#--- Python proof e-mail ;) ---
# Hi Aaron,
# You can get to the coordinates in the following way:
# First make a model from the selection you want to work on:
sel = cmd.get_model( object )
# Then you can get to the coordinates and modify them without affecting the
view:
for i in
Hi Frieda,
In addition to my previous mail, the following works for me:
sslist=[]
iterate n. ca, sslist.append( [resn,resi,ss] )
/i=1, j=len(sslist)-1
/while ij:\
if sslist[i][2] == sslist[i+1][2]:\
sslist.pop[i]\
j = j - 1\
else:\
i=i+2
Hope it helps,
Tsjerk
On 10/9/07,
Hi Tsjerk, Frieda,
I made a different solution (I can't get Tsjerk's to work, oddly - it looks
like it should step through sses correctly, but I can't see why the
sslist.pop(i) gives what it should).
Anyway, my 'versions' :) are on the wiki as:
http://www.pymolwiki.org/index.php/Ss
which
Hi Tsjerk,
When I paste your script into the command line of PyMol (MacPyMol to
be exact), this is the response:
Traceback (most recent call last):
File /home/local/warren/MacPyMOL070703/build/Deployment/
MacPyMOL.app/pymol/modules/pymol/parser.py, line 456, in parse
File string, line
Hi Tsjerk, Frieda,
I made a different solution (I can't get Tsjerk's to work, oddly -
it looks
like it should step through sses correctly, but I can't see why the
sslist.pop(i) gives what it should).
Anyway, my 'versions' :) are on the wiki as:
http://www.pymolwiki.org/index.php/Ss
which
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,
Hi Gillean,
For what it's worth, I experienced the same... No dashes in the numbers:
1-1
1--1 L
1-2
2--1 L
2-3
3--1 L
...
etc.
The double dash must come from the -1 value used as default for your SSE
class. Better double check what's going on there :)
Cheers,
Tsjerk
On 10/9/07, gilleain
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
Hi Tsjerk,
I am getting two errors. Is there a problem with line endings? I am
taking the code in emails and on the wiki and pasting it into a text
editor (BBEdit), then copying that and pasting into the PyMOL command
line. The text editor is saving the text with Unix (LF) which I take
Hi everyone,
Sorry for posting my replies to the list; I hope this is all generally
useful.
Firstly, the bug: the obvious cause is if the line if ss == currentType:
is never true. In that case, it is making a list of one-residue sses, with,
as Tsjerk correctly pointed out, the default end of -1.
Thank you very much, this works much faster than cmd.alter_state.
On 10/9/07, Tsjerk Wassenaar tsje...@gmail.com wrote:
#--- Python proof e-mail ;) ---
# Hi Aaron,
# You can get to the coordinates in the following way:
# First make a model from the selection you want to work on:
sel =
It looks like quite a few people are actually still using the
electrostatics wizard, so I updated the code on my website
(http://www.umich.edu/~mlerner/PyMOL). For what it's worth, I just use
the visualization pane of the APBS plugin these days, but I understand
if the wizard is a little cleaner
Hi,
I hoping to get into the molecular movie making business, and I'm
wondering whether, rather than specifying each movement of an object, PYMOL
can record object movements that are created using the mouse and/or
keyboard.
Thanks,
Tom Leyh
Professor of Biochemistry
The
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