Dear Kara,
It should not be that hard. What kind of a library file do u have that
xleap recognizes these structures? Are the .lib file or .prep file? I
would change all of the 'old' residue naming (which is UNK) to a new one,
and save the file. And when u load those structures in xleap again, they
will be seen in the new residue names.
For instance, I just saved the residue 'RG' in a .lib file format. In all
entry lines, u will see the name of the residue in it, such as;
!!index array str
"RG"
!entry.RG.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
"P" "P" 0 1 131072 1 15 1.166200
"O1P" "O2" 0 1 131072 2 8 -0.776000
"O2P" "O2" 0 1 131072 3 8 -0.776000
.
.
.
"HO'2" "HO" 0 1 131072 33 1 0.418600
"O3'" "OS" 0 1 131072 34 8 -0.524600
!entry.RG.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
"P" "P" 0 -1 0.0
"O1P" "O2" 0 -1 0.0
"O2P" "O2" 0 -1 0.0
.
.
.
"HO'2" "HO" 0 1 131072 33 1 0.418600
"O3'" "OS" 0 1 131072 34 8 -0.524600
!entry.RG.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
"P" "P" 0 -1 0.0
"O1P" "O2" 0 -1 0.0
"O2P" "O2" 0 -1 0.0
.
.
.
So, changing all these 'RG's into a new residue will change the name of
this residue.
If the file is in .prep format, it will look like the following:
0 0 0
leap-generated prep residue
RG.res
RG INT 0
CHANGE NOMIT DU BEG
0.00000
.
.
.
Again, changing the word 'RG' to a new file will change the residue name
for this structure.
Good luck,
On Fri, 17 Feb 2006, Kara Di Giorgio wrote:
> I've created two different residues in the past and they were both
> called UNK. I didn't think about it as they were not used at the same
> time. However, now I DO want to use them as part of the same
> simulation. How would I change the name of one of them in such a way
> that xLeap recognizes them as different. I've tried re-naming things
> in the past, but the original name seemed to stay as part of it. Was I
> incorrect? How would you suggest going about this? (Just re-creating
> one of the residues as something other than UNK isn't an easy option as
> they were difficult to set up in the past.)
>
> Any help would be greatly appreciated.
>
> Thanks,
>
> Kara Di Giorgio
> University of the Pacific
>
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>
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sun Feb 19 2006 - 06:10:22 PST
