Hi
Tom,
I
understand that it can get complicated without a
defined point of reference. And again, it’s
possible to get around it by just ‘clip off’ in
figure scripts, so this discussion is just about
details. I guess it is just confusing sometimes,
as I have seen people struggling with this before.
For
me it’s more a matter of ease-of-use. As in I
would like to have a command that writes out all
necessary settings to recreate a view of a
model/map. For example, why can the point of
reference not be (and stay) the center of the
surrounding box for the displayed model(s),
irrespective of already applied clipping planes?
And then write out the position of the clipping
planes plus the depth cue values when using e.g.
‘view matrix’ (or some other command). Like this
all the important information for recreating a
certain view (of these model(s)) could be written
out from a single command and could then be copied
into a script . Again, that would be similar to
‘get_view’ in pyMOL (https://pymolwiki.org/index.php/Get_View).
Right now, to recreate a view reproducibly looks
something like this:
-
‘view matrix’ ->
copy paste the camera values into the script
-
‘clip list’ ->
copy paste the clip values into the script after
a clip off command
-
Decide what
lighting and depth cue values -> copy paste
into script
-
Then the script
will look somewhat like this
view
matrix camera
-0.18203,-0.11049,-0.97707,-138.8,-0.96294,-0.1811,0.19988,197.66,-0.19904,0.97724,-0.073424,107.97
clip
off
clip
near -3
clip
far 30
lighting
soft depthCueStart 0.5 depthCueEnd 0.7
save
"PNG/example.png"
Which
is completely fine, but it would save some
copy-pasting if everything was accessible from a
single command.
Best,
Moritz
External
Email - Use Caution
Hi Moritz,
I agree that
absolute clip plane positions can be useful.
The question is what are the absolute
positions measure relative to? For example
if I say "clip near 8" that is supposed to
be 8 Angstroms in front of what point? The
rules the ChimeraX clip command uses are a
bit complicated because what reference point
to measure distances from is not obvious.
So if no clip planes are shown then the 0
position is the center of the bounding box
of the displayed models. If the clip plane
is shown then 0 means the current plane
position. And if you want to define your
own reference point then use the position
option "clip near 8 position /B:123@CA"
means the 0 point is at the C-alpha atom of
residue 123 in chain B.
To get
reproducible clip plane positions you need a
reproducible reference point that the
distances are measured relative to.
Not 100% sure I understand
the question correctly, but maybe
the confusing part is the following:
The clip numbers are not absolute,
but are additive. As in every time
you use the following command:
the far clipping plane would
be moved by 35. This can lead to
some inconsistencies, for example
when one uses ‘clip list’ and gets a
value of 210, and then puts that
value into a script that changes the
clipping plane several times for
different views. Safest way to not
have that problem is: put a ‘clip
off’ in front of all clipping
commands in a script. This way the
exact view will be reproduced every
time. E.g.
view matrix camera
-0.20791,2.5127e-09,-0.97815,-250.33,-0.97815,-4.5356e-09,0.20791,309.25,-9.8669e-09,1,4.8527e-09,229.38
view matrix camera
-0.96824,-0.21649,0.12504,-223.03,-0.075286,-0.22447,-0.97157,-549.26,0.2384,-0.95013,0.20104,356.85
In this example, the first
view will be at clipping near/far of
-1/134, and the second view will be
at -16/35. If one omits the ‘clip
off’, the second view would be at
clip near=-17 and clip far=169
(instead of the intended -16, 35)
For me personally absolute
values would be more intuitive (I
guess similar to pymol (which many
people might be used to), where
‘get_view’ would give you a matrix
that reproduces both view and also
clipping/fogging every time, no
matter whether there is already
fog/clipping present.)
External Email - Use
Caution
Hi Vincent,
I always save a session file
with the view for each
publication image. Trying to
do it this other way is much
harder, in my opinion, and I
have never tried it myself.
As far as I know, the "view
matrix" command should report
(and restore) the camera and
model positions, and "clip
list" report (and "clip"
restore) the clipping plane
position(s):
<https://secure-web.cisco.com/1MVnhhzN19WBilS9gDO4_Q4yCh88PWvZfX-39fwyPLIlx6y4Vz3erktHutC1_lKG0kNF5i7X1vpZ7EWpHymhI9own4UCYQDyy245qU8KiJfSeI282n3t0Lt4kYQGx7NLjSiWQYIRlp84o6PVH6X9EUHJBZzTt2SRhRejzqbrEhvgPa64B1kDYW8xNta0vRQDIBmq8mjNAC3NY5px5EfwuoG0iTlnewXuEifYJRWHp6ACyMas0YrxHVwJfshSUq8ank_K2DLemsI1f6ECTd8K7bZCVQ4RFPwUkWmX8Tr41j_tEfbkruTRSi5UoMb6FcMAsNnE9QFKwhNLqfOFG2hXo_w/https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fview.html%23matrix>
<https://secure-web.cisco.com/1rH6UOFHJhkT9dijsnzAEc3Hc8ARJKTd5xv5ALjfH1y-k5g4IK3l8co6LiNk9qjkgrwKk9eMLlyWjhtYrdPqg4Siy0MRjcp9fZngrYrOFiTM8kjV3bxH7udnPoeNhGW3st_N9PH9-pYscgbTW9E508Wf4-U5IkR2tVGRqGOimTv68XGSjgm5QqZMsIdGZUJS0Ahkn2CPJYnNE450ekgoCE5nUnXSenyXxRNbUq8__qZTIas3sBteUOb1Enmo05OXaswwSZLia_YEYuK6XbH5Ewb13Fht0YRaay0qjzUobh05clvM-qA550zp_NjZAUGpXKviIAWGEh5Io-IFqO0pUvQ/https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fclip.html>
What you showed for results
from "clip list" does not make
sense: the near and far
planes do not have a tilt
axis, so their axis will only
be 0,0,1 or 0,0,-1. But you
said "modified" so maybe you
edited it? It is impossible
for me to tell what is really
in your session if you don't
include the whole results for
clip list.
Then if you want it to look
the same you should set
exactly the same clip plane(s)
as reported by clip list. If
you have a front or back
plane, you should also set the
reported axis ("axis" option
of "clip", see help above) and
point cordinates ("position"
option of "clip").
If it is not working and you
feel it is a bug, please use
Help... Report a Bug and
attach the session, and the
details of how you tried to
reproduce it; however, that
would put your data in a
publicly available
repository. If you have a
simpler example you could
attach that to the bug report
instead.
I hope this helps,
Elaine
-----
Elaine C. Meng,
Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical
Chemistry
University of California, San
Francisco
> On Aug 28, 2023, at 7:48
AM, vincent Chaptal via
ChimeraX-users <chimerax-users@cgl.ucsf.edu>
wrote:
>
> Hi Elaine,
>
> I've been playing around
with it but I can't get to
what I want.
> The second option of
saving views works within a
session, but it is lost if I
restart ChimeraX or changes
session, so what I'm looking
for is really some numbers to
place in a script so I can
touch up my figure for
publication multiple times.
>
> Using "clip list" does
list me an offset for the
"far", as I modified it:
> Using 1 clip planes:
> far offset -1.5964, axis
0.032,-0.040,0.999, point
106.7,107.9,112.8)
>
> I am trying to reproduce
the view with:
> view matrix camera
0.051145,-0.99818,0.03201,113.43,0.99794,0.049838,-0.040387,99.325,0.038719,0.034009,0.99867,323.92
> clip front 0 far -1.5964
>
> (and varying flavors) but
it doesn't recreate the same
view. The clipping offset is
much more drastic with my
command line compared to the
manual twicking of the far
plane.
> Could you please point me
in the right direction?
> Thank you
> Vincent
>
>
> Le 22/08/2023 à 17:08,
Elaine Meng a écrit :
>> Hi Vincent,
>> You can report
current clip settings in the
Log with command:
>>
>> clip list
>>
>>
>> <https://secure-web.cisco.com/1rH6UOFHJhkT9dijsnzAEc3Hc8ARJKTd5xv5ALjfH1y-k5g4IK3l8co6LiNk9qjkgrwKk9eMLlyWjhtYrdPqg4Siy0MRjcp9fZngrYrOFiTM8kjV3bxH7udnPoeNhGW3st_N9PH9-pYscgbTW9E508Wf4-U5IkR2tVGRqGOimTv68XGSjgm5QqZMsIdGZUJS0Ahkn2CPJYnNE450ekgoCE5nUnXSenyXxRNbUq8__qZTIas3sBteUOb1Enmo05OXaswwSZLia_YEYuK6XbH5Ewb13Fht0YRaay0qjzUobh05clvM-qA550zp_NjZAUGpXKviIAWGEh5Io-IFqO0pUvQ/https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fclip.html>
>>
>>
>> More to your point,
however, you can save the
current view (which includes
the clipping plane positions)
with command:
>>
>> view name myviewname
>>
>> ....of course you can
name it something else, and
you can have multiple saved
views with different names.
Then later in the same
session, either not quitting
ChimeraX between, or from
saving a session file after
you saved the view(s) and
later restoring the session
from the file, you can get
back to that view with
command:
>>
>> view myviewname
>>
>> ...there are various
command options, like
gradually moving to the view
over a number of frames as is
often done for recording a
movie, see the help:
>>
>> <https://secure-web.cisco.com/1QzMfrb2bZI0tVknJWm-znSsYye9DecegVUfz15eWNt_8AzFuzOAXgIKZHBreojVsS73FrNrwRrBkd1UE6S9pAAamQqPRyDDZpT89CZXZntBovx5URBa_xBs8IfMrD3wLZEvvwUAzrWsz9CWHBWQL_su4yWaM0qW8ffrI5NlHt4dFq_nntTiGdUqU-BsNjJX6g-2Tp2mo_eAnYDw34TAbUD5IYF-t_5kUJrLOSpz_MWw4dELuErBKnv50drbgJl4KhiovI4fsA6zDL0ybgaxcv5n6Vm4noNShHARvqUWPNI8YAPpxGbCnOGZ8fL-rqwoVhPI7bCw8EaLQuu9syS9Fuw/https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fview.html%23name>
>>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng,
Ph.D.
>> UCSF Chimera(X) team
>> Department of
Pharmaceutical Chemistry
>> University of
California, San Francisco
>>
>>
>>> On Aug 22, 2023,
at 3:34 AM, vincent Chaptal
via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
>>> wrote:
>>>
>>> Hi,
>>>
>>> I opened the side
view dialog window and
adjusted the view planes for a
nice figure.
>>> I would like to
save the parameters so I can
go back and modify the figure
at a later stage, but the
setting are not stored in the
"view matrix" command.
>>> Could you tell me
which command can save these
settings? (I'm using chimeraX
1.5).
>>>
>>> Thank you.
>>> Best
>>> Vincent
>>>
>
> --
> Vincent Chaptal, PhD
> Director of GdR APPICOM
> Drug Resistance and
Membrane Proteins Lab
>
> MMSB -UMR5086
> 7 passage du Vercors
> 69007 LYON
> FRANCE
> +33 4 37 65 29 01
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