[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
[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 UpUp(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 UpUp(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 bernhard.lohk...@ki.se 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] 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 paul.ems...@bioch.ox.ac.uk 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] Scheme on WinCoot (Win XP)
On Thu, 14 May 2009 00:34:36 +0100, Paul Emsley paul.ems...@bioch.ox.ac.uk 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
