I just tried using the new coot_utils.py, but now most of the extensions menu actually won't show up at all, including the replace residue menu item.
If this is going to be difficult to figure out, is there a version I could go back to that might have this function intact? Thanks, Scott On Sun, Oct 10, 2010 at 5:22 PM, Paul Emsley <[email protected]>wrote: > At a guess, update coot_utils.py from the same place. > > Paul. > > > Scott Horowitz wrote: > >> Hi again, >> >> I tried the new extensions.py, but it still doesn't work, and now I get a >> different error instead: >> >> File: "C:\WinCoot\share\coot\python\extensions.py", line 581, in <lambda> >> TypeError: using_active_atom() takes exactly 1 argument (5 given) >> >> Any help on how to fix this problem would be greatly appreciated. >> >> Thanks again, >> Scott >> >> On Sun, Oct 10, 2010 at 4:17 PM, Bernhard Lohkamp >> <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> Mea culpa, >> >> I reworked using_active_atom and forgot to update some calls to it. >> >> FIX: >> >> replace extensions.py (in YourWincootDirectory\share\coot\python\) >> with the following >> >> >> http://code.google.com/p/coot/source/browse/branches/release-0.6.2/python/extensions.py >> >> or wait for a build revision 3211 or newer. >> >> B >> >> Thanks for the quick reply- I tried the replace residue box as >> well, but >> it didn't work for me either. After checking that the >> restraint did >> read L-peptide under group, the standard, unmutated amino acid >> remained >> on-screen after hitting the mutate button. Here's what it >> says at the >> bottom of the coot dos box at when I try to do this: >> >> File "C:\WinCoot\share\coot\python\coot_utils.py, line 103, in >> using_active_atom >> for <func, aa_args, extra_args> in funcs: >> TypeError: an integer is required. >> >> Any ideas on how to fix this would be greatly appreciated. >> >> Thanks, >> Scott >> >> >> On Sun, Oct 10, 2010 at 11:58 AM, Paul Emsley >> <[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>> wrote: >> >> ________________________________________ >> From: Mailing list for users of COOT Crystallographic Software >> [[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>] On >> >> Behalf Of >> Scott Horowitz [[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> >> <mailto:[email protected]>>] >> >> Sent: 10 October 2010 15:59 >> To: [email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> >> >> Subject: mutate to unnatural amino acid >> >> >> I'm trying to solve a structure with an unnatural amino >> acid not in >> the coot or ccp4 libraries, and I'd like to be able to mutate a >> preliminary structure to have this amino acid for further >> refinement. I successfully created a .cif file using >> libcheck and >> sketcher in CCP4 (specified when created to be an >> L-peptide), and by >> converting this to a SMILES file, was able to load it into >> coot and >> see it on the screen. I am also able to directly import >> the residue >> by clicking "import cif dictionary", and importing the >> files created >> using libcheck and sketcher. The following things are true >> either >> way I import the residue: In coot, when i go to edit >> restraints, it >> recognizes the residue, and I can make changes; however, >> when I open >> the simple mutate window, the unnatural amino acid I have >> imported >> does not show up. Is there another way to do this? >> >> ----- >> >> Yes , if you have a non-standard residue/monomer, you need >> to use >> Extensions -> Modelling -> Replace Residue... >> >> Section 5.17.3 in the Manual. >> >> Paul >> (from wretched Microsoft web mail) >> >> >> >> >> -- *************************************************** >> >> Dr. Bernhard Lohkamp >> Assistant Professor >> Div. Molecular Structural Biology >> Dept. of Medical Biochemistry and Biophysics (MBB) >> Karolinska Institutet >> S-17177 Stockholm >> Sweden >> >> phone: (+46) 08-52487651 >> fax: (+46) 08-327626 >> email: [email protected] <mailto:[email protected]> >> >> >> >
