Hi Kalyan,
If you are unable to read the .res file then I suspect that you had and
END without an HKLF.
Thanks to Tim this problem has been fixed now (r4161) if you're feeling
adventurous.
As for the PDB file, yes indeed, Coot will choke if you try to feed it
atoms without residue names.
Some of the Coot tools depend on standard residue names, this maybe why
things are not working for you (devil's in the details).
Paul.
On 07/05/12 10:06, Tim Gruene wrote:
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Dear Kalyan,
the reason why you cannot read in the .res-file is that you don't have
RESI-cards. They are required by coot.
For the same reason your PDB-file does not contain any information
that would allow coot to refine the coordinates.
As far as I know coot does not create restraints from the .res-file,
hence you need to give your structure residue names for which
cif-files exist with constraints.
However, I since you are working on such a small structure at atomic
resolution I suggest you use Christian Huebschle's shelxle instead of
coot as GUI for shelxl refinement.
You find it at
http://ewald.ac.chemie.uni-goettingen.de/shelx/eingabe.php
Best,
Tim
On 05/07/12 05:38, Kalyan wrote:
Hi George:
I am facing the same problem reading .pdb file generated from
shelxl in coot. I have tried inserting the space group name in the
CRYST1 record but still unable to read the file. COOT is able to
read the .res and .fcf file and I can see the map but COOT is not
allowing me to build the molecule from .res file. I am trying to
refine the solution obtained from direct methods using SHELXS. What
are the parameters that I need to change in the .res or .pdb file
to be able to modify and build the molecule in the first place. Do
I have to replace 'Q' with 'C' or some other changes, and then how
will I connect the atoms in COOT? The appearance of the part of the
.pdb file is shown below (space group name is manually inserted).
CRYST1 21.139 51.900 31.090 90.00 104.69 90.00 P 1 21/a 1
1 SCALE1 0.047306 0.000000 0.012400 0.000000 SCALE2
0.000000 0.019268 0.000000 0.000000 SCALE3 0.000000
0.000000 0.033251 0.000000 ATOM 1 S1 0
-0.215 21.413 10.717 1.000 4.73 ATOM 2 S2 0
0.551 21.040 12.581 1.000 4.64 ATOM 3 S3 0
1.526 18.258 7.542 1.000 5.05 ATOM 4 S4 0
0.802 16.539 8.374 1.000 4.95 ATOM 5 S5 0
11.171 22.546 8.376 1.000 5.35 ATOM 6 S6 0
9.747 22.514 6.903 1.000 5.85 ATOM 7 Q2 0
-1.517 23.108 -2.742 1.000 0.41 ATOM 8 Q3 0
-5.977 20.216 -0.493 1.000 1.03 ATOM 9 Q4 0
13.309 15.857 11.911 1.000 1.63 ATOM 10 Q6 0
-2.030 15.341 9.819 1.000 2.42 ATOM 11 Q7 0
0.489 22.190 6.739 1.000 2.46 ATOM 12 Q8 0
-1.247 24.612 5.096 1.000 2.29 ATOM 13 Q9 0
4.588 21.769 11.905 1.000 2.41 ATOM 14 Q10 0
-3.731 19.433 12.713 1.000 2.78 ATOM 15 Q11 0
7.498 18.251 9.847 1.000 2.39 ATOM 16 Q12 0
3.703 20.519 8.595 1.000 2.22 ATOM 17 Q13 0
0.926 24.359 15.407 1.000 2.33
Thanks,
Kalyan
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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