the manual and in various other scripts in this forum are written in scheme it would be nice to have access to at least the basic scripts (non-gui) without having to resort to re-writing them in Python. Although the rules for how to convert scripts are documented, it's still a hurdle, especially for non- programmers. About the underlying problem - the text in scheme widgets - is that a missing feature in the Windows scheme libraries or some weird bug? Thanks, -Alex On Mon, 11 May 2009 23:17:05 +0200, Bernhard Lohkamp wrote: >Hi, > >ok to clarify the situation with respect to Scheme/guile in WinCoot: > >In general it is possible to compile and run WinCoot with Scheme, >however we currently DO NOT distribute WinCoot with Scheme enabled (note >to self: change website). The reason for this is that no text can be >displayed in the Scheme (Gtk) widgets and I/we want to avoid endless >commenting on this. Maybe there should be some low level implementation >without the use of fancy (scheme) widgets, so that at least scripts can >be run.. (on my - long - list now). > >B > >> I am new to Coot - I have been experimenting with the examples on >> the wiki >> page and it appears that scheme/guile scripting does not work in >> WinCoot(0.5.2). Just wanted to confirm if I am correct. >> >> I am/was a little confused b/c it appears the libraries and paths to >> scheme/guile get installed but nothing happens if I try to run a >> scheme script. >> >> Also read the slightly cryptic message "you can install an add-on >> forscheme/guile scripting (no warranties)" in >> http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot.html >> but I haven't seen this add-on anywhere. >> >> Just wanted to avoid re-writing some nice scheme scripts I see >> here and >> there and to just get some information on the subject. >> >> Thanks! >> -Alex >> > > > >*** > >Dr. Bernhard Lohkamp >Assistant Professor >Div. Molecular Structural Biology >Dept. of Medical Biochemistry and Biophysics (MBB) >Karolinska Institutet >S-17177 Stockholm >Sweden > >phone: (+46) 08-52487673 >fax: (+46) 08-327626 >email: bernhard.lohk...@ki.se
Re: [COOT] Troubles with torsion rotations in NAD
David J. Schuller wrote: I have an NAD cofactor. Coordinates attached; they were generated by running libcheck on the CCP4 dictionary file NAD.cif (standard file taken from CCP4 6.1.0). I am trying to rotate various torsional angles. I am using the "Edit Chi Angles" feature of Coot 0.6-pre-1. Is this the best way? Behaviour seems a bit irregular. I frequently see this message (such as when attempting to rotate about var_2 NN1 <--> NC1*): first atom : NN1: not found in residue WARNING:: failure to find all atom pair in residue atoms! Atom NN1 is in my file (attached). So is every other atom which appears in a torsion line with NN1 in the .cif file. If I choose the top listed bond (var_1 NC7 <--> NC3), the nicotinamide ring rotates, but the rest of the dinucleotide doesn't. Attempting var_8 gives a CHI readout, but I can't see anything moving. Same for var_9. Dear David, This is a variant of the libcheck/refmac vs Coot NAD bug discussed previously. The cause of the problem is the 'bizarre' naming convention of the NN1 and NN7 in the NAD. Coot can't map the dictionary atom name to the name in the PDB file. So you have to help out. You need to quote the NN1/NN7 references in the cif dictionary. IIRC it should read 'NN1 ' rather than simply NN1 (same for 7). Paul.
Re: [COOT] Scheme on WinCoot (Win XP)
Alex Luso wrote: Hi Bernhard, Thanks for the clarification. commenting on this. Maybe there should be some low level implementation without the use of fancy (scheme) widgets, so that at least scripts can be run.. (on my - long - list now). Ok, I think that would be a good idea. Given the fact that almost all scripting examples on the manual and in various other scripts in this forum are written in scheme it would be nice to have access to at least the basic scripts (non-gui) without having to resort to re-writing them in Python. Almost all fancy scheme scripts have a fancy python counterpart (somewhere). In cases where that is not so, such a counterpart can often materialize if desired. Although the rules for how to convert scripts are documented, it's still a hurdle, especially for non- programmers. Yes, that is true for anything other than the most simple/trivial customizations. About the underlying problem - the text in scheme widgets - is that a missing feature in the Windows scheme libraries or some weird bug? Can you be somewhat more precise in you description of the "text in scheme widgets"? Paul.
Re: [COOT] Zinc-density
Moritz Metlitzky wrote: Hi everybody, i just installed coot and played around a bit with my structure and the Fit Protein command. Now to my question, i have a zinc atom in my structure coordinated by 3 cysteines. it refines pretty well, but when i do Fit Protein Coot always links the 3 cys directly in the zinc density, so it seems it doesn't know that a zinc is there. it is displayed as zinc and everything but it doesn't assign density to it. The trick in such a case is to change the map to which you are fitting. You should mask out the Zincs in the map. (It should be possible do select by element but how to do that escapes me for the moment (it is an mmdb atom selection string)). So probably fastest to do it by residue number: //B/23-25 or so. Then used the masked map as the refinement map of course. Paul
Re: [COOT] Scheme on WinCoot (Win XP)
On Wed, 13 May 2009 23:29:28 +0100, Paul Emsley wrote: >> About the underlying problem - the text in scheme widgets - is that a missing >> feature in the Windows scheme libraries or some weird bug? >Can you be somewhat more precise in you description of the "text in >scheme widgets"? > >Paul. I meant the issue Berhard mentions as the reason scheme is not available to Win-Coot - "missing text in scheme widgets". Just curious if that's a minor bug or something major. Incidentally, I wonder what's the best resource to look at the available functions/commands etc in coot? For instance, I was curious what parameters were acceptable for set-baton-build-params i.e. from the tutorial/manual I know "backwards" is an option. But how to reverse it back to normal? "forwards", "forward", "normal"?! I found the command in the Coot Reference Manual webpage but it didn't give me any more information. Where would I find it in the code itself? Thanks, -Alex
Re: [COOT] Fit protein suggestion/query
Oliver Clarke wrote: I like the fit protein script - at low resolution, initial rounds of fitting and refinement often result in my leucines/isoleucines having fairly implausible rotamers, and fit protein is a great way of quickly fixing up the worst of these. However, it doesn't seem to deal so well with residue types where there are many almost equally probably rotamers (eg lys, arg), and in poor density these often end up with sidechains lodged firmly in density that belongs to the neighbouring strand of a beta sheet, for example. Yes. this can happen. A bit of sphere refinement can help when this happens. I aim to improve the rotamer search for low resolution cases for 0.6. Is there any way to script a function that will allow rotamer-fitting of specific residue types (eg all except lys, arg and maybe glu and gln)? Hmm... sort of. The fit-protein and friends have been reworked recently. You can redefine fit-protein-fit-function. You will notice that there is now a test for the residue name. You will need a recent coot pre-release for this to work. Paul. (define (fit-protein-fit-function res-spec imol-map) (let ((imol (list-ref res-spec 0)) (chain-id (list-ref res-spec 1)) (res-no (list-ref res-spec 2)) (ins-code (list-ref res-spec 3))) (let ((res-name (apply residue-name res-spec))) (if (not (or (string=? res-name "ARG") (string=? res-name "LYS"))) (map (lambda (alt-conf) (with-auto-accept (format #t "centering on ~s ~s ~s~%" chain-id res-no "CA") (set-go-to-atom-chain-residue-atom-name chain-id res-no "CA") (rotate-y-scene 10 0.3) ; n-frames frame-interval(degrees) (if (string=? alt-conf "") (auto-fit-best-rotamer res-no alt-conf ins-code chain-id imol imol-map 1 0.1)) (if (>= imol-map 0) (begin ;; (refine-auto-range imol chain-id res-no "") (refine-zone imol chain-id res-no res-no alt-conf) (accept-regularizement))) (rotate-y-scene 10 0.3))) (residue-alt-confs imol chain-id res-no ins-code)) Paul.
Re: [COOT] Scheme on WinCoot (Win XP)
Alex Luso wrote: On Wed, 13 May 2009 23:29:28 +0100, Paul Emsley wrote: I meant the issue Berhard mentions as the reason scheme is not available to Win-Coot - "missing text in scheme widgets". Just curious if that's a minor bug or something major. Oh I see - yes he did say that. >>> About the underlying problem - the text in scheme widgets - is that a missing feature in the Windows scheme libraries or some weird bug? Yes, probably one of those things :) Incidentally, I wonder what's the best resource to look at the available functions/commands etc in coot? The User Manual? Hah :) (Actually, Judit Debreczeni has recently helped out in including the scripting interface documentation into the main body of the manual). For instance, I was curious what parameters were acceptable for set-baton-build-params i.e. from the tutorial/manual I know "backwards" is an option. But how to reverse it back to normal? "forwards", "forward", "normal"?! Oh, hmm... Thank you for pointing out this failing. For the record it is "forwards". I found the command in the Coot Reference Manual webpage but it didn't give me any more information. Where would I find it in the code itself? To answer the question: http://www.ysbl.york.ac.uk/~emsley/software/pre-release/ But you should not need to dig into the code. Just mention where docs are missing and I will try to fix it. Paul.
Re: [COOT] Scheme on WinCoot (Win XP)
On Thu, 14 May 2009 00:34:36 +0100, Paul Emsley wrote: >> For instance, I was curious what parameters were acceptable for >> set-baton-build-params >> i.e. from the tutorial/manual I know "backwards" is an option. But how to >> reverse it back to normal? "forwards", "forward", "normal"?! > >Oh, hmm... Thank you for pointing out this failing. For the record it >is "forwards". Thanks. Of course, I had figured it out by trial-and-error... :-) Made slightly more difficult b/c there was no error reported for a wrong parameter. I wonder if adding the function as buttons on the baton window would be useful? (i.e. "Build Backwards" and "Build Forwards" - perhaps asking for user input as to the relevant res-num or guessing it). I think O does that. Just a thought. Ok. Cheers, -Alex
Re: [COOT] coot crashes running on fedora 9 ia64
Clare Peters-Libeu wrote: First off, let me apologize for a really long message. I'm trying to get Coot running on a 64-bit machine running fedora core 9. I picked fedora core 9 because many of the graphics libraries required for Coot are already installed. However, the autobuild script fails when compiling the clipper libraries. After some research I discovered that fedora 9 use gcc4.3, but the version of clipper downloaded from Paul Emsley's site need gcc3.4 to compile (-which is perplexing because I compiled the clipper libraries from the CCP4 distribution with gcc4.3) One downloads clipper from Kevin Cowtan's site :) clipper should compile with gcc4.x (x=anything) AFAIK. Running the build-it-gtk2-simple appears to build all the packages without an error. The script exits with an error that the script can't create the $AUTOBUILD_INSTALLED/python2.5 directory. However, when I look at proper directory, the directory is indeed there and coot and coot-real are in the appropriate bin directory. The logs say that the coot-test in the script failed. Wow, does it!? I tried to disable the tests of others (i.e. not developers - it seems I failed). Forget the tests, they will fail unless you have the (frequently changing) test data sets. If I start it up manually, I see the startup image, some verbiage about proper citations, and then lines about loading a pdb library. It ends with There are 2 data in /usr/local/share/CCP4/ccp4-6.0.2/lib/data/monomers//g/GD.cif There are 2 data in /usr/local/share/CCP4/ccp4-6.0.2/lib/data/monomers//t/TD.cif There are 2 data in /usr/local/share/CCP4/ccp4-6.0.2/lib/data/monomers//u/UR.cif Reading coordinate file: /usr/local/share/coot_build/coot-gtk2/share/coot/standard-residues.pdb PDB file /usr/local/share/coot_build/coot-gtk2/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 Illegal instruction If I build it with the python option, Coot hangs when it displays the coot image. Nasty. OK, back to the non-python version for now. Please try to give us a debugging report: $ gdb xxx/bin/coot-real where thanks. Have I created a problem by using two different compilers for the libraries or is this a totally different issue? I've seen posts that refer to similar behavior that were cured with updating nvidia drivers or messing with x-windows. Is there a way to tell which it is? As far as I understand, it is usually OK to use c++ and c in different compilers - but c++ to c++ in different compilers can cause problems. My wrapper script #!/bin/bash export AUTOBUILD_INSTALLED=/usr/local/share/autobuild5/coot export AUTOBUILD_BUILD=/usr/local/share/autobuild5 export LOGS=$AUTOBUILD_BUILD/logs export NIGHTLY_DEST_DIR=$AUTOBUILD_BUILD export STABLE_DEST_DIR=$AUTOBUILD_BUILD export build_coot_prerelease=1 export LD_LIBRARY_DIR=/usr/local/lib:$LD_LIBRARY_DIR export CC=gcc34 export CXX=g++34 # # I obtained build-it-gtk-simple using # wget http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it-gtk2-simple # bash build-it-gtk2-simple > build.log That seems OK, but I would use the up to date compiler. You suggest that there is a problem with that. Let's address that problem. # # _ These are the steps that I used to install gcc3.4 Step 1: Install compatibility libraries for programs compiled with earlier versions of gcc. This may not be strictly necessary for Coot, That is true. I'm perplexed. I've download and compiled the clipper libraries using the CCP4 install script and everything went great with gcc4.3. So there appears to be a difference between the two set of clipper libraries. As far as I can tell, the CCP4 installation works fine. OK, so tell us what is going wrong when you compile clipper with g++-4.3 (send long logs (e.g 0.4-clipper.txt) to: coot-dev at ysbl dot york dot ac dot uk). I suspect a linking problem. Let's try to get everything working with the same compiler: 4.3 or so. Thanks, Paul.
