Hi Gilleain,

I tried the code with a different, single pdb file (1CRN) loaded in PyMOL, and got the same output formatting.

The original PyMOL file I am working with has seven different protein structures in it. The pdb IDs are
1ujc
1h2e
1k6m
1e58
1nt4
1dkq
1qwo
and they have been aligned to each other.

Another mystery is, in copying the code again from the wiki, now I get only a series of errors, both with my original file and with 1 CRN by itself. Did you update the wiki page, or am I losing my mind?

Is there some chance that MacPyMOL is different? Or is there a recent version I should download?

Thanks,
Frieda

On Oct 9, 2007, at 9:25 AM, gilleain torrance wrote:

Hi Frieda,

That's odd. It seems to work okay for mulitchain proteins (I'll add
some extra bits to handle chains).

The "--" in the output is weird. It suggests that either the start
numbers end in a dash or the end number start with a dash. It's
difficult to diagnose the bug, if bug there is, without the input
data.

What structure are you using this on? Does it happen with other structures?

gilleain

Hi Gilleain,

I tried pasting in the code at the first link, followed by
ss my_object
where my_object is the name of an object in the file,
and the output looks like this:
1-1
1--1 S
1-2
2--1 S
2-3
3--1 S
3-4
...etc.

Am I using ss incorrectly?

For the second link above, I do not know what command(s) to issue after I
paste in the code.

Thanks for your help,
Frieda



///////////////////////////////////////////




Frieda Reichsman

Molecules in Motion

Interactive Molecular Structures





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Frieda Reichsman
Molecules in Motion
Interactive Molecular Structures

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