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))))))
