Hi Balaji,
Balaji Bhyravbhatla wrote:
> Hello All,
> I have a couple of clarifications on using COOT.
>
> (1) when using the refmac refinement without ligand, all is well. But
> as soon as I add the ligand to the model I cannot run refmac properly.
> It comes back with an error about ligand being present. I have read a
> parameter file generated via the PRODRG server, which was labelled for
> REFMAC. I can do RSR in COOT after I read it so I know that it has
> been read properly. Any suggestions about my mistake would be welcome.
>
You also need to read in your cif file for your ligand, then Refmac
won't complain - unless there's something wrong with the naming scheme.
But if you generated your ligand with PRODRG you also have the precise
description of it as cif file. Assuming you're running Refmac within
Coot. If you run Refmac via the GUI or per script you should add in the
command LIBIN followed by the name of your cif file.
>
> (2) when adding terminal residues, i still have not found a way to
> place the residue properly. The program hints that if it fails once
> that we should try it again. But no matter how many times I have tried
> over the months I have not been able to get the terminal residue to
> show up in the right place. I am not looking for the best fit but at
> least in the right place would be nice! The residue shows up in all
> odd places, even when the density is clear.
>
Into which map are you fitting ? Check that, perhaps that 's the reason
why it misplaces you terminal residue. Usually it works pretty good for
reasonable density. You can assign the map by Calculate/Model Fit
Refine/ Select Map
> (3) I have not been able to adjust the "undo" command to go back one
> step only. Is there a way? For example, I fit a loop using the
> program, after my initial manual fitting, and did not realize that if
> I do not give a sequence COOT will replace all the residues with
> ALA's. Alas, an hours worth of work was wasted because of that and
> when I hit "undo" it took me a whole lot of steps back.
>
You can also mutate the whole subunit by mutate residue range pasting
the corresponding sequence and redo your lost work. In theory there
should have been a gziped file under coot-backup/ with the changes you
made before fitting the loop. Every single step is safed there, so you
should be able to retrieve your lost data instantenously by ungzipping
the correct file and start from there again.
Hope that helps,
Jürgen
> Thanks
>
> Balaji
>
>
>
>
--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
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