yeah, its true.
We should work out a tutorial for this kind of things. Something where
there is only one line of instruction and one line of command, like:
1) Download a file
fetch pdb1.pdb
2) Select all ASP or GLU residues:
select acids, resn ASP+GLU
3) Suggestions?
Am 02.03.11 22:36, s
On 03/02/2011 10:07 PM, Tsjerk Wassenaar wrote:
> Hey :)
>
> It's good to note that programs are written by programmers, using
> programmer's logic.
First of all, I was not complaining about the logic of the PyMOL
programmers. I tried to help find out the reason that might cause
Martin's script
Hey Hongbo,
good way of putting it. Indeed, I think thats what seemed most
intuetively to me in the beginning, and so I ended up trying to figure
out why 'AND' was not giving me the expected selection. Remembering my
boolean algebra lecture from back in the days, I suddendly realized that
it ha
Hey :)
It's good to note that programs are written by programmers, using
programmer's logic.The confusion is not so much caused by the
simplified expression, but by users with little background in
mathematics/logic assessing 'and' and 'or' from a linguistic
background. In computer science and math
I believe the confusion is caused by the simplified selection expression
in PyMOL (and some other visualization tools as well). I remember that
one of my colleagues once questioned strongly the reason of using OR
instead of AND in such situation.
The expression:
select resn GLU or resn ASP
ac
Hi,
Seems to work fine for me. I'm using version 1.3, although I doubt that this
could be
a version compatibility problem.
Could you give more specifics on how it doesn't work for you (ASPs not
colored red
or GLUs not colored red, etc.) ? Note that the parenthesis around 'resn glu'
aren't
needed.
For me,
color red, resn asp+glu
works.
Maia
Martin Hediger wrote:
> Dear all
> What is the selection syntax to select all GLU and ASP residues within
> an object?
>
> I'm trying it the way its written on the wiki:
> remove resn hoh# remove water
> h_add # add hydrogens
>
> a
Hi Martin,
On Tue, 01 Mar 2011 13:44:36 +0100 Martin Hediger wrote:
> Dear all
> What is the selection syntax to select all GLU and ASP residues within
> an object?
>
> I'm trying it the way its written on the wiki:
>
> remove resn hoh# remove water
> h_add # add hydrogens
>
Hi Martin,
To select all ASPs and GLUs just type,
select resn GLU+ASP
or
select resn GLU or resn ASP
or, if you need parentheses,
select ((resn GLU) or (resn ASP))
Maybe this will help:
# fetch a test protein
fetch 1rsy, async=0
# color all ASPs and GLUs red
color tv_red, (resn ASP or r
Hi Martin -
** Short answer:
Use `resn asp+glu` (although your original command actually works for me).
** Not-so-short answer, with a bonus question about comment syntax:
The Asp/Glu line of your script can be condensed slightly using a plus sign,
but the original syntax of that line actually
Hi Martin,
Try the following:
color tv_red, resn asp+glu
or
color tv_red, resn asp or resn glu
Cheers,
2011/3/1 Martin Hediger
> Dear all
> What is the selection syntax to select all GLU and ASP residues within an
> object?
>
> I'm trying it the way its written on the wiki:
>
> remove resn h
Hi Martin,
The wiki way should work. The only thing I can think of is that you're
not doing what you think you're doing :S
Did you copy paste the commands from the wiki? Did you get an error?
What version are you using?
> but, the selection kind of does not work for me (I'm assuming the operator
Dear all
What is the selection syntax to select all GLU and ASP residues within
an object?
I'm trying it the way its written on the wiki:
remove resn hoh# remove water
h_add # add hydrogens
as surface
color grey90
color slate, resn lys # lysines in light blue
color pal
13 matches
Mail list logo
