Re: [COOT] problem loading smiles
Hello Marian, On 12/02/13 16:58, Marian Oliva wrote: Sorry to bother you with this question but I´m having some troubles when loading smiles of new synthesize ligands for fitting. First I was using an older version of Coot and after File=smiles, an error message showed up (related to ccp4 libcheck connection). Apparently this happens when ccp4 is not installed on the computer (or so I've read after google it), I'm sorry that you had to google it. Coot should do a better job about informing you about what it needs installed - it can do it - it does it elsewhere, so there's no excuse. I've noted that a fix is required before the next release. what's a bit puzzling since ccp4 is already installed in my computer (Mac OS Lion 10.7.5) …. As I'm not an expert on computers I though this could be some kind of bug due to Lion (??) … Left hand doesn't know what the right is doing :-( I am used to starting applications from the terminal. I understand that Mac users often like icons. Anyway, I realized that there is a new version of coot (v0.7.0) and hoping this version has fixed this ghost bug, I downloaded it and installed from ccp4 coot-0.7.0-i386.dmg. Now, after File=smile, nothing happens ... and I mean nothing. Coot stays still as if I wouldn't click any button and there is no error/warning message that gives you a tip about what's the problem (but the window to paste the smile never pop-up). Sounds bad. Where did you get your Coot? From CCP4? I´m new with coot and the ligand fitting tool and I open Coot by double clicking on the Applications icon Ah! question answered... or from Phenix. Oh - OK, in that case you should use Phenix tools underneath Coot. I'll speak with Phenix people and make that happen. Maybe using scripting would avoid this problems but I´m not good at it …. yet (I'm working on it) Standard usage such as you describe should not need it. Sorry. I really would really appreciate any help/suggestion you can give me I'm not sure that I've been much help. Truth is that I don't use that code path - and haven't done for a long time. If you are starting with a SMILES string I'd recommend using Bill Scott's (latest) binary and using that, your code path goes via the 2d layout and from there uses cprodrg (for the moment). Here a bit of helpful script - put it in ~/.coot-preferences Paul. (if (defined? 'coot-main-menubar) (let ((menu (coot-menubar-menu Ligand))) (add-simple-coot-menu-menuitem menu SMILES - 2D (lambda () (generic-single-entry SMILES string Send to 2D Viewer (lambda (text) (smiles-to-ligand-builder text) (add-simple-coot-menu-menuitem menu Residue - 2D (lambda () (using-active-atom (residue-to-ligand-builder aa-imol aa-chain-id aa-res-no aa-ins-code 0.015))
Re: [COOT] problem loading smiles
On Fri, Feb 15, 2013 at 5:24 AM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote: Anyway, I realized that there is a new version of coot (v0.7.0) and hoping this version has fixed this ghost bug, I downloaded it and installed from ccp4 coot-0.7.0-i386.dmg. Now, after File=smile, nothing happens ... and I mean nothing. Coot stays still as if I wouldn't click any button and there is no error/warning message that gives you a tip about what's the problem (but the window to paste the smile never pop-up). Sounds bad. Where did you get your Coot? From CCP4? FYI, this sounds like the problem I see with the Python scripting menu item - absolutely nothing happens. I'm using the version distributed by CCP4. or from Phenix. Oh - OK, in that case you should use Phenix tools underneath Coot. I'll speak with Phenix people and make that happen. I may be misunderstanding - is it possible that the Phenix plugin is breaking Coot? We haven't seen this happen before, but that doesn't mean it can't ever happen... -Nat
Re: [COOT] problem loading smiles
On 15/02/13 15:11, Nat Echols wrote: On Fri, Feb 15, 2013 at 5:24 AM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote: Anyway, I realized that there is a new version of coot (v0.7.0) and hoping this version has fixed this ghost bug, I downloaded it and installed from ccp4 coot-0.7.0-i386.dmg. Now, after File=smile, nothing happens ... and I mean nothing. Coot stays still as if I wouldn't click any button and there is no error/warning message that gives you a tip about what's the problem (but the window to paste the smile never pop-up). Sounds bad. Where did you get your Coot? From CCP4? FYI, this sounds like the problem I see with the Python scripting menu item - absolutely nothing happens. I'm using the version distributed by CCP4. I support Bill Scott's binaries. or from Phenix. Oh - OK, in that case you should use Phenix tools underneath Coot. I'll speak with Phenix people and make that happen. I may be misunderstanding - is it possible that the Phenix plugin is breaking Coot? We haven't seen this happen before, but that doesn't mean it can't ever happen... Possibly. Depends on what you are doing :). Are you intercepting new_molecule_by_smiles_string() and replacing it with your own function? Cool! Paul.
[COOT] problem loading smiles
Sorry to bother you with this question but I´m having some troubles when loading smiles of new synthesize ligands for fitting. First I was using an older version of Coot and after File=smiles, an error message showed up (related to ccp4 libcheck connection). Apparently this happens when ccp4 is not installed on the computer (or so I've read after google it), what's a bit puzzling since ccp4 is already installed in my computer (Mac OS Lion 10.7.5) …. As I'm not an expert on computers I though this could be some kind of bug due to Lion (??) … Anyway, I realized that there is a new version of coot (v0.7.0) and hoping this version has fixed this ghost bug, I downloaded it and installed from ccp4 coot-0.7.0-i386.dmg. Now, after File=smile, nothing happens ... and I mean nothing. Coot stays still as if I wouldn't click any button and there is no error/warning message that gives you a tip about what's the problem (but the window to paste the smile never pop-up). I´m new with coot and the ligand fitting tool and I open Coot by double clicking on the Applications icon or from Phenix. Maybe using scripting would avoid this problems but I´m not good at it …. yet (I'm working on it) I really would really appreciate any help/suggestion you can give me Thx Marian
