Re: [ccp4bb] about coot
Dear Paul, Thanks for your reply. Because I have some code in ~/.coot related to the graphic, when I ran coot in --no-graphic mode, coot would crash. If I delete the ~/.coot file, coot will be ok at no-graphic mode. Another question: Many functions in coot, such as refine-zone or refine-auto-range, have a parameter called altconf, which is a string, but what's the meaning and function of altconf? Does it mean alternative conformation? And what kind of string will be used as correct argument in these functions? Thanks for your help. Best wishes, Q. Cai On 11/23/2012 07:32 PM, Paul Emsley wrote: On 23/11/12 08:54, Qixu Cai wrote: I have some problems about coot. 1, How to run the Extensions -- All molecule -- Stepped refine at no-graphic mode of coot? (let ((imol (read-pdb coot-download/3rso.pdb)) (imol-map (make-and-draw-map coot-download/r3rso-refmac.mtz FWT PHWT 0 0))) (map (lambda (chain) (fit-chain imol chain)) (chain-ids imol))) 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? All and more, I think. They are in coot-top-dir/share/coot/python 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that?
Re: [ccp4bb] about coot
On 23/11/12 11:40, Armando Albert wrote: Dear Paul, 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that? You may want to open a different session in the same directory and not spoil the one you are using for refinement If you want to prevent the reading of the state script in the current directory use --no-state-script Paul.
Re: [ccp4bb] about coot
On 25/11/12 11:53, Qixu Cai wrote: Dear Paul, Thanks for your reply. Because I have some code in ~/.coot related to the graphic, when I ran coot in --no-graphic mode, coot would crash. fail with an error message I hope you mean. If I delete the ~/.coot file, coot will be ok at no-graphic mode. Yes, that can happen if you do not protect gui code. Another question: Many functions in coot, such as refine-zone or refine-auto-range, have a parameter called altconf, which is a string, but what's the meaning and function of altconf? Does it mean alternative conformation? Yes. And what kind of string will be used as correct argument in these functions? , A or B, typically. Paul.
Re: [ccp4bb] about coot
Dear Paul, Sorry to bother you again. In the scheme script you provided, it seems that the imol-refinement-map is not set. Is it necessary to add this code: (set-imol-refinement-map imol-map) to the script? Thanks for your reply. Best wishes, Q. Cai On 11/23/2012 07:32 PM, Paul Emsley wrote: On 23/11/12 08:54, Qixu Cai wrote: I have some problems about coot. 1, How to run the Extensions -- All molecule -- Stepped refine at no-graphic mode of coot? (let ((imol (read-pdb coot-download/3rso.pdb)) (imol-map (make-and-draw-map coot-download/r3rso-refmac.mtz FWT PHWT 0 0))) (map (lambda (chain) (fit-chain imol chain)) (chain-ids imol))) 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? All and more, I think. They are in coot-top-dir/share/coot/python 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that?
[ccp4bb] about coot
Dear all, I have some problems about coot. 1, How to run the Extensions -- All molecule -- Stepped refine at no-graphic mode of coot? 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? 2, And is there any option to prevent coot auto-loading ~/.coot file? Thank you very much for your help! Q. Cai
Re: [ccp4bb] about coot
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Q. Cai, ad 1) maybe Paul knows better, but 'stepped refine' sounds to me like coot refines step by step and displays the steps inbetween, which means that the combination with no-graphic mode makes little sense, doesn't it? You can run refmac5 directly from a script instead. ad 2) the scripts are located in coot/wheezy/share/coot/[python|scheme] relative to your coot installation directory unless you tell coot otherwise with your personal setup ad 3) you can remove or rename that file Cheers, Tim On 11/23/2012 09:54 AM, Qixu Cai wrote: Dear all, I have some problems about coot. 1, How to run the Extensions -- All molecule -- Stepped refine at no-graphic mode of coot? 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? 2, And is there any option to prevent coot auto-loading ~/.coot file? Thank you very much for your help! Q. Cai - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQr081UxlJ7aRr7hoRAvdsAJ9WQzLd736L37mW6ebd7PmticL8CwCeI/DS 7FQzwGMbz1G9LXBNsiCpVjo= =R8Xt -END PGP SIGNATURE-
Re: [ccp4bb] about coot
On 23/11/12 08:54, Qixu Cai wrote: I have some problems about coot. 1, How to run the Extensions -- All molecule -- Stepped refine at no-graphic mode of coot? (let ((imol (read-pdb coot-download/3rso.pdb)) (imol-map (make-and-draw-map coot-download/r3rso-refmac.mtz FWT PHWT 0 0))) (map (lambda (chain) (fit-chain imol chain)) (chain-ids imol))) 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? All and more, I think. They are in coot-top-dir/share/coot/python 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that?
Re: [ccp4bb] about coot
Dear Paul, 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that? You may want to open a different session in the same directory and not spoil the one you are using for refinement Armando I am out of the lab El 23/11/2012, a las 12:32, Paul Emsley pems...@mrc-lmb.cam.ac.uk escribió: On 23/11/12 08:54, Qixu Cai wrote: I have some problems about coot. 1, How to run the Extensions -- All molecule -- Stepped refine at no-graphic mode of coot? (let ((imol (read-pdb coot-download/3rso.pdb)) (imol-map (make-and-draw-map coot-download/r3rso-refmac.mtz FWT PHWT 0 0))) (map (lambda (chain) (fit-chain imol chain)) (chain-ids imol))) 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? All and more, I think. They are in coot-top-dir/share/coot/python 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that?
