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CCP4BB  May 2012

CCP4BB May 2012

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Subject:

Re: ShelXL and Coot

From:

Tim Gruene <[log in to unmask]>

Reply-To:

Tim Gruene <[log in to unmask]>

Date:

Mon, 7 May 2012 11:06:23 +0200

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text/plain

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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

GPG Key ID = A46BEE1A

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