[Chimera-users] BIOMT matrix in Chimera?

[Elaine Meng]

On Jul 27, 2008, at 10:38 AM, Francesco Pietra wrote:
>
> Hi Elaine:
> After a brief playing with Multiscale Models, I was considering your
> last suggestion below. I modeled each chain separately, also because
> the X-ray diffr data show some conformational differences. Modeling
> gave very good DOPE score. Now the problem is appending Chain B to
> chain A, etc (each chain opens correctly in Chimera). I have a Python
> script (not tried yet) to insert the Chain identifier (which Modeller
> did not print), update the Atom serial number, and then append the
> files. May I ask, in view of Chimera, if the "Atom number + 1" printed
> in Modeller pdb files at column 80 can be left at it is, i.e. not
> updated on appending the files? I forgot about that and I have already
> problems enough with the script at my minimal level with Python. I
> assumed that Python identifies the columns one unity less than PDB
> numbering. Finally, do you know what means "1SG" at columns 74-76 of
> Modeller pdb files?


Hi Francesco,
I don't know what MODELLER puts in those columns after "B- 
factor" (61-66, which may actually contain the "modeller error  
profile," since a homology model doesn't really have B-factors).   
Maybe you could ask the modeller people.  However, for Chimera  
purposes they could be omitted (changed to blank).

According to the description of ATOM lines:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html
67-76 is supposed to be blank, 77-78 element symbol, 79-80 charge. I  
believe Chimera tolerates lines without the last few columns, as long  
as the X,Y,Z coords are still there. If your files have stuff in the  
later columns, it might still be OK, just try opening them in Chimera  
to see.

My suggestion of modeling the multimer from a template multimer would  
still incorporate the chain differences - you would still use A as the  
template for A, B for B, etc.  However, I don't know how to make  
modeller do that.

> Following the "appending" plan below, is it correct to
> append pdb files lacking all hydrogens (as provided by Modeller) and
> then rely on Amber's LEAP to complete the multimer?
> francesco

I don't know what you mean by "complete the multimer" - if just adding  
hydrogens, you can do that with AddH in Chimera (or addh command).   
That does not use leap/amber.
Best,
Elaine