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Here it is, step-by-step:<br>
<br>
1) Create a PDB file with FUC, GAL, GLA (copy-paste from your email),
zz.pdb, renumber residues (just to look nice);<br>
<br>
2) Run <br>
<br>
phenix.refine --show_defaults=all > params<br>
<br>
and edit "params" file to define custom bonds;<br>
<br>
3) Run <br>
<br>
phenix.ready_set zz.pdb <br>
<br>
to get zz.cif file for GLA<br>
<br>
4) Add dummy CRYST1 record to zz.pdb<br>
<br>
5) Create dummy set of "Fobs":<br>
<br>
phenix.fmodel zz.pdb high_res=3 label=f-obs r_free=0.1 type=real
output.file_name=zz.mtz<br>
<br>
6) Run phenix.refine to idealize the geometry of zz.pdb:<br>
<br>
phenix.refine zz.{cif,pdb,mtz} strategy=individual_sites
main.bulk_sol=false output.prefix=zz_idealized params
refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None
main.number_of_mac=50 --overwrite<br>
<br>
The file zz_idealized_001.pdb is the answer.<br>
<br>
All above mentioned files are here: <a class="moz-txt-link-freetext" href="http://cci.lbl.gov/~afonine/tmp2/">http://cci.lbl.gov/~afonine/tmp2/</a><br>
<br>
Let me know if you have any questions.<br>
<br>
Pavel.<br>
<br>
PS> It will be much easier to do in future -:)<br>
<br>
<br>
On 4/27/10 4:21 PM, Hansman, Grant (NIH/VRC) [F] wrote:
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<div class="Section1">
<p class="MsoNormal">How do I make trisaccharide, tetrasaccharides,
etc from single
monosaccharides? I.e., how do I join the monosaccharides. Do I use
ideal coordinates?
Can I join them in coot? I want to make HBGA Trisaccharide B.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">That is, I want to join FUC-GAL-GLA, it would be
FUC (C1)-GAL
(O2)-GAL (C2) then GAL (C3)-GAL(O3)-GLA(C1)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 1 C1
FUC A 1 1.410
0.468 -0.410 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 2 C2
FUC A 1 0.120
0.513 -1.233 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 3 C3
FUC A 1 -0.831 -0.576
-0.728 1.00 10.00
C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 4 C4
FUC A 1 -1.016
-0.402 0.783 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 5 C5
FUC A 1 0.359
-0.379 1.454 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 6 C6
FUC A 1 0.185
-0.241 2.967 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 7 O1
FUC A 1 2.007
-0.823 -0.535 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 8 O2
FUC A 1 0.424
0.284 -2.610 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 9 O3
FUC A 1 -2.094 -0.452
-1.385 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 10 O4
FUC
A 1 -1.700
0.824 1.044 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Courier New";">ATOM
11 O5 FUC A 1
1.116 0.724 0.961 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Courier New";"><o:p> </o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 1 C1
GAL A 1 1.384
0.161 -0.445 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 2 C2
GAL A 1 0.328 -0.139
-1.512 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 3 C3
GAL A 1 -0.975
0.575 -1.139 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 4 C4
GAL A 1 -1.360
0.176 0.289 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 5 C5
GAL A 1 -0.177
0.454 1.220 1.00 10.00
C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 6 C6
GAL A 1 -0.563
0.093 2.655 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 7 O1
GAL A 1 2.612
-0.476 -0.802 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 8 O2
GAL A 1 0.785
0.328 -2.782 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 9 O3
GAL A 1 -2.011
0.186 -2.044 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 10 O4
GAL
A 1 -1.686 -1.213
0.327 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 11 O5
GAL
A 1 0.945
-0.328 0.819 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Courier New";">ATOM
12 O6 GAL A 1
0.539 0.355 3.526 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Courier New";"><o:p> </o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 1 C1
GLA A 1 1.424
-0.489 -0.382 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 2 C2
GLA A 1 0.392
-0.498 -1.512 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 3 C3
GLA A 1 -0.650 0.592
-1.244 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 4 C4
GLA A 1 -1.222
0.387 0.163 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 5 C5
GLA A 1 -0.068
0.330 1.166 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 6 C6
GLA A 1 -0.630
0.161 2.579 1.00
10.00 C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 7 O1
GLA A 1 2.043
0.797 -0.316 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 8 O2
GLA A 1 1.044
-0.242 -2.757 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 9 O3
GLA A 1 -1.700
0.498 -2.209 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 10 O4
GLA
A 1 -1.958 -0.836
0.206 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">ATOM 11 O5
GLA
A 1 0.783
-0.771 0.859 1.00
10.00 O<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Courier New";">ATOM
12 O6 GLA A 1
0.446 0.112 3.517 1.00
10.00 O</span><o:p></o:p></p>
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