Hi Evan:
I ran pdb2pqr by hand and I think the Zn and CTP is problematic:
REMARK 5 WARNING: PDB2PQR was unable to assign charges
REMARK 5 to the following atoms (omitted below):
REMARK 5 7220 ZN in ZN 154
REMARK 5 7221 ZN in ZN 154
REMARK 5
> However, step 6. (apply) results in this:
>
> Selector-Error: invalid model "and".
> ( ( Model and _mutate_sel ) )<--
>
> Anyone with any ideas?
Unfortunately, "model" is a PyMOL selection language keyword. Everyone,
please avoid naming your models "model", if possible -- that will save you
Per,
No, looking through the code, there doesn't seem to be anything like this
available yet, other than 3D visualization of the alignment (lines drawn
between atom centers).
What you are presumably looking for is the length of those lines. hmm...
Cheers,
Warren
--
DeLano Scientific LLC
Subs
Evan,
This appears to be a problem with file format incompatibility between PyMOL
and the psize.py script. I suspect that rounding off the atom coordinates
will eliminate it:
alter_state 1, all, (x,y,z)=(int(x*1000)/1000.0, int(y*1000)/1000.0,
int(z*1000)/1000.0)
Cheers,
Warren
_
F
With a certain file 1za1 from pdb when I try to run apbs I get the
errors below. Other files are OK. Any suggestions?
error: 1
ValueError Exception in Tk callback
Function: at 0x182892b0> (type: )
Args: ()
Traceback (innermost last):
File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymo
Thanks to all, redirecting didn't work but it seems fine now after
restarting kde. Don't know what's different though.
On 20/09/2007, DeLano Scientific wrote:
>
> Try redirecting stderr and stdout to a file -- the process may be getting
> suspended by the shell due to output.
>
> csh/tcsh:
>
> p
