[COOT] Export residue density fit values to file
Dear all, Is there a way in Coot to export the Residue Density Fit values as calculated by the Validate Density fit analysis to a text file? Basically a simple output with residue number and density fit value would suffice. I've been looking into the different scripting possibilities of Coot, but being a new user, I've not been able to figure this out... Many thanks, Sander Nabuurs.
Re: [COOT] Key-binding for changing active map/molecule color
Victor Alves wrote: Hi I have looked at the reference manual and can't seem to find a way to fulfill my desire to change colors of the active map or molecule at key-press. All the commands I found use imol which means you have to know the exact number. If you're launching Refmac from within Coot, its useful that Coot changes the map and molecule colors (as it does automatically) but sometimes I don't like the chosen colors and would like to change them, just by pressing a key. So, I would like to add a key binding to set the current (active) map to a certain color and likewise do the same for the active molecule. Something like: (add-key-binding Blue Map b (lambda () (set-map-colour *_active-imol_* 51 128 178)) instead of having to use imol. Hi Victor, First, to make the new maps from Refmac be the same colours as the previous one, add to your ~/.coot file: (set-keep-map-colour-after-refmac 1) Secondly, to answer your question: (add-key-binding Blueify the Latest 2foFc Map b (lambda () (let loop ((l (reverse (map-molecule-list (cond ((null? l) 'no-map) ((= (map-is-difference-map (car l)) 0) (set-map-colour (car l) 0.1 0.5 0.68) (graphics-draw)) (else (loop (cdr l))) i.e. we have to find the value of active-imol and we do that by working backwards through the list of map molecule numbers and finding the first one that is not a difference map. Note the colour scales go from 0 to 1. Paul.
Re: [COOT] Key-binding for changing active map/molecule color
2009/2/24 Victor Alves vdal...@fmv.utl.pt: Hi I have looked at the reference manual and can't seem to find a way to fulfill my desire to change colors of the active map or molecule at key-press. All the commands I found use imol which means you have to know the exact number. If you're launching Refmac from within Coot, its useful that Coot changes the map and molecule colors (as it does automatically) but sometimes I don't like the chosen colors and would like to change them, just by pressing a key. So, I would like to add a key binding to set the current (active) map to a certain color and likewise do the same for the active molecule. Something like: (add-key-binding Blue Map b (lambda () (set-map-colour active-imol 51 128 178)) instead of having to use imol. Thank you Victor Alves This message was sent using IMP, the Internet Messaging Program. This would colour the last non-difference map: (add-key-binding Blue Map b (lambda () (let loop ((map-imol-list (reverse (map-molecule-list (if (not (null? map-imol-list)) (if (= (map-is-difference-map (car map-imol-list)) 0) (set-map-colour (car map-imol-list) 51 128 178) (loop (cdr map-imol-list)))
Re: [COOT] Key-binding for changing active map/molecule color
Dear Paul and Judit Thank you so much! Its a pleasure doing business with you :-) Victor - Victor Alves, DVM, PhD Auxilliary Professor Veterinary Medicine Faculty - UTL Lisbon, Portugal Quoting Paul Emsley paul.ems...@bioch.ox.ac.uk: Hi Victor, First, to make the new maps from Refmac be the same colours as the previous one, add to your ~/.coot file: (set-keep-map-colour-after-refmac 1) Secondly, to answer your question: (add-key-binding Blueify the Latest 2foFc Map b (lambda () (let loop ((l (reverse (map-molecule-list (cond ((null? l) 'no-map) ((= (map-is-difference-map (car l)) 0) (set-map-colour (car l) 0.1 0.5 0.68) (graphics-draw)) (else (loop (cdr l))) i.e. we have to find the value of active-imol and we do that by working backwards through the list of map molecule numbers and finding the first one that is not a difference map. Note the colour scales go from 0 to 1. Paul. Quoting Judit Debreczeni judit.debrecz...@googlemail.com: This would colour the last non-difference map: (add-key-binding Blue Map b (lambda () (let loop ((map-imol-list (reverse (map-molecule-list (if (not (null? map-imol-list)) (if (= (map-is-difference-map (car map-imol-list)) 0) (set-map-colour (car map-imol-list) 51 128 178) (loop (cdr map-imol-list))) This message was sent using IMP, the Internet Messaging Program.
[COOT] Stereo projection with Coot
Does anyone know if Coot will work with the DepthQ 3D projector (www.depthq.com) and an appropriate NVIDIA graphics card, such as the FX3700?
Re: [COOT] Stereo projection with Coot
Yep it does. On linux there may be issues, because the drivers may or may not support swap-eyes. The problem is that the images are out of sync with the glasses, or to be more precise, the left image is displayed when the right shutter on the glasses is open. That was the case with the version we are having, not sure if the latest projector is better. This is not a problem if the app allows you to swap eyes, like Pymol. I don't think coot has that capability (yet?) HTH Carsten -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:c...@jiscmail.ac.uk]on Behalf Of Evan Kantrowitz Sent: Wednesday, February 25, 2009 1:37 PM To: COOT@JISCMAIL.AC.UK Subject: [COOT] Stereo projection with Coot Does anyone know if Coot will work with the DepthQ 3D projector (www.depthq.com) and an appropriate NVIDIA graphics card, such as the FX3700?
Re: [COOT] Stereo projection with Coot
Schubert, Carsten [PRDUS] wrote: Yep it does. On linux there may be issues, because the drivers may or may not support swap-eyes. The problem is that the images are out of sync with the glasses, or to be more precise, the left image is displayed when the right shutter on the glasses is open. That was the case with the version we are having, not sure if the latest projector is better. This is not a problem if the app allows you to swap eyes, like Pymol. I don't think coot has that capability (yet?) I don't really understand - do you mean simply that the object is back to front? (ie. the front clipping plane is at the back?) If so I would try: (set-hardware-stereo-angle-factor -1.2) (something negative anyway). Paul.
Re: [COOT] python or scheme?
Markus Dehnhardt wrote: Dear cooters, I am new to coot, but I have already discovered how powerful extensions and key bindings can be. My question is quite simple: if I want to generate my own extension or keybinding, which scripting language is better suited? I am not very familiar with either but willing to experiment. There were similar questions already on this mailing list but there are a couple of things that are not clear to me: Some of the documentation is for python some for scheme: the scripting interface is python and the reference manual is scheme. Are all functions awailable for both? Or does one have any advantage over the other? Sigh... Well, you are not the first person to be confused by this. The state of the scripting documentation has been reported as problematic for a while. I don't know what do to about it that does not involved a lot of work. Yes, the User Manual is mostly written with schemey examples. The reference manual I have not looked at for years :-/, the scripting interface page is also automatically generated and provides an interface from a C-programmers point of view - which is very like that for Python. I use often this quite often. The scripting interface for functions written in scheme/python should equivalent access to functions that do the same thing. The syntax of the function calls can be readily converted between scheme and python. There are notes available on how to do this. The functions that we saw today, for example, could have equally well have been written in python. What is other users preference: python or scheme, and why? For those who are not influenced by me, python I'd say. And they chose python because it is more readily picked up for those with an imperative or object-oriented mind-set. Like the dolphins, I'd choose scheme for exactly the same reasons. How often do people, other than developers, create extensions? Hard to say, but my feeling is not often enough. And that is, I suppose, is due to the poor state of the scripting/extension documentation. That and the fact that it takes an investment of time to learn the scripting language, the Coot extensions API and the GUI toolkit. And finally to the scheme scripters: how did you learn scheme? The Little Schemer and Ken Dybvig's The Scheme Programming Language. To answer your question: python or scheme? Yes! We provide the best 2 languages so that you have the choice. How to choose? Read The Little Schemer - if you think it is delightful and stimulating, use sheme. If you think it is hateful, irrelevant and full of irritating silly parentheses, use python. HTH, Paul.
Re: [COOT] python or scheme?
2009/2/25 Frank von Delft frank.vonde...@sgc.ox.ac.uk: I'm totally not with Paul on this one (is scheme object-oriented???), and eternally grateful to him and Bernhard for implementing python scripting. I think that the point was that scheme is not imperative and not particularly object-oriented (but allows both). Once you understand how python fits, it's spectacularly powerful. If you want a list of all commands available in the python interpreter -- some native python, some from the scripting -- you can run the following in the python script window: import inspect; inspect.currentframe().f_globals.keys() It doesn't tell you what the functions do or the arguments are (it's possible in theory, haven't figured it out yet though), but it's a start. You can do that in scheme too (in the scheme scripting window): (apropos-internal ) It will be a rather long list, but it will give you a hint what to google for. Another couple of hints: - there is no command completion in the scheme scripting window, there is in python - wincoot doesn't do scheme, but does python. - you can't do all gtk2 things from scheme (as coot doesn't come with guile-gnome), there's no such limitation in python. Hopefully one day there will be no such differences...? But I feel that these shouldn't put anyone off. Scheme is still fun and well worth picking up. J.
[COOT] OS X coot-0.6-pre-1-revision-1876 - minor bug
I just upgraded via fink and now in the Display Manager I am unable to chose which map to bind to the scroll wheel. I can properly bind using the HID--ScrollWheel--Attach scroll wheel to which map? pulldown, but not from the radio button in the Display Manager window. Thanks, Scott
