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]>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]>> wrote: >> >> ________________________________________ >> From: Mailing list for users of COOT Crystallographic Software >> [[email protected] <mailto:[email protected]>] On Behalf Of >> Scott Horowitz [[email protected] <mailto:[email protected]>] >> >> Sent: 10 October 2010 15:59 >> To: [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] >
