Re: [COOT] current Spacenavigator support
Murray, Michael (NIH/NIEHS) [F] wrote: Hello all, I am thinking about purchasing a Spacenavigator from 3Dconnexion. I vaguely remember Paul mentioning something about the device in a recent talk but I can't quite remember the context. I was wondering if it was compatible and/or useful with Coot. There was apparently some discussion on the board about support in 2007 but I don't see any mention since. Any information would be appreciated. This would ideally work on a Mac running OS X 10.5 but I could always dual boot into Linux if necessary. Hello Michael, Yes I did mention it. Under Things to come. There is no way it will work currently. (2007? Eek!). I look forward to having a play with one - it will give my left hand something other to do than prop up my head... Oh, and in the meantime, if you are using a Mac, you could amuse yourself with a set of PowerMates. They work nicely with Coot. Paul.
Re: [COOT] sequence view problem
I saw this myself this morning on my Mac. I don't know what the problem is but I think I can reproduce it. I'll follow this up. Paul. Kay Diederichs wrote: Hi Bernhard, when I do that, the contents of the hollow area of the window changes (but the sequence is still not visible). The changed contents appears to belong to other windows that I sweep across. best, Kay Bernhard Lohkamp schrieb: Kay, we saw a similar thing at the Workshop in Chicago (although different binary and OS). What happens when you move the window out of the screen and back? That worked then, but is certainly not a long term solution ;-) B using the latest binary coot-0.6-pre-1-revision-2109-binary-Linux-x86_64-centos-5- gtk2.tar.gz on a 64bit CentOS-5.3 machine I get an empty sequence view window. With empty I mean that at the place where the sequence should appear on a white background, the window is empty (hollow, so to say) and the contents of the window beneath it is visible (see attached screenshot). I had the same problem with previous coot versions. Anything I can do about that? thanks, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature smime.p7s.
Re: [COOT] sequence view problem
Kay Diederichs wrote: when I do that, the contents of the hollow area of the window changes (but the sequence is still not visible). The changed contents appears to belong to other windows that I sweep across. Thanks, it was a canvas geometry problem when there was only one chain (not tested before bizarrely enough). Fixed now (rev 2122). Paul.
[COOT] nightly pre-release binaries, summary page
Our nightly builds summary page and web server is in a state of disrepair. As a work-around you can still get your binaries here: http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ Paul.
Re: [COOT] nightly pre-release binaries, summary page
Kay Diederichs wrote: Paul Emsley schrieb: As a work-around you can still get your binaries here: http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ If this is the work-around, then which is the real one? Seeing as you ask, the new real one is/will be here: http://www.biop.ox.ac.uk/coot/devel/build-info.html BTW if the York server is out of business: I mirror all new files appearing on the York server, at ftp://turn5.biologie.uni-konstanz.de/coot/software/ (so that site has a binaries/nightlies/pre-release subdirectory as well) Right, fine. Paul.
Re: [COOT] Visualising Probe Dots
Alex Theodossis wrote: Is it possible to change the dot density of the Probe output, when running it through Coot? You mean (i) the dot size? No - not yet. (ii) the dots density? Yes, you can fiddle with arguments to *probe-command* in the probe function in xxx/scheme/generic-objects.scm (i.e. add -density30 after ALL). Paul.
Re: [COOT] Loading monomers (Bug!!)
Frank von Delft wrote: Hi, maybe it's fixed in pre-release, but in our version of coot (v0.5.2): When you load a monomer (e.g. NAP), and coot finds that monomer-NAP.pdb already exists in the working directory, it will simply load that file, rather than generating a new one. This is a profoundly evil bug: It is a feature... to me, load monomer does not mean load the next convenient file in the working directory, it means load the monomer from the dictionary. (Just wasted a day or so trying to find out why my NAP won't real-space refine :) :-( It does say that that is what it will do in the Importing Monomers section of the manual. Wasn't your 'suspicious' radar tweaked by the fact the solution appears instantly, rather than taking 30 seconds (for libcheck to run)? Hmmm... Perhaps the status bar should say that it is loading pre-generated files... (or something). P.
Re: [COOT] Stop real space refine tools with a keystroke?
Francis E Reyes wrote: Is there anyway to do this? Sometimes (err I mean a lot of times) I'm building into a low res map, trying to real space refine or regularize several residues in a stretch and Coot gets stuck (still iterating but not moving the atoms on screen anymore). Can I press escape or something to stop the iterations and prompt me whether I want to accept the solution? Not exactly that - but you can press Escape to abandon the current refinement. P.
Re: [COOT] Syntax of mutate_by_overlap.
Ian Tickle wrote: All - can anyone help me with the syntax of the 'mutate_by_overlap' scripting command. I need to mutate a CYS to a chemically-modified entity that I've called CYD. I made a Refmac dictionary entry for this which I read in it's accepted. I'm using WinCoot so I understand I must use Python syntax. I've tried the following: mutate_by_overlap(0,A,17,CYD) That's what I would have used. That should not give a python error (I don't have a working pythonic coot to hand to test :-/) I guess the problem is that coot does not know how to make your CSD. Perhaps if generated the monomer-CSD.pdb and libcheck_CSD.cif (and put them in the current directory) it would work. and in the text window: get_monomer (CYD) This is not a guile command! What does it mean by an integer is required? :-( I don't know - that is a strange thing to say. Paul.
Re: [COOT] Probe pointer distances using scheme?
Stephen Graham wrote: Hi all, I'd like to add a key binding to toggle the 'Pointer distances' on or off. I have found the scheme command (set-show-pointer-distances istate) which I can use to turn them on/off, but I couldn't find an equivalent (show-pointer-distances) function to get the current state [like the (set-show-environment-distances istate) and (show-environment-distances-state) function pair for environmental distances]. Could someone please point me towards the correct function to grok the current pointer-distances state and/or could I ask for such a function to be added to the TODO list? There isn't one - I'll add it now. Pick up a new binary in the morning. Paul.
Re: [COOT] Coot with stereo LCD on OS X
William G. Scott wrote: The latest PyMOL and Coot both work great in stereo. I would go so far as to say these look as good as they did on my ca. $12K (1999 dollars) SGI R1s with Sony trinatron monitors [...] Wow. That's pretty good. You encourage me to fix the naive stereo rotation. Item scheduled for 0.7 then. For me, the reference stereo image is Frodo on a ES PS390. You might like to tweak the eye angle: set_hardware_stereo_angle_factor(1.45) # or some such (I am presuming that you are using the pythonic version). Thanks to Paul (and Warren) for implementing this. For stereo support of Zalman M220W in Coot, credit should entirely go to Bernhard Lohkamp. Regards, Paul.
Re: [COOT] can't edit DNA chi angles
Scott Classen wrote: Hello, I'm using coot 0.6-pre release 2172 via fink after selecting a DNA base to edit and selecting the chi angle that I would like to move I get the following errors when I drag the mouse: Urgh. Me too. Sorry about that (wretched chi-angle code). I suspect 0.5.2 is not so horrific. P.
Re: [COOT] Zalman Coot
Coot will only work with Zalman with revision 2134+ Paul. William Scott wrote: I should add that I can only confirm that it works post revision 2134 The latest in fink is 2172. I'll make a new intel stand-alone if that helps. On Aug 5, 2009, at 11:46 AM, Jürgen Bosch wrote: My coot is 0.6-pre-1 rev 2037
Re: [COOT] click on residue get geometry analysis?
Francis E Reyes wrote: Is there a shortcut for this? No. I'm looking for something similar to the analysis you obtain after a real space refine. There is no pre-refinement analysis (i.e. validation). It would be a nice thing. It is on the list (with 3D markup). Paul.
[COOT] Old Coot - an apology
Dear all, The time is almost upon us for the Old Coot timer to go off in the 0.5 series. When we released 0.5 in Sept last year, I thought that 11 months would be comfortably enough to get 0.6 out. But alas no, there is no new version available. I did consider making a fake 0.5.3, and reset the timer there, but rejected the idea because it would be a cheat - there would be no new features (and would take time too). I also considered releasing what we have, but rejected that too - the chi angle code really does need fixing (indeed, the chi angle code is the only thing blocking 0.6). You can also remove the old coot warning by running the attached script (gziped to get it past the stupid email attachment filter). You can also remove it by hand: edit xxx/share/coot/scheme/coot-gui.scm and comment out (with a ;) the (old-coot?) line [1]. I hope that the new version will be available in less than 2 weeks. Thanks for your patience, Paul. [1] I don't mean the (define (old-coot?) line remove-old-coot-warning.sh.gz Description: GNU Zip compressed data
Re: [COOT] Guile library dependencies in Coot
Teemu Ikonen wrote: Hi, I recently compiled Coot-svn (manually) in Ubuntu and was somewhat annoyed by all the Guile library dependencies which are not available as distribution packages. [snip] Teemu and I corresponded off-list. I will try to move Coot toward using less unconventional packages - including the replacement of guile-gtk with guile-gnome [1]. [1] the name is mis-leading perhaps - guile-gnome is actually the guile interface to the GTK+/Gnome library stack - not to GNOME itself. Paul.
Re: [COOT] ccp4mg
Wu, Zhongren wrote: I am using ccp4mg to get nice graphics for presentations. I have no problems to get movie.gif files for structure rotations. However, when use animation, I ran into a lot problems. I followed the instructions closely and get morph files (pdb format) from the yale.edu server. But ccp4mg refuses to take them, complaining the wrong format. I hope somebody can help me out. Hello Zhongren Wu, If ccp4mg complains about the format of the PDB file(s) it is probably right. The devil is in the detail - what does it say? If I had to guess, I'd say that the files from they yale.edu are not sanctioned PDB format. Paul. p.s. slightly ironic that you should ask about ccp4mg here. There is a mailing list for ccp4mg questions: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=CCP4MG
Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
Engin Ozkan wrote: Hi everybody, Using the revision 2283 on 10.5, I am seeing this whenever I am closing the application: /sw/bin/coot: line 5: 19785 Segmentation fault /sw/bin/coot-real $@ Yep, coot shuts down with a segmentation fault. I haven't tested most functionality and it has not affected my use of coot yet, but I assumed it might help to report it. This seems to be the same bug observed by Christian on a 10.4 machine, because I get the similar Preferences crash. Empty 0-coot.state.scm is also probably due to the crash during exiting. Dear MacCoot-bug-finders, It would be very useful (making the difference between a bug being probably not fixable to probably fixable) if you could send me the core dump analysis of coot. Coot will leave a core dump in /cores - at least it does for me (look for the latest one) $ gdb /sw/bin/coot-real /cores/cores. where send me that text output. Thanks, Paul
[COOT] call for beta testers [was Re: buggy coot 0.6-pre-1 r2264 on OS X 10.4.11]
On Sep 11, 2009, at 7:36 AM, Benda, Christian wrote: Dear Bill, Thanks for your quick reply! I installed the new revision but it doesn't seem to make a difference (to my problems). I guess you're right and it's because I am still running 10.4 - think it's time to upgrade to 10.6, finally! Again, many thanks and best regards, William G. Scott wrote: Paul just pulled off a heroic fix (rev 2310). Please try that. So the last couple of days have been a bit frustrating for me, but a good deal of credit goes to Bill of course. Anyway... the time is approaching for a new point release. While there are still a couple of issues on the list to be addressed, feedback on the current pre-release would be appreciated. Mac users will need Bill's latest and greatest, others can use the binaries on the pre-release page: http://www.biop.ox.ac.uk/coot/devel/build-info.html If possible, please restrict your comments to issues in 0.6, not missing features or features for 0.7 - there will be time for that after 0.6 is out and working. Thanks, Paul.
Re: [COOT] call for beta testers [was Re: buggy coot 0.6-pre-1 r2264 on OS X 10.4.11]
Miguel Ortiz Lombardia wrote: Dear Paul and Bill, rev 2310 from fink works properly now on mac (intel) os 10.5.8 Thank you a lot for solving this problem so quickly (and heroically)! Some issues, then. When launching coot I get this error: INFO:: loading preferences file /Users/mol/.coot-preferences/coot_toolbuttons.py Running python script /Users/mol/.coot-preferences/coot_toolbuttons.py Traceback (most recent call last): File string, line 1, in module File /Users/mol/.coot-preferences/coot_toolbuttons.py, line 1, in module coot_toolbar_button(Side-by-side/Mono, side_by_side_stereo_mono_toggle(), stereo-view.svg) NameError: name 'coot_toolbar_button' is not defined Oh dear.. and yes, my side-by-side/Mono button is gone Due to above I guess. Then, a debug warning, I put it here in case it may ring a bell somewhere: load extensions.scm DEBUG:: in safe_python_command_with_return() pValue is 0x162f52c DEBUG:: in safe_python_command_with_return() pValue is 0x162f52c DEBUG:: in safe_python_command_with_return() pValue is 0x162f52c DEBUG:: in safe_python_command_with_return() pValue is 0x162f52c INFO:: loading preferences file /Users/mol/.coot-preferences/coot-preferences.scm Agreed, debug be gone. Other issues: * Residue Info window is not updated when ab alt-conformation is added Fair enough. For 0.6.1 * If an alt-conf is added and then an auto-fit-rotamer, the occupancies get mangled (for a two-conf case, one goes to 0.0 occupancy and the other to 1.0) Confirmed. That's a baddie! - Thanks. * The labels 'Maximum' and 'minimum distance to protein atoms' in the 'Find waters' dialog are swapped. Or, at least, Minimum is set to 3.40 and maximum to 2.20, which makes no sense to me (but see the neuronal awakeness alert above) Shock again! Yes, confirmed. I've had a setting in my .coot file for years, so I've not noticed this. And a good thing found in this version: bond parameters preferences (width) is now taken into account!!! OK. good. Thanks for the feedback.
Re: [COOT] secondary structure view
Paul Emsley wrote: Eleanor Dodson wrote: The manual suggests the sequence view will be coloured according to secondary structure, but that doesnt seem to be true for me Thank you - if it is easy to fix, I'll do it shortly. If not, I'll schedule it for 0.6.1. It *was* easy. Rev 2339. Also introduced is print_header_secondary_structure_info(imol) which reports the SS info in the header. However, if you want to *add* SS info into the header, you can't do that in Coot (nor, AFAICS, in mmdb). Paul.
Re: [COOT] (transparent) sphere
Bernhard Lohkamp wrote: You currently cannot create a sphere as such (certainly not transparent). But you there is some workarounds: 1.) create a generic object and add a dot (although the dot will be a square esp when larger) along these lines (well, a sphere of dots): http://www.biop.ox.ac.uk/coot/extras/generic-object-sphere-dots.scm Hi, is there a way to display a sphere with given radius at a specific position in coot? preferably semi-transparent? Otherwise I'd have to import a map into rasmol and I find that a little cumbersome. Cheers, Tim
Re: [COOT] coot on 10.6 crashes with refinement
Meghan Miller wrote: Hi, I recently updated my iMac to 10.6. After updating the OS I installed fink, which I used to install and compile coot (version 0.6 pre). However, when I try to do any refinements (i.e. rotamers, mutate and align, etc.) the screen closes and I get the error message terminate called after throwing an instance of 'std::runtime_error' what():Failed to get a good fitting result /usr/local/xtal/coot/bin/coot: line 7: 12973 Abort trap /usr/local/xtal/coot/bin/coot-real $@ Hi Meghan, Mac Users in General (with crashes): For Future reference, please state the revision number and turn on developer mode on the crash reporter: /Developer/Applications/Utilities/CrashReporterPrefs.app And send the goobledegook to me or here, not Apple. At a guess though, I'd bet this is a stream problem again - I don't know why that is happening for some macs. I have tried add improvements for this (of course, I can't test them) - so you will need (or please try) a revision later than 2411. Thanks, Paul.
Re: [COOT] Debian AMD64 Coot
Bryan Krantz wrote: Does anyone know of the proper patches to apply to the ia386-libs to allow Coot to run properly on Debian Lenny AMD64? It appears that the 32bit libraries under ia386 have serious flaws and issues. I would advise that you build 64 bit binaries yourself. I develop Coot on 64 bit Ubuntu using build-it-gtk2-simple. It should just build out the box. You may need to install these beforehand: patch m4 g++ libxext-dev libxmu-dev libxt-dev libc6-dev libglu1-mesa-dev mesa-common-dev libgtk2.0-dev libgnomecanvas2-dev I'm guessing that the dependencies are the same as Ubuntu. Paul.
Re: [COOT] Disulfides across a crystallographic symmetry
Mark Nance wrote: Hi Cooters, I have a pair of disulfide bonds which link two monomers in separate asymmetric units. There is a single monomer in the asymmetric unit, and two monomers come together to form disulfides between Cys 26-Cys45, and Cys45-Cys26. For the record, you can't refine symmetry-related disulfides in Coot (yet). Paul.
Re: [COOT] How to turn off display of negative contour level?
Ian Tickle wrote: is there an easy way to turn off the display of the negative contour level for a difference map after it has been read in? I found a function 'set_map_is_difference_map()' to effectively turn on the negative level, but I couldn't see one to turn it off, maybe something like 'toggle_map_is_difference_map()' ? After 6 years of that begin available, that is the second such comment I heard. The first was a week ago. Probably I will add set_map_is_not_difference_map(). And a toggle function should be added too, I guess. (So the answer is no, you have to get it right when you make/read-in the map). Paul.
Re: [COOT] keyboard shortcut for Rotate/Translate Zone
Ben Eisenbraun wrote: On Fri, Nov 13, 2009 at 10:56:55PM +, Judit Debreczeni wrote: 2009/11/13 Ben Eisenbraun b...@crystal.harvard.edu: I'm trying to add a keyboard shortcut for Rotate/Translate Zone. Try this: (add-key-binding Rotate-Translate Zone r (lambda () (do-rot-trans-setup 1))) That's it. Thanks Judit! :-) For extra fun check out the nudge-residue feature in the recent pre-release builds (Ctrl arrow keys).
Re: [COOT] ramachandran fit error
Andreas Förster wrote: I have a structure with three chains in the asymmetric unit. When I select Refine/Improve Ramachandran Plot from Extensions/All Molecule, coot does its thing until it reaches the end of the second chain, then stops with the errors pasted below. ... Any ideas why the coot extension should fail while the scheme function executes happily? Oh, I should say I'm using coot 0.6-pre-1 rev. 2189 Ancient Coot :) OK, I'll take this to mean please make it trivially easy for me to update my Coot Paul.
Re: [COOT] Non-standard residue
S. Shunmugasundararaj wrote: Is it possible to mutate a residue to a non-standard residue in coot? Yes. Section 5.6.13 of the Coot User Manual. You could have found it by searching for mutating to a non-standard residue Extensions - Modelling - Replace Residue... Paul.
Re: [COOT] How to make a map file readable
pebbleped...@gmail.com wrote: Hi all I am trying to find out if coot can export a map file that in text format. I have created a difference map from two cns maps and want to export it also in cns format (can be read in text eidtor). But till now, I can only save it in xx.map format that in ASCII format. Can't be done. However, you can export a CCP4 map and convert that to text using CCP4's maptona4. How useful that would be, I don't know. Paul.
Re: [COOT] Electron density map for ligand
pebbleped...@gmail.com wrote: Hi all I want to know possible method to get electron density map for ligand only. The material are 2mFo-DFc map downloaded from EDS server and also coordinates from PDB. The electron density map contains protein, water and ligand. I want to build a electron density map only for ligand. How can I do that with help of some usual softwares like coot, ccp4 Section 6.16 of the User Manual. You can use any arbitrary atom selection. Paul.
[COOT] Release 0.6
We are please to announce the release of coot-0.6 Source here: http://www.biop.ox.ac.uk/coot/software/source/releases/coot-0.6.tar.gz Binaries from here: http://www.biop.ox.ac.uk/coot/software/binaries/releases/ Paul. -- Release 0.6 o FEATURE: User-defined clicks [Joel Bard]. o FEATURE: SHELXL interfaces allows the user to modify the input before running the SHELXL executable [Tobias Beck]. o FEATURE: Now compatible with Zalman M220W. o FEATURE: Post-manipulation function hook added [JED]. o FEATURE: Sphere (residue selection) refinement. o FEATURE: function to (re-)calculate probe dots around a give point [Joel Bard]. o FEATURE: monomer and residue selection dipoles. o FEATURE: Interactive map sharpening [Randy Read, Alex Brunger]. o FEATURE: LINK bonds are are now represented. o FEATURE: Backrub rotamers at low (2.7 or worse) resolution. o FEATURE: Baton build parameters (e.g. backwards) now have a GUI [Phil Evans]. o FEATURE: Move waters to surround protein [Garib Murshudov] o FEATURE: rotate/translate zone by residue ranges o FEATURE: Rigid-body fit by residue ranges. o FEATURE: Multi-select on reading coordinates is enabled. o FEATURE: Immediate access to coordinates from CIF dictionaries that contain coordinates (no need for LIBCHECK in such cases). o FEATURE: Nudge-residue (bound to Ctrl-arrow keys). o FEATURE: A dialog has been added from map averaging [Bob Nolte]. o FEATURE: Rename residue [Alexander Schiffer]. o CHANGE: partial charges added to electrostatic surface calculation. o CHANGE: shift-click and ctrl-click in the file selectors now work for reading in several coordinates files [Roberto Steiner]. o CHANGE: SEGIDs are more intelligently inherited [Steven Sheriff, Bob Nolte]. o CHANGE: Transformed make take the cell and symmetry of the reference coordinates. o CHANGE: Transformed maps take on the cell and spacegroup of the reference coordinates. o CHANGE: Coordinates Molecules transformed by LSQ take on the cell and spacegroup of the reference coordinates. o CHANGE: Pukka-puckers? fixed and re-enabled. o CHANGE: Ramachandran Plots now have molecule name labels [Wendy Offen]. o CHANGE: The save coordinates dialogs active item is the first molecule with unsaved changes (rather than simply the first molecule) [Herb Klei] o CHANGE: Go To Blob now goes to the front blob, no matter what the density level of blobs/density behind it is [JED]. o CHANGE: Don't display the geometry distance if the molecule corresponding to the start or end point is not displayed [JED]. o CHANGE: Using the internal alignment, the weights of the affine gap penalty have been changed to favour mutations and larger gaps rather than several small gaps. o CHANGE: the restraints editor now uses strings (positive/negative/both) rather than number to represent the sign for chiral volumes [Andrew Leslie] o CHANGE: the restraints editor now adds a new entry to the dictionary when the comp-id is changed. o CHANGE: Additional representations now have an All off button. o CHANGE: Chi angles rotation now include a reverse fragment option. o CHANGE: Add strand here moved next to Add Helix Here. o CHANGE: Convert PDB format 3.x prime atom names to star names (to correspond to current Refmac dictionary). o BUG-FIX: TER records are removed on addition of waters [Herb Klei]. o BUG-FIX: Align vs PIR file improved [Bob Nolte] o BUG-FIX: Single HETATMs now are refined by rigid body (as waters are) when using Refine Zone. o BUG-FIX: new atoms (and waters) are added as HETATMs if appropriate [David Mathog]. o BUG-FIX: TER records for water chains are no longer tested in water validation tests [Herb Klei]. o BUG-FIX: NCS chain jumping now works on heterodimers [Jianghai Zhu]. o BUG-FIX: The Chain Reordering function in Extensions has been fixed. o BUG-FIX: Torsion angle refinement convergence improved [JED]. o BUG-FIX: Ramachandran Green spot no longer disappears on refinement. o BUG-FIX: Limit the sequence view canvas X parameters, so that we don't get X11 errors and crash [Felix Frolow]. o BUG-FIX: Additional representations appear in both eyes in side-by-side mode. o BUG-FIX: Delete-atom spewing binary fixed [JED].
[COOT] Coot 0.6, new paper
Dear All, Our new paper has been accepted and is now in press. Please (if you want to cite coot) update your citation. About - About - References I think that this is particularly important for users of WinCoot and Coot on Mac OS X, because the paper includes Bernhard Lohkamp and Bill Scott as authors. Citing this paper (rather than the 2004 one) is the appropriate way to acknowledge their contributions. Coot 0.6.x will be the last to be built with gtk1, we will relieve ourselves of that burden in 2010. Paul.
Re: [COOT] karmic
Ed Pozharski wrote: In Ubuntu 9.10, coot appears to be fully compatible with compiz when running on Intel graphics card. So there is no need to disable the visual effects anymore. Hoorah! So will we get to see a youtube video of coot running an all molecule script (say), each face of the cube doing a different chain? Hehe... Paul.
Re: [COOT] Mask the map
pebbleped...@gmail.com wrote: hi all, I have a question about how does coot mask the electron density map. I have a ccp4 electron density map file with parameters like this: Parameters as read from the map file Origin .. -167 -36 -35 Extent ..10974 113 Grid 15652 112 Cell axes ... 100.74 32.81 72.69 Cell angles . 90.00 90.71 90.00 UVW (fast, medium, slow) Y X Z OK, so right there is the problem. Coot uses clipper's crystallographic maps - using maps that are not the asymmetric unit can be confusing, there are 2 copies of symmetry-related density. So this electron density map has 109*74*113=911458 grid points and its origin located at point -167 -36 -35 After I mask part of the density map (around chain B) and only leave electron density around chain A, I export it. Now its parameters are like this: Parameters as read from the map file Origin .. 0 0 0 Extent ..15652 112 Grid 15652 112 Cell axes ... 100.74 32.81 72.69 Cell angles . 90.00 90.71 90.00 UVW (fast, medium, slow) Y X Z OK, so a P1 asymmetric unit. So now the masked map has 156*52*112=908544 grid points with origin locate at point 0 0 0 Before I do tests, I guess how coot to do mask is: to find out grid points around selected atoms from model and set the density value to be zero then save the map like this: 1.11.1 2.12.1 3.1 0.0 4.14.1 5.15.1 Yes, if I understood correctly. So then I can compare the two maps to check out at which point the mask is placed. But actually, the masked map have different points with the initial map. Symmetry-related density, I would guess. Does anyone know how can I get a masked map with same grid points as the initial map and the only differences are density values at some grid point were set to be zero? The first map should be the asymmetric unit (again, if I understood correctly). Paul..
Re: [COOT] Release 0.6
Maia Cherney wrote: I suggested some time ago to include Go to atom button in the bar beside Display manager, as this is one of the most used buttons. Paul liked the idea, but I don't see it in the new release. For the record, I should reply to this. I did consider this option. I thought that it would be a useful addition. But only marginally so, seeing as there is already a menu item and a keyboard accelerator (F6) to show the dialog. Added to that, I rarely close (and then re-open) the go to atom dialog. Therefore it got shelved. It may well appear in 0.6.1. Paul.
Re: [COOT] Proxy server setting
Arnaud Basle wrote: Is it possible to tell coot to use a proxy server? No. Well, yes, strictly, but it won't listen. Ask again in a few days though. Paul.
Re: [COOT] Release 0.6
Victor Alves wrote: The thing is I can't find neither a stable 0.6 binary for ubuntu (32 bits) with python AND gtk2, Not all the target platforms built 0.6 correctly. We are investigating. I think that the Ubuntu 32-bits build is a virtual machine in York. It's a bit non-trivial to debug. and also in nightly builds, the binary-Linux-i686-ubuntu-8.04.3-python-gtk2 http://www.ysbl.york.ac.uk/%7Eemsley/software/binaries/nightlies/pre-release/coot-0.6-pre-1-revision-2537-binary-Linux-i686-ubuntu-8.04.3-python-gtk2.tar.gz *2537 *is way outdated compared with the latest build: 2568 Related to above. Paul.
Re: [COOT] hydrogen restraints
Sara Zueger wrote: Hi everybody, Hi Sara, as I did not find a final solution to the hydrogen restraints problem (flying or exploding during real space refinement) in any of the mailing lists, I wanted to pick this topic up again. If one adds hydrogens by phenix.ready_set or reduce the labels for these hydrogens on let's say a Cbeta atom will be HB2 and HB3 (according to the pdb v3.2 convention). However, the coot/ccp4 library names them HB1 and HB2, so there are no restraints for HB3 atoms. I see that probably this naming problem can be overcome by using phenix.reduce -OLD, or renaming them manually in the pdb file (but if one deposits the structure to PDB does one have to name them back again?). Is there already some new solution? There is not a solution yet. And how about hydrogen restraints for the most N-terminal amino acid, where one has H1, H2 and H3? How are these handled? There seem to be no restraints for those as well, because they also fly around during real space refinement. Same situation. We need to do some drudge work to convert the hydrogen names in the libraries. AFAICS it is straightforward, but just hasn't been done by anyone in the CCP4/Coot community. I wonder what dictionary the Phenix fellow use? If they have updated the dictionary to 3.2 format, perhaps we could use their copy too. (However, we deal with this, it should be done by the end of the 0.7.x series.) Paul.
Re: [COOT] Dock sequence
Phil Evans wrote: How does the Extensions-Dock sequence command work? I've got a polyAla model, so I open the dialog, import a sequence file, click the Sequence closest fragment or Sequence all fragments! Then I get in the terminal window something like Sequence: ??QKDIGVKPEFSFN?? Confidence: 0.508934 From: LQQKDIGVKPEFSFNIP Chain id: 0 Offset: 114 but nothing seems to have happened. has it failed? or worked? OK, well that interface could do with improving. As could the documentation - thanks for prodding me. It has failed. It needs 0.9 or greater confidence before it will add the sidechains (this basically Kevin's buccaneer code). Paul.
Re: [COOT] How to mask a map considering the symmetric operations?
Or to put it slightly differently: the masking of symmetry-related density works (only) when the cell and symmetry of the map is the same as the cell and symmetry of the atoms for the mask. Paul. Bernhard Lohkamp wrote: Hi, you dont say how you obtained you map. Usually in Coot, thanks to clipper, the maps extend over the whole crystal space, i.e. you have the same map in all asu. However this only works if the map is either generated by Coot itself (from an mtz file) or if you read a map file which covers only/exactly the asu (or unit cell). I assume you didnt use either of these. So, please try that and you will get the same, masked map around all molecules incl the symmetry related ones. Alternatively you could write out the symmetry related molecules and masked them again. B Hi all, I am looking for a strategy to obtain a density map which only contain densities where no assignment was made in the model. When I load a PDB file and its corresponding density map to coot, I can mask all regions contain the model. And then several parts were left around the edge of the model. However, these parts are not totally the one where no assignments was made, because some of them belong to the adjacent asymmetric unit part. I can display these parts by using cell and symmetry function in coot and can see the model overlap with the map. But how can I also make masks on them and let only the part where no assignments was made left from the whole map. That is how to mask the model and also its images. Thanks
Re: [COOT] deleting atoms from alternate conformations
wtempel wrote: Hi all, judging from what I see being used by my colleagues, COOT is well on its way to world domination. Like Linux (haha). Anyway, suppose I have split a residue, say lysyl, to model alternate conformations of its side chain. Suppose further that I would like to remove NZ from conformer B. Upon doing so, the current COOT implementation will remove the atom. Good. It will also remove the confID from what was conformer A's NZ atom and re-set its occupancy to 1. On the latter part, intuition tells me that instead, conformer A's atoms should be unaffected, namely keep their confID and sub-unity occupancy. My questions: 1) What behavior is expected by other COOT users in comparable situations? Would the answer be different if a C or an O had been deleted? I'd rather ask: is Coot doing the right thing in such a case? I suspect that Garib or Pavel may know. 2) Should a few folks align themselves with my opinion, can COOT's behavior be modified without unintended side effects? Yes. Specifically, I like COOT's current behavior when Delete Residue is applied to alternative conformations: Delete the conformer completely and set the remaining conformer's atoms to Occ=1 and remove the confID. I think that that is just doing the above for many atoms. Paul.
Re: [COOT] coot question
Katarina M wrote: Hi all, I am running coot version 0.6 pre on Mac OS X 10.5.8. Everything was working fine upon installation for couple of months and all of the sudden after trying to real space refine a residue funny looking dots would appear around it (as is shown in the attached photo). It appears that these dots are somehow showing the interaction with the neighboring residue or water molecules. Could anybody help me with turning off this feature? They are probe dots. Presumably you installed it or molprobity and coot started using it. Somewhere you have set: (set-do-probe-dots-post-refine 1) so you could try finding that and commenting it out or simply add (set-do-probe-dots-post-refine 0) to the end of your ~/.coot file. Re: the image, I would be tempted to move the CG and NZ to the left somewhat, and the CD, CE to the right. Paul
Re: [COOT] COOT for MAC OSX, baton
Lei Jin wrote: I have two questions here: 1. Where is the COOT for MAC OSX? I just could not find it, although I could find COOT for Windows and Linux at http://www.biop.ox.ac.uk/coot/software/binaries/releases/ See the FAQ: http://www.biop.ox.ac.uk/coot/doc/coot-faq.html#SEC3 2. Using baton to build Calpha model (tracing the polypeptide chain): after skeletonizing the map, when I use baton, I have to choose a few positions determined by the program for the end point of the baton. How can I rotate the baton and decide where the end point is by myself? See Section 5.7 of the User Manual. http://www.biop.ox.ac.uk/coot/doc/coot/Baton-Building.html#Baton-Building Lots of snow here. Nottingham? Hmm Paul.
Re: [COOT] Coot 'Feature' Request
Antony Oliver wrote: I'm using Coot on OS X - so I don't know whether this is a 'feature' of this version (fink built) - but the dialog boxes, particularly the save dialog, always appear behind the main window. It is possible to change this behaviour, so that it appears in front? Apple bug. It works fine on all other X servers (AFAIK). It used to work on Macs too (Pather, maybe Tiger, and IIRC Leopard used to work before they updated X11 for it). Paul.
Re: [COOT] Nucleic acids residue names
Miguel Ortiz Lombardia wrote: Dear all, Is there a way to ask Coot to write pdb coordinate files with nucleic acid residue names in 'standard' PDB format? That is: DA, DC, DG, DT, A, C, G, T... No. It's on the list. I will use the PDB-approved nomenclature. Sorry, this may have been solved already, but I just found an old message (http://www.ysbl.york.ac.uk/~emsley/coot/mbox-2006/0227.html) with a perl solution put forward by Bill Scott. I wonder if a preference setting could be changed so there is no need to resort to external file editing. Not yet. Paul.
Re: [COOT] Macros in COOT
Dear Andrew, Having worked with O for many years I am only now getting serious with COOT. There are a couple of things that I would like to do that don't seem to be available (as far as I can tell), but which may well be possible using Macros. Unfortunately a quick Google has not revealed anything about how to use macros in COOT, but a colleague suggested they need to be written in Python or another language that I had not heard of before. Your colleague is correct. The other language is a form of Lisp - you will have heard of that. So my first question is where can I find a low level description of how to write macros with some examples (I know nothing about Python, except that it is fashionable) ? It is fashionable - or at least is was 2 years ago. Now the cool kids favourite is ruby (on rails) I understand. We don't use the word macros because that would be confusing given the extant Lisp macros, which are part of the language. You can learn about programming python in many ways of course (not least the python tutorial, which is what I read first) http://docs.python.org/tutorial/ The coot python extensions are described in the documentation. There is a standard trivial formatting change that has to be made to get the syntax right for python, see Python Scripting here: http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-faq.html There is a growing collection of coot scripts in the Wiki http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT There are specifically two things I want to be able to do: 1. Do an LSQ superposition using specified residues in multiple chains (superposing one oligomer on another). Something like this then? clear_lsq_matches() # specs for reference then moving add_lsq_match(20, 90, A, 20, 90, A, 1) add_lsq_match(20, 90, B, 20, 90, B, 1) add_lsq_match(15, 75, D, 15, 75, D, 1) apply_lsq_matches(1, 2) which presumes that the reference molecule is in 1 and the moving molecule 2. 2. To do a LSQ superposition of a homologous structure onto my working structure using ± N residues about the current position, where N is a variable (not essential, could be fixed) and the current position is the last residue that I clicked on. That is more involved - and more useful because it can be dynamic . Something like the following perhaps (in scheme, just for amusement (not tested)). You will need to set imol-ref, perhaps by reading in the reference pdb, as demonstrated below. The function is bound to Shift-Y. Paul. - (define dynamic-lsq-range-extent 2) ;; +/- 2 residues either side of centre residue (define imol-ref (read-pdb reference.pdb)) ;; convert between the input reference chain id and the chain id of ;; the moving molecule that corresponds to that chain ;; (define (mov-match-chain ref-chain-id) ref-chain-id) (define (dynamic-lsq-match) ;; get the current residue and use that to make residue ranges for ;; an LSQ fit ;; (using-active-atom (clear-lsq-matches) (add-lsq-match (- aa-res-no dynamic-lsq-range-extent) (+ aa-res-no dynamic-lsq-range-extent) aa-chain-id (- aa-res-no dynamic-lsq-range-extent) (+ aa-res-no dynamic-lsq-range-extent) (mov-match-chain aa-chain-id) 1) (apply-lsq-matches aa-imol imol-ref))) (add-key-binding Dynamic LSQ overlay Y dynamic-lsq-match) Paul.
[COOT] Release 0.6.1
We are pleased to announce the release of Coot-0.6.1 Source code: http://www.biop.ox.ac.uk/coot/software/source/releases/coot-0.6.1.tar.gz Binaries http://www.biop.ox.ac.uk/coot/software/binaries/releases/ (the building on additional platforms is underway): Paul -- Release 0.6.1 o FEATURE: Quick-save - bound to Ctrl-S. o FEATURE: Binary updates (pre-releases) now available. o FEATURE: tutorial data can be loaded from a Extensions menu item o FEATURE: A means to set the refinement weight so that the resulting chi squareds are 1.0 (or close) [Katya Heldwein] o CHANGE: Save dialog positions now also saves the Edit Chi Angles dialog position [Markus Rudolph]. o CHANGE: Coot can now go through proxies (http_proxy environment variable) to get News. o CHANGE: Baton manipulation is now possible when the skeleton runs out. o CHANGE: Hydrogen representation now thin and grey monotone. o CHANGE: Interface to sidechain docking improved [Phil Evans]. o CHANGE: Updates to sync with new EDS (Electron Density Server). o CHANGE: Filenames of mtzs and pdb in the current directory are now stored as relative in the state file [Andre White]. o CHANGE: Default image type for screenshot is now PNG [Joel Bard]. o CHANGE: --python --no-graphics results in a python prompt at the command line [Gabor Bunkoczi]. o BUG-FIX: Check waters by difference map now works again [Misty X]. o BUG-FIX: SSM alignment crash fixed [Ed Pozharski]. o BUG-FIX: Splitting a sidechain with zero occupancy no longer leaves atoms with negative occupancy [Takaaki Fukami]. o BUG-FIX: Shift-spacing through waters, deleting active water now goes to previous atom [Ingo Korndoerfer]. o BUG-FIX: No torsion restraints added when the esd of the torsion is 0 (Phenix compatibility) [Joel Bard]. o BUG-FIX: Rotamers and Edit Chi now works for MSEs [Clemens Vonrhein]. o BUG-FIX: Hydrogen environment distances now are synchronised with the display of hydrogens [JED]. o BUG-FIX: Phosphate-backbone mode enabled for symmetry [Miguel Ortiz Lombardia]. o BUG-FIX: Carbon-Iodine bond length limit lengthened. o BUG-FIX: Go To Atom dialog is updated after simple mutation of a base [Miguel Ortiz Lombardia] o BUG-FIX: Coot no longer things that a SHELXL BLOC card is an atom [Zbigniew Dauter]. o BUG-FIX: sugar chains now find the linkage type better (rather than forcing seemingly-random chain breaks) [JED]. o BUG-FIX: Go to Atom keyboarding chain-id superfluous functions removed [JED].
Re: [COOT] Autosave
Victor Alves wrote: About Auto-save. I tried it, after modifying the PDB model I was working on, but apparently this didn't save those changes to my current opened PDB file. It just writes a coot.state.scm file. Am I right? Well, I can't say that you're wrong, but for me, modified models are written out to the default save file name (e.g. xxx-coot-1.pdb) before the state file is saved. Paul.
Re: [COOT] coot 0.6.1 and libldap-2.2.so.7 at Fedora10
Hi Martin, Martin Moche wrote: Dear Coot Users, I am trying to run, coot-0.6.1-binary-Linux-i386-fedora-4-gtk2, at my Fedora10 Linux machine... Eeek - Stop right there! The correct solution is to use the Fedora 10 binary. ... which seems not to to be in place yet... OK, it is now, please look here for binaries: http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/ Paul.
Re: [COOT] Macros in COOT--use VB to write python code
Goodness, sounds like fun. Coot does have an alignmutate function of course, but you don't get to fiddle with the sequence alignment - Coot uses its own alignment [1]. My understanding is that should be fine for ~70% sequence identity or better. My feeling though is that it is not widely used. So my question to the community is: Is there a need to be able to use an alignment rather than simply a target sequence? Thanks, Paul. [1] courtesy of mmdb Wes Ozarowski wrote: Dear Andrew, Since I don't have the time to learn python fully and because there is not too many of examples of python scripting available for Coot, thus I use my expertise of VB to help me write the correct syntax for python script. then paste it into notepad and run it as a python script from Coot's GUI. For example I will paste an amino acid sequence of homologous proteins from ClustalW into an excel spreadsheet, then using VB to write a program that will put each amino acid into it's own spreadsheet cell as separate objects with some fancy colors ( as color codes) to make it pretty. Now, I can do all sorts of analyses of these sequences, like find the ones that are non-homologous between two proteins, put them in a table, let VB write the python syntax for goto and mutate_autofit of all these specific amino acids, paste it into notepad and wala ! i have automation. That is ,I can goto (thus observe visually the mutational changes for oddballs) and mutate_autofit about 300 amino acids in about 10 min, rather than spending hours doing it manually. Wes In a message dated 1/19/2010 10:56:53 A.M. Central Standard Time, and...@mrc-lmb.cam.ac.uk writes: Having worked with O for many years I am only now getting serious with COOT. There are a couple of things that I would like to do that don't seem to be available (as far as I can tell), but which may well be possible using Macros. Unfortunately a quick Google has not revealed anything about how to use macros in COOT, but a colleague suggested they need to be written in Python or another language that I had not heard of before. So my first question is where can I find a low level description of how to write macros with some examples (I know nothing about Python, except that it is fashionable) ? There are specifically two things I want to be able to do: 1. Do an LSQ superposition using specified residues in multiple chains (superposing one oligomer on another). 2. To do a LSQ superposition of a homologous structure onto my working structure using +/- N residues about the current position, where N is a variable (not essential, could be fixed) and the current position is the last residue that I clicked on. Thanks Andrew
Re: [COOT] americanisms in 0.6.1....
Kevin Cowtan wrote: Ezra Peisach wrote: I move that the names in the scheme scripts be changed to the american names and that a new script British.scm be put in place. Well, that's just crazy talk. The scripting interface should clearly use the established language of science, which transcends national boundaries and has been the lingua franca for the bulk of the history of science. I therefore propose that Coot scripting interface be translated to Latin. There may be some technical neologisms which do not yet have appropriate Latin equivalents. I'm sure these people will be glad to help... http://www.vatican.va/roman_curia/institutions_connected/latinitas/documents/index_en.htm At some stage I (at least) would like to have the GUI translated into various languages. We have a start for Spanish and French and I'd like others, for example Chinese, Japanese and Portuguese, So we'll be putting out a call for translators later (Latin_Vatican is a possibility). No time to look at this before next year though. Paul.
Re: [COOT] key binding to delete waters
david lawson (JIC) wrote: Dear All, I would like to set up a key binding to delete the water molecule I’m centred on, but I can’t get the guile syntax right. Can anybody help? A good question for bioklatch, http://www.bioklatch.com/ IMHO. I'll answer it there too, if someone asks it. (add-key-binding Delete this water D (lambda () (apply delete-atom (active-residue (Perhaps it should be in the Wiki too). Paul.
Re: [COOT] Transforming maps
Marko Hyvonen wrote: (transform-map-using-lsq-matrix 1 A 1 200 0 A 1 200 2 (molecule-centre 1) 10) All seems to go fine, except that the map matches correctly only part of the transformed molecule, and it looks like when the map is extended by symmetry, things fail Yes, the transformed map only makes sense 10A around the centre of molecule 1. Make sense, but it does not quite do the correct thing. If I use: (read-pdb test.pdb) (read-pdb reference.pdb ) (auto-read-make-and-draw-maps test.mtz) (transform-map-using-lsq-matrix 1 A 118 349 0 A 118 349 2 (molecule-centre 1) 10) (set-rotation-centre 34.0726.71 0.6102)# centre of molecule 1 the result is: http://www-cryst.bioc.cam.ac.uk/node/199 still can't see anything (other than window dressing). This is centred on the point around which the map is created (based on coot output), and you can see clearly density is lacking from one side of the image, very close to the centre. that sound like the radius is too big. I am sure there is trivial solution to this, but I can't think of it now. Use a bigger radius? Dynamically set the position to which you transform maps? Dynamically? Me? That would be great. Hmm... Can I centre on a residue or calculate a centre from a set of atoms? Yes. go-to-atom-chain-residue-atom-name molecule-centre Also, is the lsq matrix from the transform-map-using-lsq-matrix stored anywhere, No, sadly not. It returns the new molecule number of the map. You can generate an lsq matrix using: (clear-lsq-matches) (add-lsq-match bla bla..) (define my-matrix (apply-lsq-matches imol-ref imol-mov)) and can I use it for other transformations? Yes, indeed.
Re: [COOT] problem with refining DNA
Miguel Ortiz Lombardia wrote: Le 4 févr. 2010 à 04:37, Norman Zhu a écrit : hello there I am in the process of refining a protein structure complexed to DNA promoter site. I ran into difficulty as i try to move a few bases into patch of electron density that is obviously meant for them. dragging the bases with real space refine zone and/or regularize zone neither break open the phosphate back bone bounds or turn everything into knots. I know there is nothing wrong with the naming convention of my bases since I changed them from DT to Td after similar blog. Any suggestion on this matter would be greatly appreciated. Norm Hi Norm, Depending on the resolution of your data you may need to turn down the matrix weight in refinement parameters. I tipically put this down to 30 (compared to the default value of 60) and for really lower resolution (say 3 or worse) I may go as down as 20. I frequently use 6.0 or even 2.0 sometimes. Paul
Re: [COOT] DNA structure refining problem
Norman Zhu wrote: This email is a continuation of an inquiry I post last week. The problem I had and still is i can't use the real space refine zone and regularization zone functions on a DNA structure. Whenever i ask the computer to fit the bases into the electron density it would give me a solution that would only satisfies the needs of the purine and pyrimidine bases but at the expense of the sugar and phosphate back bone. The devil's in the detail. Do you atom names in the pdb file match the atom names in the Refmac dictionary? Perhaps you use prime names and the dictionary uses * names. Upgrading to a recent pre-release should help with the diagnostics. Paul.
Re: [COOT] anomalous difference map
Kay Diederichs wrote: I was under the expression that coot automatically calculates an anom diff map when the DANO label is used. Depends what you mean by automatic, but I would say not. Open MTZ, use the Expert button, that will enable anomalous labels (as I suspect that you know). However I can find nothing to that effect in the documentation. http://www.biop.ox.ac.uk/coot/doc/coot/Create-a-Map.html#Create-a-Map What's missing? Have I been looking at ordinary diff maps when when using DANO and PHWT in coot? No, I don't think so. I think that I might be missing your point. Paul.
Re: [COOT] anomalous difference map
subh wrote: Hi, I am trying to open my phased mtz file in coot to see the anomalous difference map.But it does not open when I choose Open mtz, .cif etc. While I can open the map by choosing auto open .MTZ it doesnot give me the choice to select the maps that I want to see. I knew that if I could open the mtz file through open .mtz,ciff etc ruther than auto open, i should get the expert selection. You should indeed. Click on the Expert button on the MTZ column selector and it will allow you to choose anomalous labels.
Re: [COOT] chain coloring
Sebastiano Pasqualato wrote:
Hi Paul, hi all,
besides for the principal task of building molecules, I like using coot for
studying structures.
I would however be very happy to give a given chain a determined color, rather
than having colors attributed by the program.
Well, you (only) have
Edit - Bond Colours - { pull the slider }
that's all you have for now - and for at least the next year.
(those settings get saved to the state file, btw)
By the way, I don't know if that's a problem of mine only, but with the new version
of coot (I'm currently using Bill Scott install of Coot 0.6.1 on MacOSX 10.6.2) when
I try to change chain colors with the Edit--Bond colors--Molecule colors I
only have one of the chain of a molecule that has the color changed, the others stay
of the color they were.
If I understand you right, that should not be - and indeed does not
happen for me. (You are in Bonds (Colour by Molecule) mode, right?)
Paul
Re: [COOT] ncs ghost control
Eleanor Dodson wrote: This seems to be lost ?? /y/programs/xtal/coot/coot-Linux-i386-fedora-10-gtk2-python/share/coot/python reads pdb and says: ... INFO:: NCS chain comparison 306/307 INFO:: NCS chain comparison 304/307 INFO:: NCS chain comparison 306/307 INFO:: NCS chain comparison 305/307 INFO:: NCS chain comparison 306/307 INFO:: fill_ghost_info Constructed 5 ghosts Ghost 0 name: NCS found from matching Chain B onto Chain A Ghost 1 name: NCS found from matching Chain C onto Chain A Ghost 2 name: NCS found from matching Chain D onto Chain A Ghost 3 name: NCS found from matching Chain E onto Chain A Ghost 4 name: NCS found from matching Chain F onto Chain A Molecule 0 read successfully then reads some monomers ... then NCS_controller display chain toggled for imol 0 chain 1 state 1 ncs_control_display_chain There are 5 ghosts ighost: 0 name: NCS found from matching Chain B onto Chain A chainid: B target chain id: A display_it_flag 1 ighost: 1 name: NCS found from matching Chain C onto Chain A chainid: C ... then when I try to display it: INFO:: NCS chain comparison 306/311 First atom of 2340 in first selection 1/D/501/1PE/ OH2 altLoc :: segid :D: pos: (43.244,-35.506,-4.711) B-factor: 18.28 First atom of 2316 in second selection 1/A/501/1PE/ OH2 altLoc :: segid :A: pos: (-4.313,-18.187,34.044) B-factor: 21.72 WARNING:: no points to do matching find_ncs_matrix returns (LSQ) | 0, 0, 0| | 0, 0, 0| | 0, 0, 0| ( 0, 0, 0) WARNING:: Junk NCS matrix No NCS matrix defined Admittedly the pdb begins with the ligand numbered 501 then goes back to 1 2 3 etc.. Has that upset it?? That would be my guess - 60-70% probable I estimate - such is the nature of mmdb atom selection... Paul.
Re: [COOT] hydrogens hanging after removal of alternate conformation
Garib Murshudov wrote: Just for info: There is new version of the dictionary that is compliant with pdb v3. It works with new version of refmac and should work with phenix also. It seemed to work with coot also. www.ysbl.york.ac.uk/refmac/data/refmac_experimental/remfac_dictionary_v5.18.tar.gz I should warn that we are still working on this dictionary but it should be usable now (if you use refmac then you will need newer version of refmac also available from the same page) That should of course be http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac_dictionary_v5.18.tar.gz
Re: [COOT] error saving coordinates in Shelx format
Alice Dawson wrote: I'm running Coot 0.6.1 on a Mac (running 10.5.8), installed via Fink. I'm running some Shelx refinements. When I try to save the coordinates (as a .ins, from a .res that I read in) I get this error (first-coords-imol) (first-unsaved-coords-imol) INFO:: Setting fileselection with file: benz32_bind-coot-0.ins save coordinates for molecule 0 to file /Users/axdawson/work/ptr1/ Coord_submission/pemet/benz32_bind-coot-0.ins /sw/bin/coot: line 5: 26481 Bus error /sw/bin/coot-real $@ This happens even when I make no changes to the coordinates before trying to save. It doesn't happen with pdb format coordinates. Any ideas? Dear Alice, I think that this is the same problem that Derek Logan complained about recently. I did investigate the problem and it seemed to result from setting the precision or other output format specifiers for the floating point numbers in the .ins file. I don't know why Coot on a Mac should do this - I suspect a Mac problem rather than a Coot problem. I have patched things up in the pre-release to not crash on writing the .ins file - but that doesn't help a great deal because the resulting .ins file is empty. Real solution still pending. I'm hoping the Bill and I can find some time to bash on it soon. Paul.
[COOT] simplify CA-Mainchain selection [was Re: a request]
Dear Eleanor, Eleanor Dodson wrote: When converting from CA to Main chain it would be wonderful to just have to select a CHAIN - not click on the first and last residues.. In that I cant think of any time when you would want to only convert a limited span of residues.. On reflection, I agree with you and will schedule this for implementation. It is part of a larger request to allow many functions to be specified by residue identifier, rather than clicking eg real space refine from /A/10 to /A/17 set occupancy to 0.0 for /A/10 to /A/17 These function are described (to varying degrees) in the manual. (db-mainchain imol chain-id resno-start resno-end direction) (refine-residues imol residue-list) (refine-zone imol chain-id resno-start resno-end alt-conf) (zero-occupancy-residue-range imol chain-id resno-start resno-end) (fill-occupancy-residue-range imol chain-id resno-start resno-end) Paul.
Re: [COOT] add terminal residue residue type
Dear Dirk, Dirk Kostrewa wrote: another point for your wish-list: when I add a terminal residue, an alanine is added that I have to mutate into the proper amino acid type in a second step. I would find it very useful, if a popup-window would ask me, which amino acid type I want to add. This would have two advantages: I don't have to mutate the amino acid afterwards, Extensions - Dock Sequence - Associate Sequence. Then, when you do an add terminal residue, Coot does an on-the-fly sequence alignment to find out the next residue type and makes the mutation for you. and, maybe, the real space positioning would be even better. yes, I think it is. Paul.
Re: [COOT] pointer distances, recording water
Maia Cherney wrote: Hi Paul, the format of the file got screwed. I am resending the file in the attachment. I would like to repeat the description of the problem. There is a difference in recording of water molecules in coot and in phenix. The example is given in the attached pdb file. Certainly HETATM is correct for waters. Ancient Coots used to write ATOM. I'd be surprised if recent Coots don't add waters as HETATMs and don't strip the TER before adding a water. Paul.
Re: [COOT] Coot balking at SHELX refined anisotropy
SIPPEL,KATHERINE H wrote: Hi all, I am running Coot 0.6.2-pre-1(revision 2816). The OS is Open Suse 11.1. Every time I try to open a SHELX refined pdb file with ANISOU cards I get this error ERROR 14 READ: Unmatch in different records for the same atom Then it lists the line number of the first ANISOU card. If you remove all the ANISOU cards it works. If you open an anisotropically refined pdb from PHENIX it works. I've even checked the spacing in the pdb file to make sure its correct. I can not see any difference between the SHELX and PHENIX derived coordinates. I'm sure this is some simple idiocy on my part but if you have any ideas I'm all ears. Hi Katherine, Sounds to me (if I understand correctly), although I hesitate to suggest it, that the output PDB from SHELX is not conformant with the current standard (it's in good company, Refmac too had a similar problem). The formating of the ANISOU cards is quite particular and I invite you to have another look there. If you like, you can send me a few lines of Phenix PDB that work and the corresponding lines of the SHELX file that do not. Paul.
Re: [COOT] Coot balking at SHELX refined anisotropy
SIPPEL,KATHERINE H wrote: Thanks for all of the replies. It turns out with the updated COOT that ANISOU cards require an element type (column 77-78). For the record, it is not fundamentally the update of Coot that has changed things, it's that recent versions of Coot use recent versions of mmdb which implements the PDB standard. It will still open ATOM card lines without it, mmdb is somewhat forgiving and (I believe) infers elements from atom names. Hmmm... but not for ANISOU cards, I wonder if anything can be done... hence the confusion. The output pdb from SHELXL refinement doesn't write this column which is why COOT was having issues. .. was conforming to the standard I think you mean :-)
Re: [COOT] rotate/translate button
Jan Abendroth wrote: since a few versions, the linux distribution of coot seems to have lost the handy rotate/translate button in the toolbar on the right side of the main window. It is not an option under preferences either. However, it is still around in the osx version from Bill. Are there any tricks to get this button back? Coot is built on many different OS types, using the given (or supplied) version of GTK+. Some old operating systems have a version of GTK+ that does not include a ``ToolMenuButton'' (newer operating systems do, of course) - and it is under such widget that the Rotate/Translate function has moved. The Coot build system detects old versions of GTK+ and skips over the MenuToolButton code, so the button does not appear in the main window. However, on all systems, the Rotate/Translate mode selector can be found as a menu to the right of the ``Rotate/Translate Zone'' button on the Model/Fit/Refine dialog. So, if you want a Rotate/Translate Menu Tool Button in the main window, don't use an old OS. I've added this answer to the FAQ. Paul.
Re: [COOT] command line and customized options (bug/feature?)
Ed Pozharski wrote: It appears that when loading model/map from command line (via --pdb and --auto options) coot ignores the parameters defined in $HOME/.coot . Mine has the (set-map-sampling-rate 2.5) setting for smoother maps, but when I use the command line to load pdb/mtz files, the maps look more like sampling rate 1.5 . I agree that it should work this way round. Paul.
Re: [COOT] What kind of maps produced in coot when refmac is run?
Francis E Reyes wrote: What kind of maps are produced in coot when refmac is run from within it? Sigma-weighted 2fo-fc's ? SigmaA, yes, Standard refmac maps: 2mFo-DFc, mFo-DFc.
Re: [COOT] problem reading bond mmCIFLoop and bonds/angles not drawn
Christian Benda wrote: Hi, we have a recurring problem with our coot installations (coot version 0.6.1rev 2740 on Mac OS X 10.6.3). For some users when they start coot, they get a list of error messages in the terminal (see below) and structures are displayed without most of the bonds drawn (only crosses where atoms are and some bonds). The error messages are pasted below. It seems like the problem occurs only for those users, who also work on a Mac OS X 10.4 coot (before or in parallel, on a second work station but a network file system). In one case, we could solve the problem by deleting .coot-preferences in the users home directory. But after a few days the problem came back. For another user, this didn't help at all and a third user doesn't have this problem altogether (on the same workstation using the same coot). There is also no second or stand alone coot installed which could interfere. Any hints on what we can do? My guess would be that this is the same reason as bad bonds being drawn, section 3.4 of the FAQ: http://www.biop.ox.ac.uk/coot/doc/coot-faq.html#SEC26 Paul.
Re: [COOT] Unmodeled blobs behaviour
Jan Dohnalek wrote: I have noticed that Coot puts me in irrelevant places when I use the Unmodeled blobs validation. It does its job but then the list of blobs sends me to perfectly interpreted places and I cannot see any uninterpreted blobs... I don't know why this should be, I have not seen it before. Paul.
Re: [COOT] Using RSR for ethylene glycol and building a oxidized cysteine
Craig Smith wrote: Hey gang, Hey indeed. Buenos días, in fact. I have an ethylene glycol that I trying to build into my structure. I used File - Get monomer and entered EDO and deleted the hydrogens. I can move EDO into density using rotate/translate zone but I'm having problems with RSR zone. Is there a connectivity or parameter file I need to import into COOT? How do incorporate this file(s) into REFMAC5 for refinement. That all sounds like hard work. I'd do: Extensions - Modelling - Add Other Solvent Molecules - EDO You do not need to do anything for Refmac, it should just work. I also have an cysteine that appears to be oxidized. How do I build that? Extensions - Modelling - Replace Residue - CSO (or some such). Paul.
Re: [COOT] latest coot on rhel 5 32-bit
Andreas Förster wrote: Hey cooters, I'm trying to replace my current coot (centos4 binary, version 0.6, revision 2540 with guile 1.8.7 and python 3.6.0 embedded) with a more recent binary. The OS is RHEL 5.2 to 5.4, 32-bit. I download version 0.6.2, revision 2939, python, unpack but can't start the program because of a library conflict. Error while loading shared libraries: libldap-2.2.so.7. This library is apparently provided by openldap-2.2.xx. On my machines, openldap-2.3.xx is installed, providing libldap-2.3.so.0 and the like. How to make this work? What I do in such cases, is go to the libs directory in the coot directory and do something like $ ln -s /usr/lib/libldap-2.3.so.0 libldap-2.2.so.7 It's a hack, admittedly. And why does the new coot use the old library when the old coot used to use a more recent one? I don't know off the top of my head.
[COOT] beta testers for 0.6.2
Hi Cooters, We are approaching the release of 0.6.2, which will be the last version using gtk1 and guile-gtk. I want to move on to concentrating on a project, rather than tweaking the 0.6.x series. So this is a call for beta testers to make sure that 0.6.2 is ship-shape (and I mean by that, that we need to find bugs, not missing features [1]). If you'd like to give it a go, please pick up the latest dev builds from here: http://www.biop.ox.ac.uk/coot/devel/build-info.html Thanks, Paul. [1] although of course sometimes that's a fine line.
Re: [COOT] how to set the refinement map
Seth Harris wrote: Actually I do have a map button. Hmm... I see. But I'd rather write something in a script somewhere once than click the button and confirm the click EVERY time I start the program! OK, I'm not understanding you then. If you start from fresh and you read in more than one map before refining anything, then of course Coot will not know which map to use. Understandable it seems to me. And typically one does not do that very often - certainly not every time. If you use the state script, the state script contains the setting for the refinement map. If you write your *own* script then you can easily set the refinement map as you read in your interesting mtz file: (set-imol-refinement-map (make-and-draw-map x.mtz 2FOFCWT PH2FOFCWT 0 0)) Hmmm, I had tried the (set-imol-refinement-map 1) in my .coot but obviously the problem was the map did not yet exist. indeed. So close! A monkey in the wrench... but it works beautifully if I put the (set-imol-refinement-map 1) into a coot_refinement_map.scm file and then my script adds the --script coot_refinement_map.scm option to the command line launching the program (at the end, I guess, to be sure the map is already loaded by then). That will do then? A small thing, but it felt time to get it right! It is not clear to me if you need to get it right or you have succeeded in getting it right... Paul.
Re: [COOT] beta testers for 0.6.2
Ed Pozharski wrote: 1. This does not include autobuilder bugs, right? sigh yes, I do mean autobuilder bugs too - as long as it's not about SuSe. 2. What is the bug reporting procedure - just email the list? Yes - or me, or coot-dev at ysbl dot york dot ac dot uk if you wish.
Re: [COOT] Coot 0.6.0 and sequence view
Stefan Becker wrote: recently I installed Coot 0.6.0 and had so far no problems using it. Now I wanted to use it combined with shelxl refinement but encounter the problem that the Sequence view window in the Coot 0.6.0 version doesn´t present the chains as in earlier versions. I must number chains in Coot e.g. 1001, 2001, 3001 etc. for creating the shelxl .ins file. Now the sequence view in the new Coot version positions the chains along a number line and this line stops after 3245, so that I cannot see e.g. the glycerols that are in the 3000 range and the waters that are in the 4000 range. With the older Coot versions this was not an issue. There all chains were listed in rows below each other and there was no number line. Confirmed - even in the latest 0.6.2 pre. This needs to be fixed. Thanks, Paul.
Re: [COOT] mon_lib_list.cif?
Hi Scott, Congratulations for being up to date with you pre-release version. AD, CD, GD and TD are the filenames that Refmac uses to hold restraints for Ad, Cd, Gd and Td. The PDB standard names are DA, DC, DG and TD so it is not clear to me what your custom cif files contain. Coot renames residue name to match the dictionary. I'd be very surprised indeed if Coot changed the atom names (as you said it did). The Right Way, it seems to me, to fix this, is to on-the-fly change the dictionary identifiers to the PDB standard (this is what I believe Phenix does). This update is tentatively scheduled for 0.8. For the moment though, for handling cif/dictionary/atom-naming convention problems with Coot, I recommend the remediator. If Coot is really renaming the atoms (other than the coventional hydrogen name de-mangling), I'd like to know about it of course. Paul. From: Scott Classen [sclas...@lbl.gov] Sent: 25 May 2010 19:16 To: Paul Emsley; William Scott Cc: COOT@JISCMAIL.AC.UK Subject: mon_lib_list.cif? Hi all, I just updated to 0.6.2-pre-1 (build 2965) via fink I am using the PDB v3 atom names for DNA so I copied over my custom cif files to replace: /sw/share/coot/lib/data/monomers/list/mon_lib_list.cif /sw/share/coot/lib/data/monomers/a/AD.cif /sw/share/coot/lib/data/monomers/c/CD.cif /sw/share/coot/lib/data/monomers/g/GD.cif /sw/share/coot/lib/data/monomers/t/TD.cif coot fires up OK. no complaints about the cif files, but coot is renaming my DNA atoms to version 2 atom names when it reads the PDB in.
Re: [COOT] mon_lib_list.cif?
On 26/05/10 16:01, Scott Classen wrote: If I inspect the residue by looking at residue info I see that the atom names now have * instead of ' and the phosphate oxygens are O1P O2P instead of OP1 OP2. You are right of course, I'd forgotten how much Coot munges it into to make it match the dictionary. On 02/06/10 20:23, Scott Classen wrote: Just to reiterate When coot (0.6.2-pre-1 Miramar (revision 2965) ) imports a DNA with PDB v3 atom/residue names it converts them to v2 atom/residue names... except for the C7 of Thymidine which remains C7 instead of being renamed C5M. Yes indeed - this was mentioned a short while ago on the Phenix list. I think I'll add a temporary fix to do this renaming. The right way (as Phenix does it, I believe) is to the fix the dictionary to match the model, not the other way round. Paul.
Re: [COOT] To mutate non-standard nucleic acids
Briefly, this is not the way that Coot wants you to do it. Coot wants you to Replace Residue (under modelling). Make sure that your restraints for the modified residue have the group DNA (or RNA), not monomer. Paul. From: Mailing list for users of COOT Crystallographic Software [c...@jiscmail.ac.uk] On Behalf Of Mary Varughese [elizabethvj1...@gmail.com] Sent: 02 June 2010 11:19 To: COOT@JISCMAIL.AC.UK Subject: To mutate non-standard nucleic acids We are working on modified nucleic acids. Using a pdb file of a modified nucleic acid, I want to cut and change the positions of the residues in the nucleic acid chain. I tried it with calculate-- model/fit/refine--rotate/translate zone, although we cut and place it at the correct distance no bond is forming. Is there any way i can do this?
Re: [COOT] Save Coordinates (as) ...
Dear Dirk, Miguel, Tim, Dirk Kostrewa wrote: another point for your wish list: usually, I save coordinates quite frequently during a model building session, giving always the same name for that session like myproject-coot6.pdb. Coot always asks me to select a file name and appends -coot-0 before the .pdb, which I find quite tedious. There are 3 potentially tedious things going on here: (1) coot not overwriting the input file (2) coot choosing a new file-name for saving that you don't like (3) coot giving you a dialog AFAICS, Coot will never overwrite the input file (without specific user intervention to do so) - not while I have a say about it, that is. I am prepared to compromise about (2), giving you a temporary file name that gets overwritten (which is of course, not the input file), xxx-coot-tmp-0.pdb, perhaps. As to (3), that is already done away with, using quick-save-as (Ctrl-S). This is, I think the 3rd case of implementing a feature that I doubted and resisted in the face of community pressure, but then having implemented, went on to enjoy myself - I use it many times a day. And note that (unless you tell it otherwise) coot does a back-up of the model before every modification - that is what fills the coot-backup directory. My suggestion is: offer both a Save Coordinates, with only an initial query for the output file name, and a Save Coordinates as ... option. That would offer the user to either quickly overwrite the initial output file or save the coordinates to a new output file name. I don't entirely agree with that. Or perhaps I do as long as the initial output file name is not the same as the input file name. Paul.
Re: [COOT] Too maye open files
On 16/06/10 09:57, Guillermo Carrasco wrote: Hi, I'm the system manager of a network in which we are using coot. A few days ago a user sent me a message telling that when he has been working with coot for about 3-4 hours, he get an error message like this: E: client-conf-x11.c: XOpenDisplay() failed W: core-util.c: Failed to open configuration file '/users/USERNAME/.pulse/client.conf': Too many open files W: client-conf.c: Failed to open configuration file '/etc/pulse/client.conf': Too many open files W: shm.c: Failed to read /dev/shm/: Too many open files I don't know what's happening, can anyone help me please? Thank you very much. That looks to me like a PulseAudio error. And (sad to say) as yet, Coot doesn't do sounds. I mean to say, that that error message does not look like it comes from Coot. Paul.
Re: [COOT] Failure to mount /home/emsley delays coot startup
On 23/06/10 13:26, Schubert, Carsten [PRDUS] wrote: I wonder if anyone has a solution to this problem. We are starting to run coot (0.6.2 pre) on SuSe Enterprise 10.x edition machines. The load times per session are approx 2 minutes, before coot is up and running. Hideous. But I'd mostly lay that at SLED's door, rather than Coot's. Loading with the older RedHat EL 4 machines is almost instantaneous from the same server. A bit of digging revealed that per load of coot ca 3100 lines of error messages are created in /var/log/messages dealing with the inability to find /home/emsley. It was my understanding that the use of LD_LIBRARY_PATH should trump the built-in paths (I mean that the build-in paths should not even be looked up because dynamic libraries are resolved by using LD_LIBRARY_PATH directories). It would seem that SuSe does not do that. Is there any way to get rid of these references in the pre-compiled binaries? Not that I know of (other than by editing). Where should I start digging? It's build into the libraries at a low level. We discussed a means to address this with relative paths a little while ago - that solution has yet to be explored and implemented. I suppose the easiest solution would be to create a /home/emsley and be done with it, urgh. but our IT guys won't do it unless this is the last resort. I am sympathetic that that. Any help to fix this annoyance would be greatly appreciated. You could binary edit the coot-real executable and replace directories that do not exist on your system with others that do (keeping the string length the same). It may help if I made SuSe-specific binaries - one day I'll get a SuSe box (or virtual machine). Or you could build the binaries yourself. Paul.
Re: [COOT] Help with phi psi values
Hi Mark, On 23/06/10 23:24, Dr. Mark Mayer wrote: I'd like to print out phi psi values for selected residues and would appreciate advice how to do this. Clicking on Measures/Residue Info... window brings up Chi values, but not phi/psi. Indeed - phi/psi values have been requested - they are on the TODO list - I'll add a nice coloured square too - to represent Ramachandran goodness. From the graphics window I can click on a CA atom; with dynarama window open the plot for that resiidue is highlighted green; next I click on residue in dynarama window and phi psi values are written to X11 terminal. This fails when residue is in densely populated section of rama plot, since clicking often pick up another residue; its also an inelegant way of doing this. You can zoom in/out on the Ramachandran plot with +/- keys. But basically, there is no way in Coot yet to do what you want to do. Perhaps the log files of procheck will do for you? Paul.
Re: [COOT] Key-binding for changing active map
On 29/06/10 18:06, goncalve wrote: does any one have a script file where we can add a binding key for each of the current 2foFc and FoFc maps ? ;; fix the problematic standard definition of is-difference-map? ;; (temporary hack) ;; (define (is-difference-map? imol-map) (if (not (valid-map-molecule? imol-map)) #f (= (map-is-difference-map imol-map) 1))) ;; here's the keybinding: Shift S (add-key-binding Swap Refinement Maps S (let ((local-ref-map #f)) (lambda () (let ((map-list (map-molecule-list))) (if (not local-ref-map) (if (not (null? map-list)) (begin (set! local-ref-map (car map-list)) (set-imol-refinement-map local-ref-map))) (let f ((l map-list)) (cond ((null? l) (format #t Failed to swap maps~%)) ((and (is-difference-map? local-ref-map) (not (is-difference-map? (car l (set! local-ref-map (car l)) (set-imol-refinement-map (car l))) ((and (not (is-difference-map? local-ref-map)) (is-difference-map? (car l))) (set! local-ref-map (car l)) (set-imol-refinement-map (car l))) (else (f (cdr l))
Re: [COOT] How to quit from Coot script
On 08/07/10 06:50, Ian Stokes-Rees wrote: I have just written my first Coot script, but I cannot get Coot to exit when the script completes. I have tried variations of: nothing (exit) (exit 1) (quit) (quit 1) but I always end up at the coot prompt. My script consists of about 6 lines which run just fine and output a bit to the terminal as they progress. When they finish, I am stuck with: (coot-real-exit 0)
Re: [COOT] preferences, etc. : bond thickness
On 15/07/10 09:32, Huw Jenkins wrote: I have noticed this too - I think it's because when you start coot with the command line argument '--pdb filename.pdb' the pdb is read*before* coot.py, coot-preferences.scm or ~/.coot so the bond preferences are only applied to the next pdb opened from within coot. For the record, I think that it should read the pdb files after reading .coot.py - it is not trivial to fix. Paul.
Re: [COOT] alternate conformers and ramachandran map
On 15/07/10 15:54, Ed Pozharski wrote: Are alternate conformers supposed to show up in Ramachandran map? Yes. I have a disordered loop which I modeled in two conformations and number of outliers reported magically goes down. After clicking few times on residues in the loop coot crashes but only when mouse pointer is moved over to the map dialog. I think that this is fixed in rev 3034. I am running 0.6.2. revision 3011. Hmm. Also, in this revision there is a problem with sequence dialog - the first ten residues are shifted out of the dialog on the left side. Baah - wretched fonts! Does this make it better? xset +fp /usr/share/fonts/X11/75dpi/ Paul.
Re: [COOT] application of crystallographic symmetry operators
On 04/08/10 11:50, Ingo P. Korndoerfer wrote: i was struggling with a detail yesterday and haven't really gotten anywhere (well yes, i have done it another way, now, but still think it should work as i describe below). when i click on a symmetry mate, coots shows me the symmetry operators applied to generate this one, in my case like [-X+1/2,Y+1/2,-Z (-1 -1 -1)] (or so, from memory) now i tried to use this symmetry operator to generate a new molecule. it would apply the first part, but completely ignore the second part. that is fine, since the funny translation term in () ... well ... i can see coot could possibly not handle that. but then i also tried -X-1/2,Y-1/2,-Z-1 Yes, that is exactly what you are supposed to do. and that would not make any difference. That is a bug then :-(, sorry. Yes, I can reproduce. so before trying much more, could anybody confirm to me, that really, i should be able to simply copy the symmetry operator coot shows me, when i click on a symmetry mate and use it AS IS, to GENERATE that symmetry mate, or at least confirm, that my second approach was not completely off. or, if not, would it be conceivable to have coot show exactly what i need to input to generate this mate, or vice versa, interpret it's own output correctly. or would it be conceivable, that rather then entering a symmetry operator, i would simply click on the symmetry mate that i would like to generate and it fills in the proper operator for me ? File - Save symmetry coordinates should do that You'll need to then File - Read coordinates, sightly inelegant. (I suspect that this might have been the other way) Paul.
Re: [COOT] Stand-Alone Coot - OS X : correction
On 04/08/10 02:40, William Scott wrote: Dear Coot OS X people: Yesterday I put a package on the server that wrongly installed into /Library instead of /Library/Coot If you installed it, you can either install the replacement or manually move bin, share, etc and lib into /Library/Coot (which you probably need to create). http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot#Version_0.6.2-pre-1-3072 http://sage.ucsc.edu/%7Ewgscott/xtal/wiki/index.php/Stand-Alone_Coot#Version_0.6.2-pre-1-3072 And just to encourage you to try out Bill's handywork, there is something new (eye candy?) under Display Manager - [Maps] Properties
Re: [COOT] scheme : draw C-alpha : specifying range
On 06/08/10 18:20, Lepore, Bryan wrote: i'd like to do this : (graphics-to-ca-plus-ligands-representation range ) some things i tried, with error output, are range=0-20, (unbound-variable) range=* (expecting exact integer)-means no range possible? where can i read about the syntax because it seems not the same as for (multi-read-pdb a*.pdb .) ... Sorry, Coot is just not built to do this sort of thing. There are a number of stock representation for a given molecule, I mean you can only change the style on a molecule-by-molecule basis - no sub-selection. There are additional representations (typically ball and stick for a given residue (range)). That's it. graphics-to-ca-plus-ligands-representation expect an integer - the molecule number (i.e. it is one of a limited number of representation styles for the given molecule). With my ccp4 hat on, I'd recommend ccp4mg 2.4.x for this sort of thing. Paul.
Re: [COOT] application of crystallographic symmetry operators
On 04/08/10 11:50, Ingo P. Korndoerfer wrote: when i click on a symmetry mate, coots shows me the symmetry operators applied to generate this one, in my case like [-X+1/2,Y+1/2,-Z (-1 -1 -1)] (or so, from memory) now i tried to use this symmetry operator to generate a new molecule. it would apply the first part, but completely ignore the second part. that is fine, since the funny translation term in () ... well ... i can see coot could possibly not handle that. Hi Ingo, This is now fixed in rev 3092 (I'd got the fractional and orthogonal translations mixed up :-/ ). Thanks, Paul.
Re: [COOT] scheme : draw C-alpha : specifying range
On 06/08/10 18:51, Lepore, Bryan wrote: (graphics-to-ca-plus-ligands-representation range ) Sorry, Coot is just not built to do this sort of thing. FWIW, (graphics-to-ca-plus-ligands-representation 0 ) (graphics-to-ca-plus-ligands-representation 1 ) (graphics-to-ca-plus-ligands-representation . ) (graphics-to-ca-plus-ligands-representation n ) Oh (with a bit of off-list chat) I see what you mean. You want: (define my-range (model-molecule-list)) ;; just an example, (range 1 5) is another (map graphics-to-ca-representation my-range) Paul.
Re: [COOT] scheme : ^e (C-e) equivalent?
On 06/08/10 18:57, Lepore, Bryan wrote: by the way, is there a ^e (C-e) equivalent in scheme? i.e. where does scheme get its key bindings from? I have not yet enabled user-defined control key bindings (it's on the list). Did I interpret your question correctly this time? Hmm... maybe not. Maybe you want to advance to end of line in the green scripting window? Can't be done. It would be a cool thing to have (as would command completion). Paul.
Re: [COOT] views
On 13/08/10 17:43, Lepore, Bryan wrote: was wondering how to get a view that loops, i.e. starts over. i.e. something like in vmd where you flick it and it spins indefinitely. Well, there is Draw - Spin View On/Off. That's about as close as it gets. Paul.
Re: [COOT] scheme : (toggle-idle-function) for Spin View?
On 13/08/10 19:57, Lepore, Bryan wrote: trying to see if (toggle-idle-function) will do Draw-Spin View. didn't find it in the scheme manual (June, 21 2009 ). this should be able to do in scheme, yeah? (toggle-idle-spin-function)
Re: [COOT] handling LINK records between symmetry-related atoms
On 13/08/10 22:47, Alejandro Buschiazzo wrote: Dear all, I have this protein with zinc atoms that interact with some atoms from neighbor molecules related by crystallographic symmetry. When I add the proper LINK records in the pdb (i.e. including the corresponding symmetry operators in the sym1 and sym2 fields, right justified columns 60 - 65 67 - 72), coot represents these link bonds between atoms of the same ASU..the ones linking symmetry-related atoms become of course 'very long' in some cases... am I doing something wrong? No. Short-sighted-programmer error :) is there any workaround? No. Well, not other than deleting the LINK records. I'll address it shortly. Paul.
Re: [COOT] COOT/X11 Freezes after several corrections use molprobity
On 24/08/10 08:33, Miguel Ortiz Lombardía wrote: Le 23/08/10 18:58, Joseph P. Noel a écrit : Hi All. I am running the latest release of COOT on my Mac running 10.6.4 from X11 quartz installed using Bill Scott's fink instructions. It runs fine. I have just begun using scripts generated by Molprobity or just looking through my models to make corrections based upon the drawing of probe dots. That all works fine as well. However, I have found that COOT and X11 freezes after several corrections of sites (on average I would say about 10-15 corrections). Everything freezes - screen and X11. I have to then force quite X11 to regain control of things and start fresh. I began by just using the COOT backups or saving a new set of corrected coordinates after each fix but obviously this will take quite some time to thoroughly improve a large model. I am including the recommended .coot file I found on the Molprobity site. If anyone has any suggestions on how to eliminate these freezes I would be eternally grateful! (define *probe-command* /Users/sandiegonoels/Sites/molprobity3/bin/macosx/probe) (define *reduce-command* /Users/sandiegonoels/Sites/molprobity3/bin/macosx/reduce) (set-do-probe-dots-on-rotamers-and-chis 1) (set-do-probe-dots-post-refine 1) Cheers! Joe Noel Hi, We have experienced the same problem. But we haven't found a way to reproduce the freezes consistently... If Coot freezes or crashes, that's Bill's or my responsibility. If X11 freezes or crashes it's Apples - I don't know much about that. It might help if you do *not* do either or both of these: (set-do-probe-dots-on-rotamers-and-chis 1) (set-do-probe-dots-post-refine 1) At a guess the rotamers and chis setting would be more sensitive. Don't forget to Ctrl-S for quick-save-as. Paul.
Re: [COOT] Visualize NCS operators
On 04/09/10 18:44, Florian Schmitzberger wrote: Dear All, I was wondering if there was an easy way in COOT to visualize NCS operators (e.g. 2-fold rotational axis between two NCS groups). Cheers, Florian P.S.: DM writes out NCS operators as .vu files that can be viewed in xfit. Hi Florian, Sorry for the delay. Coot has the function: (read-vu-file file-name object-name) This is not documented for some reason, I'll have to see about that. (I haven't tested this function for years). Paul.
