Re: [COOT] coot read-only switch
-- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: 07 November 2014 10:13 To: COOT@JISCMAIL.AC.UK Subject: [COOT] coot read-only switch Hello, does Coot have a 'read-only' command line option, i.e. so that it does not modify anything in the current directory? I often just want to look at a PDB-file and would prefer not to end up with coot-backup and all the other files. While these are not exactly what you are after, these may be of some help: 1. the backup dir can be set to be any directory, e.g. /tmp/, so that it doesn't fill the working dir with its droppings, by setting the relevant environment variable: https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Environment-Variables 2. backups can be switched off completely: https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Backup-Functions The options listed with 'coot --help' don't seem to list one of such kind. Regards, Tim -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [COOT] Add other solvent molecules setting
Yes, it can be added to the .coot file like this: (append! *solvent-ligand-list* (list TRS)) or like this for multiple molecules: (append! *solvent-ligand-list* (list TRS XXX YYY)) -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Ulrich Gohlke Sent: 14 February 2013 10:48 To: COOT@JISCMAIL.AC.UK Subject: [COOT] Add other solvent molecules setting Dear crystalleagues, in Extensions - Modelling - Add Other Solvent Molecules..., is there a way to add common compounds such as TRS to the pre-selected molecules permanently, i.e. one doesn't have to Add a new Residue Type every time Coot is started? Can this be added to the .coot file or something? Cheers, Uli --- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.de http://www.mdc- berlin.de/en/research/research_teams/macromolecular_structure_and_inter action/
Re: [COOT] refine/improve Rama
-- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Ed Pozharski Sent: 16 September 2011 18:25 To: COOT@JISCMAIL.AC.UK Subject: [COOT] refine/improve Rama Is there some way to do the Refine/Improve Ramachandran plot not on the whole molecule? The underlying command stepped-refine-protein-for-rama doesn't seem to have any other options but the imol, so obviously no luck. I also tried set-refine-ramachandran-angles 1 which, afaiu, should turn Ramachandran restraints on, but I don't see any difference (in fact, when I refine a zone the residues move away from allowed angles). I thought that this could be combined with stepped-refine-protein, but that one would also tackle the whole thing, and one cannot narrow its action to a zone. I could, of course, delete the elements I don't want refined and later reinsert them. Another workaround (maybe) is to fix the atoms I don't want to move (in which case it'd be totally awesome if one could fix all the atoms in a zone at once - is this possible?). So, perhaps a future version may allow for all of these operations (e.g fit-protein, stepped-refine-protein, stepped-refine-protein-for-rama) tp be applied to a zone? Please? Having to refine a couple of large low resolution beasts right now, I sympathise with your distress. I am not sure if this is of any help, but a naive solution could be: --- (define (stepped-rama-refine-zone imol chain-id res-start res-end) (make-backup imol) (let ((current-backup-state (backup-state imol)) (current-replacement-state (refinement-immediate-replacement-state)) (current-rama-state (refine-ramachandran-angles-state)) (imol-map (imol-refinement-map))) (turn-off-backup imol) (set-refine-ramachandran-angles 1) (set-refinement-immediate-replacement 1) (set-go-to-atom-molecule imol) (if (valid-map-molecule? imol-map) (map (lambda (residue) (set-go-to-atom-chain-residue-atom-name chain-id residue CA) (refine-auto-range imol chain-id residue ) (rotate-y-scene 25 0.3) (accept-regularizement)) (number-list res-start res-end)) (format #t No valid refinement map.~%)) (if (= current-replacement-state 0) (set-refinement-immediate-replacement 0)) (if (= current-backup-state 1) (turn-on-backup imol)) (if (= current-rama-state 0) (set-refine-ramachandran-angles 0 --- What might also help is to turn on the secondary structure restraints and set the refinement matrix to low -- they seem more powerful than rama restraints to me. And if I am allowed a couple of feature requests along similar lines: 1. automatic detection of secondary structure restraints to be used -- coot knows about secondary structure elements (it can e.g. colour the chain according to those), it might as well use that knowledge to automatically restrain the main chain torsions. (I admit I quite often forget to change helix to strand or vice versa as I walk along the chain.) 2. stepped refine to work on nucleic acids 3. nucleic acid main chain torsion and ring pucker restraints PS. Well, I was told long time ago that restraining Ramachandran angles is a BAD idea because they should only be used for validation. But this is 3A data. Well, more recently, we were asked what we would pick if we had the choice: better models or perfect validation tools...
Re: [COOT] python commands for showing / hiding a molecule
http://biop.ox.ac.uk/coot/doc/coot.html#set_002dmol_002ddisplayed Pythonic: set_mol_displayed(imol, state) state is 1 for display and 0 for hide. set_mol_active(imol, state) might also be useful in the same context. -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of R.D. Oeffner Sent: 17 June 2011 12:20 To: COOT@JISCMAIL.AC.UK Subject: [COOT] python commands for showing / hiding a molecule Dear all, I'm sure there is an embarrasingly simple answer to this question but does anybody know how to show and hide a molecule programmatically from a python script run by Coot? I can easily load a molecule with the read_pdb(filename) command. But the Display Manager doesn't tell what command Coot is doing under the hood for hiding or showing the molecule. Many thanks, Rob -- Robert Oeffner, Ph.D. Research Associate Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162
Re: [COOT] change names of maps?
http://www.biop.ox.ac.uk/coot/doc/coot.html#set_002dmolecule_002dname Works for maps too. JED. -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:c...@jiscmail.ac.uk] On Behalf Of Francis E Reyes Sent: 26 October 2010 16:49 To: COOT@JISCMAIL.AC.UK Subject: [COOT] change names of maps? Hi All maybe a feature request or maybe it's already implemented. Can we change the names of loaded maps to whatever we want? I tried to do it under display manager but it wouldn't let me. Running Coot 0.6.2-pre (rev 3186). F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [COOT] Coot, delete a chain
How about this: 1. click on the bin in the toolbar and select Delete zone 2. go to the first residue in the chain (in the Go to atom window or with ^g), click on the residue 3. similarly, go to the last one and click that - Coot should delete the chain (it will take a while...) It that seems a little fiddly, try this: --- (define (delete-chain imol chain-id) (if (and (string? chain-id) and (number? imol)) (let* ((n-res (chain-n-residues chain-id imol)) (start (seqnum-from-serial-number imol chain-id 0)) (end (seqnum-from-serial-number imol chain-id (- n-res 1 (delete-residue-range imol chain-id start end --- where imol is the molecule number and chain-id is the chain you want to delete. using it like e.g.: (delete-chain 0 A) JED. How nice would it be to be able to delete chains/residues in the go to atom window... or renumber residues and change chain IDs and copy fragments by simple drag-and-drop... sigh. -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:c...@jiscmail.ac.uk] On Behalf Of Maia Cherney Sent: 31 January 2010 20:07 To: COOT@JISCMAIL.AC.UK Subject: Re: [COOT] Coot, delete a chain Hi all, Is there a way to delete the whole chain of a complex? Or all solvent atoms at once? Maia
Re: [COOT] Stepped version of sphere refine?
Recently, someone (I'm sorry, I can't recall who, and I couldn't find the post in question) posted a extremely useful scheme script to refine residues in a sphere centered around the active residue. That was Paul. (Who else? ;-) ) I was wondering if anyone knows of a way to alter the script (reproduced below) from a key binding to a scheme function, such that it can then be called with 'stepped-refine-protein-with-refine-func'? If no one got back to you on this one in the meantime, you might try something like the following quick-and-dirty approach: --- (define (stepped-sphere-refine imol) (let ((imol-map (imol-refinement-map))) (if (not (valid-map-molecule? imol-map)) (info-dialog Oops, must set map to refine to) (let ((current-steps/frame (dragged-refinement-steps-per-frame)) (refine-func (lambda (chain-id res-no) (set-go-to-atom-chain-residue-atom-name chain-id res-no CA) (let ((active-atom (active-residue))) (if (not (list? active-atom)) (format #t No active atom~%) (let* ((centred-residue (list-head (cdr active-atom) 3)) (other-residues (residues-near-residue imol centred-residue 4)) (all-residues (if (list? other-residues) (cons centred-residue other-residues) (list centred-residue (format #t imol: ~s residues: ~s~% imol all-residues) (refine-residues imol all-residues) (accept-regularizement) (rotate-y-scene 30 0.6))) (set-dragged-refinement-steps-per-frame 100) (stepped-refine-protein-with-refine-func imol refine-func 1) (set-dragged-refinement-steps-per-frame current-steps/frame) --- JED -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
Re: [COOT] Dropping Gtk1 version [was Re: overlapping buttons in molprobity check script]
Is there any particular reason to hang onto the gtk1 port? Seems like all it does is generate bug reports. Indeed. Is there anyone who needs the GTK1 version? (And if so, why?) Thanks, AFAIR Redhat 8 (which is without gtk2) is still used in a number of labs (and esp. industry - Judith, Tardeusz?!), B Indeed. In general, I have the impression that redhat 8 bins can come quite handy when a more appropriate build is not available: mostly for fossil and misbehaving RHEL systems, but for those too where the plug's been pulled on the build machine (e.g. F8) etc. I understand that gtk2 versions have more functionality but there are a few of us out there who'd still like to have access to regular redhat 8 builds for the above reasons or for troubleshooting. It feels somewhat unfair to say that gtk1 bins only generate bug reports -- gtk2 do too for that matter, perhaps a different set... but that deserves another post... JED -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
[COOT] get-monomer crash
A bit related to the thread about dropping gtk1 versions: has anyone experienced this and perhaps could provide a fix/explanation? Symptoms: (get-monomer three-letter-code) makes gtk2 (!) centos-4 coot crash on RHEL4, e.g. with GOL: --- (monomer-molecule-from-3-let-code GOL ) throw from within critical section. /xtal/work/JED/coot/coot-Linux-i386-centos-4-gtk2/bin/coot: line 124: 23850 Aborted $coot_real $* coot-exe: /xtal/work/JED/coot/coot-Linux-i386-centos-4-gtk2/bin/coot-real coot-version: /xtal/work/JED/coot/coot-Linux-i386-centos-4-gtk2/bin/coot-real core: #f No core file found. No debugging --- Interestingly, get_monomer(three_letter_code) is fine, so is get-monomer in gtk1 redhat-8 coot, same machine, same circumstances. It gets more confusing: even though get-monomer fails, I can get away with replacing get-monomer with (monomer-molecule-from-3-letter-code three-letter-code ) in my scripts and extensions. The only thing I can think of is that this is a guile-issue, as centos-4 builds come with guile 1.8.5 while redhat builds have guile 1.6.8. Plus, I haven't come across anything that would give the above error message, other than libguile's throw. What do guile-experts say about this? I can't get my head around the difference between monomer-molecule-from-3-letter-code and get-monomer. Aren't they supposed to be one and the same thing? Why not use monomer-molecule-from-3-letter-code only? thanks, JED -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
Re: [COOT] problem in loading icons
I was wondering if anybody observed this before. When I start coot I get this messages (a long list of errors for the whole content of the folder /sw/share/coot/pixmaps/): Error loading icon: Couldn't recognize the image file format for file '/sw/share/coot/pixmaps/add-alt-conf.svg' Well, it is probably not more than a shallow consolation to know that it does happen on certain RHEL4 machines using centos builds as well... so you are not alone asking this question. JED -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and confidential and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
Re: [COOT] Coot 0.5 and colours
To answer your question then, there is no way in 0.5 to turn back to the old behaviour. It might be possible in new versions to enable this, but currently I am against the idea. Running the file through pdbset solves the missing element identifier problem -- not elegant, but quick and easy. Running the remediator script from the Richardson lab is a good solution too for other pdb version related issues (e.g. when 0.5 coot draws bonds between vicinal H atoms with old-style names): http://kinemage.biochem.duke.edu/software/remediator.php Another remark on colours in 0.5: redhat8 (non-pythonic) binaries on RHEL4 seem to have lost colours -- the model/fit/refine window, scripting window etc are all grey. JED
