Subject: build pdb's? Responses

From: David Smith <[email-masked]>
Date: Fri, 14 Jun 2002 16:07:13 -0400

A few of you asked to see the responses I got, they are shown below.
Thanks for everyones input.  If in one knows if any other free software
please let me know.

Thanks,

David Smith

------------------------
> Hello CCL'ers,
> 
> Does anyone know of a windows based freeware that allows one to build
> pdb files from scratch.
> 
> Thanks to all,
> 
> David
> 

------------------------
Weblab lite viewer (accelrys.com) will import files in a variety of
formats
and export in PDB, among others.  It has a quick-3D build, so you could
draw
a structure in ISIS Draw (free), save as a molfile, import to Weblab,
and
export as pdb.  Most structures built that way would need modeling...

Babel will also convert many more filetypes, but it has limited
"modeling"

You might check something like Tinker, for doing the modeling.

>From this molfile:

  -ISIS-  06110217412D

 23 26  0  0  0  0  0  0  0  0999 V2000
   -2.7473   -0.0666    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7484   -0.8940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0336   -1.3069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0354    0.3461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3200   -0.0630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3198   -0.8940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5297    0.1940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0410   -0.4781    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
   -0.5315   -1.1539    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
   -0.1934   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6363   -2.0015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1268   -1.3257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7876   -0.5608    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
    1.2713    0.1075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0919    0.0196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5754    0.6871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2385    1.4411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4133    1.5236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9335    0.8551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4618    0.3457    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
   -3.4620    1.1707    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1762   -0.0670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8786    0.9292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  8 13  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  3  6  2  0  0  0  0
 13 14  1  0  0  0  0
  6  9  1  0  0  0  0
 14 15  2  0  0  0  0
  8  7  1  0  0  0  0
 15 16  1  0  0  0  0
  7  5  1  0  0  0  0
 16 17  2  0  0  0  0
  8  9  1  0  0  0  0
 17 18  1  0  0  0  0
  1  2  2  0  0  0  0
 18 19  2  0  0  0  0
 19 14  1  0  0  0  0
  5  4  2  0  0  0  0
  1 20  1  0  0  0  0
  4  1  1  0  0  0  0
 20 21  1  0  0  0  0
  5  6  1  0  0  0  0
 20 22  1  0  0  0  0
 20 23  1  0  0  0  0
M  END

I generated this pdb file from weblab:

REMARK   Accelrys ViewerPro PDB file
REMARK   Created:  Tue Jun 11 17:41:21 Pacific Daylight Time 2002
ATOM      1  C1  MOL     1       6.797  -7.842  -0.066  1.00  0.00
ATOM      2  C2  MOL     1       6.835  -9.225  -0.278  1.00  0.00
ATOM      3  C3  MOL     1       8.025  -9.941  -0.154  1.00  0.00
ATOM      4  C4  MOL     1       7.955  -7.143   0.269  1.00  0.00
ATOM      5  C5  MOL     1       9.133  -7.863   0.385  1.00  0.00
ATOM      6  C6  MOL     1       9.164  -9.225   0.183  1.00  0.00
ATOM      7  C7  MOL     1      10.492  -7.326   0.747  1.00  0.00
ATOM      8  C8  MOL     1      11.323  -8.478   0.059  1.00  0.00
ATOM      9  C9  MOL     1      10.531  -9.726   0.413  1.00  0.00
ATOM     10  C10 MOL     1      11.003 -10.975  -0.327  1.00  0.00
ATOM     11  C11 MOL     1      12.485 -11.208   0.088  1.00  0.00
ATOM     12  C12 MOL     1      13.368  -9.965  -0.276  1.00  0.00
ATOM     13  C13 MOL     1      12.832  -8.677   0.424  1.00  0.00
ATOM     14  C14 MOL     1      13.798  -7.501   0.144  1.00  0.00
ATOM     15  C15 MOL     1      15.155  -7.778   0.011  1.00  0.00
ATOM     16  C16 MOL     1      16.067  -6.755  -0.226  1.00  0.00
ATOM     17  C17 MOL     1      15.629  -5.441  -0.332  1.00  0.00
ATOM     18  C18 MOL     1      14.276  -5.154  -0.203  1.00  0.00
ATOM     19  C19 MOL     1      13.369  -6.181   0.035  1.00  0.00
ATOM     20  C20 MOL     1       5.499  -7.090  -0.191  1.00  0.00
ATOM     21  C21 MOL     1       5.288  -6.248   1.082  1.00  0.00
ATOM     22  C22 MOL     1       4.311  -8.044  -0.428  1.00  0.00
ATOM     23  C23 MOL     1       5.623  -6.090  -1.355  1.00  0.00
TER

If you want residue info, etc, I doubt you'll find anything free besides
some modeling program like ECEPP.

---------------------------------

ArgusLab will write PDB files for any structure you can construct.
ArgusLab is not free, but it's darned inexpensive (probably less than
what an 
average Seattle coffee junkie spends on latte's and biscotti at
Starbucks each 
month :)

You can obtain ArgusLab at http://www.arguslab.com

Cheers,
Mark Thompson

---------------------------------
Dear David,

Try our program VEGA (http://users.unimi.it/~ddl). It is really free!!!

Best regards

Giulio Vistoli

---------------------------------
David, 
 
May not be of use to you, but Molekel (http://www.cscs.ch/molekel/)
allows you to build PDB files from
many types of input (including, i think, XYZ files which are easy to
build by hand).  At any rate, I would
be interested in hearing a summary of responses.
 
Best regards,
Gary

-------------------------------

DH