Hello Luc
I assume that you want to highlight the residue that already belongs to one of
the chains.
Try this:
zap ;
load myprot.pdb
wireframe off ; spacefill off ;
select *:B ; cartoon ; color dimgrey ;
select *:A ; cartoon ; color lightgrey ;
select 153:A; spacefill 23%; wireframe 0.15 ;
Dear Mathew,
That's not one of Jmol features, although as you have found you may get
some results playing with the lighting options.
Right now I cannot provide advice on that, but maybe this
http://wiki.jmol.org/index.php/Lightweight_JSmol#Model_rendering
gives you what you need, as long as you a
Oh yes!
Go to the documentation page,
http://chemapps.stolaf.edu/jmol/docs/
and search for "outline"
and you have
set celShading TRUE
set celShadingPower (integer)
Is that what you were looking for? So it seems to me
-
Dear Jmol experts,
You'd know I've never managed to grasp the quaternion math in JmolScript, I
am hoping I can solve this problem without it --or with help from some of you.
1. I have two pdb files of (partially) the same protein, that I need to align.
This I can do using the "compare" command
Thanks, Bob
Aha, the mysteries of matrix multiplication :-D
I circumvented my problem creating dummy atoms and applying the rotation
to them. But anyway I'd like to do it this way.
Still, I cannot make it work
rotaProt = compare( {*.CA/2.1 & polymer=8} {*.CA/1.1 & polymer=8} )
show rotaProt
Hi Bob
Yes, it's working perfectly. Thanks!
Note: new p1 is different than old p1 (as you said) but it does not match p11
This is with 14.4.0_2015.10.13 application
rotaProt = compare( {*.CA/2.1 & polymer=8} {*.CA/1.1 & polymer=8} );
show rotaProt;
// rotaProt =
[[-0.7424616,0.2323488,-0.628303
Hi Kilian
I'm afraid the succession of spheres is Jmol's only way of producing curved
lines (also used for protein cartoons and traces)
Have you tried adjusting set antiAliasDisplay ?
Baerwinkel escribió:
> Hi fellow Jmolers!
>
> I am preparing some structure plots with Jmol and PovRay, and
Hi
I have reports from 2 different people, accesing different pages of mine.
When gzipped pdb files are involved, Safari fails to load the model into
html5-JSmol
At least one of them reports "unrecognized file format" inside the Smol panel
Chrome works in the same systems.
So I think the
> I think I will add a
>
> load BINARY option that explicitly identifies files as binary so that JSmol
> will process them
> correctly regardless of their file name.
That sounds a very good idea, Bob.
It would need to be compatible with using other qualifiers, "load append" at
least.
Yes, my
Wow!
Thank you, Eric.- I can't imagine how that happened. Supposedly I just
copied and pasted the url.
mol uses the gzipped files -- and fails to load in Safari, it seems.
mol-2 uses plain text pdb files
So Safari loading of binary files is broken, isn't it?
-
Hi Gabriel
This may be the reason --not sure.
Proteopedia is using a "simplified model" approach; proteins are loaded only
with alpha carbons and ligands. That is meant to increase the speed of
loading and so start-up. not sure if it will affect rotation.
You can test: in Proteopedia, first l
Hi Jmolers
I'd like to use a loop to define a series of points (using atom expressions)
and then use that series to draw a polyline.
No problem in defining the series of points.
But then I need to pass them to either
DRAW myline diameter 0.3 curve
or to the VERTEX components of the CGO comm
Thank you, Rolf
I had forgotten about the script() function. Yes, that will probably do it.
I will try...YES!
Thanks
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Hi Rick
draw fixed
should work for that
http://chemapps.stolaf.edu/jmol/docs/#draw
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Simon,
although you seem to have the solution, I'd like to give my view
As I understand it, "zoom 100" will fit the model in spacefill into the window,
at any rotation angle; maybe yor perception is due to your having a single
"best" orientation, for which there may be empty margin left.
I do n
Hi all
I recently found about "load async", which I had never used before. I want to
try it for not hijacking the page while JSmol is loading big models.
However, I am using "load append" to sequentially load 2 or 3 models, which
I then align.
Is there a way to use both keywords, async and appe
Thank you, Bob
You're right
I thought I had tred it both ways. It seems I did not
Solved!
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Rolf,
maybe I'm being naïve but, Couldn't you use _modelNumber to limit the
action of the display command?
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There is some documentation on how to use the WebGL modality of Jmol,
features, limitattions, at
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/WebGL
You are welcome to report there about your experience.
On 11 Dec 2015 at 11:33, Robert Hanson wrote:
> Don't forget that there is a WebGL o
I can confirm that adding Pruvacy Badger to my Firefox (42.0, after a long
history of auto updates) prevents JSmol from loading
Tested in my own pages as well as
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
Disabling the extension immediately cures the problem (on page reload, no
need to qu
Thanks for sharing your report, Vinushka
I've added it on
http://wiki.jmol.org/index.php/Compatibility
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Hi Daniel
There are a few commands in Jmol that allow moving a part of the loaded
model(s), by first selecting them
However, note that moving a molecule in 3D manually to gain some position
with respect to another is far from easy or intuitive. All is 3D, while you
mouse moves in a 2D space.
T
Hi Ashok
You need to invoke a Jmol script from your Javascript. Probably the best way
is to use EvaluateVar()
see
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Functions#evaluateVa
r
Maybe like this:
var x = Jmol.evaluateVar(myJmol,
' "O[C@](F)(Cl)I".find("smiles","O[C@](F)(Cl)I") ')
> Should I have to include any javascript or jar
> files related to SMILES?
> Currently, I use src="JSmol/JSmol.min.js">.
No, that's enough, as long as you are also definining properly the path to the
"j2s" folder inside the "Info" variable
I am not sure what may be the effect of a hidden JSm
Ashok,
I see 2 sources of problem in your code:
1) You cannot call compareSmiles() before the Jmol Object has finished being
created
2) Where do you expect to see the output of compareSmiles() ?
This, for example, works for me in the page (no need for the console):
function go1() {
doc
For some reason, the double @@ is breaking the string
See it with:
function compareSmiles(key, ans) {
var v = " 'KEY'.find('SMILES','ANS')>0"
.replace(/ANS/,ans)
.replace(/KEY/,key)
.replace(/\\/g,"");
alert(v)
}
---
.replace(/\\/g, '');
ans = ans.replace(/\\/g, '');
Jmol.script(jmolApplet0, "smiles1 = '" + key + "'; ");
Jmol.script(jmolApplet0, "smiles2 = '" + ans + "'; ");
return Jmol.evaluateVar(jmolApplet0, "smiles1.find(
quot;:[{
"entity_id":1,
"weight":17801.109,
etc
Now the question: how to extract parts of the data, like the value for the
"weight" key?
I tried things like
print f["weight"]
print f["2k8v"]["weight"]
print f["2k8v&quo
Excellent!
Thanks a lot, Rolf
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Those formats hold actual scalable,
drawn objects that are calculated by Jmol from the internal data of the model
and its current display, but not just from the look of them on screen.
·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-
David Leader wrote:
> Ok. Apologies for my naivety. I guess I wasn't thinking about 3D graphics
> properly. Just assuming
> because the image was generated from vector-type commands that it could be
> converted into 2D
> vector commands.
More or less that is what is done by the export modules
This is undocumented (I will fix that in the Wiki), but I found it in the
Export to
Web templates, so it must work. Please give it a try
Info.makeLiveImg = "whatever.png"
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(addition to my former message)
Info.makeLiveImg = "path/to/myown.png"
Make sure to include the path to your file (relative to location of
JSmol.min.js
as the other paths in Info)
Now documented:
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Startup_period
-
Dear Bob,
Jaime Prilusky and I are observing that the History button from JSmol
console displays 2 or 3 times the same script that has supposedly been run
once.
In several broswers, but not in all pages and not with Jmol-Java
Could this be some kind of artifact, or is the code really being
Thanks, Bob
Cool? probably, but for me right now I'd rather say complex
Anyway, our worries were that the file could be retrieved twice. From your
explanation I gather it's not the case, so OK
However, I think Proteopedia scripts are not using load SYNC, and for sure
my pages are not using th
oops...
So we need to find the "magic"
I think this is interesting to have. Feature request!
There it goes, https://sourceforge.net/p/jmol/feature-requests/230/
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Thanks, Bob, I will try to investigate further with your suggestions
Updating my version of JSmol affects my whole site and I must do that
cautiously.
The debug option in serach will be easy to include
Anyway, as I said, your page
http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
also shows t
No, two different images:
- the cover image, covers the whole JSmol
- the one talked about now is a small icon, blue circular arrow, displayed on
top of the cover, lower left
On 15 Jan 2016 at 15:55, Robert Hanson wrote:
>
> Should be Info.coverImage:
>
> coverImage: null, // URL for image to
Dear Eric
I assume by "average" you mean the same as the midpoint beween both
points.
You can do it with
x = {gly6:a}.xyz
y = {asp13:a}.xyz
print {x,y}.xyz
print {(gly6:a,asp13:a)}.xyz
and it turns out that, funnily enough, Jmol is clever once more:
print (x+y)/2
:)
--
Hi all
I need to find out the numer of Jmol objects existing so far in a page.
I was expecting this to work
alert( Jmol._applets.length )
However, it returns 'undefined'. I can see that Jmol._applets does exist as a
Javascript object. Some posts in the users list say it is an array of objects.
Well, it does not work. "i" is higher than the nr of Jmol objects
> BTW, this works though it's unnecessary convoluted in my opinion
> var i=0;
> for (j in Jmol._applets) { i++; }
> alert(i)
i comes out as 0, 3, 5, 7 ...
That's because each item in Jmol._applets is kind of multi
OK,
Thanks Bob
I understand there are functional reasons behind that construction.
I still think this needs a rather convoluted method for something that is
conceptually simple: how many Jmol objects in a page.
And I am not too happy hard-coding this to using internal variables and
findin
Hi Ashok
> Is it possible to combine Jmol script and PDB file into a single file and
> load it into JSmol?
It is, indeed
http://wiki.jmol.org/index.php/File_formats/Scripting#Script_inline_within_a_
molecular_coordinates_file
or you prepare everything in the Jmol application and then export t
Hello Luciano
As you imagine, JSmol objects are not like image elements.
The canvas has no title or alt, so JSmol cannot have it either since it draws
on a canvas element.
But there are some similar options --though not completely what you wish.
Please see
http://wiki.jmol.org/index.php/Jmol_Ja
Dear Jmolers,
Luciano's recent message reminded me to share with you a recent
development of mine. I found a cool and simple trick to display a progress
image (animated spinner) while JSmol is being constructed and inserted in
its place in the page, that goes away automatically when that inser
El 26 Jan 2016 a las 19:42, Robert Hanson escribió:
> great idea! Can you set up a page that does that, and I will add your
> changes. Try adapting
> test2.htm, as it loads the library JS files in readable form.
Excellent! I will do that
·
Dr. Angel Herráez
Biochemistry and Molecula
. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871 Alcalá de Henares (Madrid), Spain
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Dear Henry,
I agree this is a prickly issue.
>From my limited experience with Java Web Start, my opinion is that it is not
practical at all. You must wait for a lengthy download, then it will open, it
leaves whoever knowns which and how many files in your computer, next
day you use that page y
Dear Frieda,
I'm afraid the Mouse Manual page is quiet old. I cannot really help you on
whether JSmol must behave (it should in principle).
As an alternative: it is easy to insert a slider in the page using just html5
tags
and to bind it to a JSmol script, so offering a more intuitive interfac
Dear Jmol users,
Last Thursday we had a rather intensive attack on the Jmol Wiki by means
of rogue users signing up and littering with junk pages. So I asked Nico to
block new users.
I am working with him to find out the best solution that willl allow
functionality
without the burden of contin
Dave,
I also think that Jmol.script should work
Do you have more than one JSmol object in the page?
If you were using "jmol_target" in your page it suggests so.
So you must make sure what name/id your object has (that's what "myJmol"
refers to)
--
Eric,
I guess the algorithm for trace etc expects always a sequential order and not
a cyclic one.
I suppose you could create a new Calpha (or a whole residue) that overlaps
res#1, assign it res#19 and maybe trick Jmol in that way to draw the trace
On 16 Feb 2016 at 17:18, Eric Martz wrote:
>
Hi Simon
I am not sure what 'wait image' you are exactly referring to.
Jmol-14.4.3_2016.02.28-binary contains these 3 in the jsmol/j2s/img folder:
play_make_live.jpg
JSmol_spinner.gif
cursor_wait.gif
The 3rd I believe is a cursor that will display (at the position of the mouse
pointer) while J
some more thoughts:
1. Use Jmol 14.5 which has all this implemented
2. try
Info.appletLoadingImage = "none"
(whithout any underscore)
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> Thanks Angel - its the cursor_wait.gif that is the problem (i.e. it shows up
> as a missing image in
> the bottom-left corner of the 'applet' canvas while JSmol is loading etc.)
No, that space is not for cursor_wait but for play_make_live
> I can work around this by creating a ./j2s/img/ fol
Hello Christian
That is a feature of JSmol that may or not be enabled. It may involve one of
these options:
- coverImage
- deferApplet
- deferUncover
(most probably the 2nd) They are described in
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Startup_period
It seems that the desi
Rojan ,
why the difference in file name between your 2 examples?
./chpdb/a0/1a0b.A.pdb
./test/1a0b.pdb
Could that be the cause the file is not found?
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Rick, I think this same message used to be shown by Chrome (which uses a
similar engine to Safari)
If the model loads fine, then it's a spurious message that can be suppressed
adding some code to the page source. I haven't got it at hand right now
Maybe searching the list archive for that phrase
Hello Sarabjeet
I have no experience with electron density maps, but a little cleanup of your
code
might help:
Hello Sarabjeet
I have no experience with electron density maps, but a little cleanup of your
code
might help:
Hi again, Sarabjeet
I see several problems there:
1. You cannot break lines within a JmolScript
2. You cannot nest double quotes inside double quotes
3. You need proper JSmol syntax for the button
Even if you prefer using Jmol-Java, it is better you use the new JSmol
syntax. Just specify "java"
Hi Sarabjeet
You can load 2 or more files using
load files "file1.pdb" "file2.pdb" "file3.pdb"
then you need to use this to display them all:
frame all
However, they usually come in very different orientations and positions in
space, so maybe you will not see the "superimposition" you may
Hi John
It is the same way. You can put the Jmol.getApplet() call inside each table
cell.
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Functions#getApplet
You will need to use/define 4 different variables for the 4 JSmol objects. A
single Info variable may be shared by all.
---
Hi Phil
Several ways of picking ligands -- depends a little on your definition which is
not always what Jmol understands by "ligand"
You can do
select ligand
but that may not match all that you expect. It's a synonym for
not protein and not nucleic and not water
Particularly, my experience i
Hi Vincent
This is a wild guess, but maybe you should try the CAP or SLAB options of
the isosurface
http://chemapps.stolaf.edu/jmol/docs/#isosurfaceconstruction/mappingparam
eters--generalshapesandvolumetriccubefiledata
Hi Phil
> OK. It does not work with my implementation on any of the browsers on the
> mac, but it does with
> your jsmol.htm file. So it's me:-(
gzipped files must go via jsmol.php at least for some browsers. With local
pages and files I usually have problems loading locally (since php is not
Dear Phil,
I don't remember seeing that post
A search for "database" on the Jmol Wiki brouth this
http://wiki.jmol.org/index.php/Database_Connection
although not fully up to date, I see
--
_
perly configured in your pages
See
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Reading_binary_files
and particularly the use of "serverURL",
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Files_and_paths
or send us one of your URL to check what is happening
·
Dr
Hi John
First of all, those instructions are meant for pople who already have an (old)
setup of pages that run Jmol Java applets using the Jmol.js file
If you are writing pages anew, you'd better forget about Jmol2.js
If you are indeed going to use Jmol2.js to quickly adapt your old pages, see
Hi Chris
I had something similar recently. The hint I got was to use the script()
function in Jmol.
This seems to do what you need:
(in Jmol script)
var c = script("show chain");
(in _javascript_)
var chains_list = Jmol.evaluateVar(
jmolApplet0, 'c');
alert(chains_list);
That
Hi John
I did not remember about this command. but it should work
http://chemapps.stolaf.edu/jmol/docs/#bondorder
> substituted "connect (all) (all) single modify" and got the desired
> single bond.
If you need to change to this command, I suggest that you use a more
specific one:
connec
Hello, Birgit, and welcome
> Is it possible that I need a special file with more informations than just
> the structure of the
> moelcule?
Yes. Many file formats do not include partial charge information, and so Jmol
cannot draw the MEP.
For example, MOL2 format will contain partial charges.
Dear Birgit
The MOL2 format will contain partial charge data for each atom, but not the
MEP. Jmol calculates the MEP coloring from the charges.
I am not sure the MEP data can be saved to file. You can save the
isosurface (with the color map, possibly) from Jmol using either "write
isosurface" c
I haven't seen the original message, so I cannot judge fully what the problem
is.
I do not think that defaulting to StOlaf will be good. People will not realize
that is a temporal solution, and it will stay forever as such.
Based on my experience in courses, one cause of trouble is to work in
Hello Harish
As Bob said, you probably haven't got the needed files in the right place.
A few tips that might help you solve this problem:
1. things may work differently if you run the page locally or from a web
server. Please be specific about this.
2. the Chrome browser limits access to loca
Mark, your code looks good.
You could also use the "script" parameter in Info to set up the commands
you need
Like this:
Info.script = "set spinFps [frames-per-second]; set spinX
[degrees-per-second]; set spinY [degrees-per-second];
set spinZ [degrees-per-second]; spin on; "
---
Y 10; set spinZ 0; spin on;"
·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871 Alcalá de Henares (Madrid), Spain
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Hello Jyoti
It's hard to say without seeing the files.
1. Which file format is your data saved to?
2. In some file formats, vibrations are stored in different models ("frames")
in
the file. By default Jmol displays only the first frame. Try advancing to other
frames, either with the buttons
w
in this list or by adding content in the above Wiki page.
Thanks
·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871 Alcalá de Henares (Madrid), Spain
---
Hi Chris
#1 You can color the isosurface when you create it, in the same command,
though I often find this tricky to achieve.
#2 Much more friendly for me is to color later, you must use the object ID
notation, that also works for draw among other commands: just add a dollar
sign before
On 13 May 2016 at 20:42, Robert Hanson wrote:
> The only thing that looks odd to me is that unitcell, boundbox, and axes have
> checkboxes at the
> top and submenus on the bottom.
That's right, but it was already that way; I've only changed the positions.
So maybe we should merge the checkboxes
> So maybe we should merge the checkboxes into the submenu. I see we
> have "Hide" inside the subenu, which overlaps with what the checkbox does.
That fusion seems sensible to do. Please see the update at
http://wiki.jmol.org/index.php/Custom_Menus/Proposals
More opinions?
I certainly would prefer to have Java available in the distribution. For large
proteins and complexes there is still a significant difference in performance.
Maybe the nonsigned variant can be dropped / separated into the other
download
On the other hand, I would vote for not having the extra f
Thanks for that huge addition of features, Bob.
Robert Hanson wrote:
> new feature: additional predefined sets for periodic table:
> "@nonmetal
> _H,_He,_B,_C,_N,_O,_F,_Ne,_Si,_P,_S,_Cl,_Ar,_As,_Se,_Br,_Kr,_Te,_I,_Xe,_At,_Rn",
> "@metal !nonmetal",
This is now documented at
http://wiki
Rolf,
> thought jQuery is needed for an operative JSmol.
JSmol uses a jQuery included into its files (that's why there are *.nojquery
alternative files).
That jquery folder is sort of a backup copy, but not used in the standard
operation.
See http://wiki.jmol.org/index.php/Jmol_JavaScript_Obj
(moving this thread to Jmol-users list)
Hi Klaus
Maybe you could achieve that by setting
set scaleAngstromsPerInch
That is compatible with a less than 100% apparent size while zoom is off.
You will need to figure out the value you need.
On 21 May 2016 at 9:30, Klaus Schaper wrote:
> Hi ev
Dear Eric
> Currently, rendering is simplified (even at platformSpeed 10) during
> rotation.
Are you aware that using negative values in hermitelevel does NOT simplify
the rendering during mouse rotation? I wonder if that's also the case for
automated rotation like in capture
Hello Eugene
You should better use the jmol-users list for this kind of questions. I am
moving the discussion there.
> I'm performing animating vibrations in crystal files in XYZ format which
> is simple and well documented. But every time I'm loading the file I
> should provide unit cell vect
Dear Eric
I think it's this:
set displayCellParameters false
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Hello Eugene
> I've found the answer really helpful but using magic word "jmolscript:"
> as a second line one loose the possibility of multi models in a single
> XYZ file feature which is very useful in analysis of phonon vibrations.
I believe the 2nd line is meant for comments, that's why J
El 30 May 2016 a las 15:32, Roginskii Eugene escribió:
> And there is no other possibility to construct supercell rather than
> using "load" command?
I have no direct experience with unit cells, but this seems to be the solution:
unitcell RANGE {nnn yyy scale}
Creates a block of unit cells
Thanks Stefan
The idea is that users will add whatever content to the wiki themselves, but
since we had to somewhat restrict user sign-up because of sappmer, I have
just gone and added your site myself.
Anyway, if any of you Jmol users wishes to contribute to the wiki and have
trouble signing u
Hello Vincent
Try reading these:
http://chemapps.stolaf.edu/jmol/docs/#loadcrystallographicoptions
http://chemapps.stolaf.edu/jmol/docs/#unitcell
> Recently I try to visualize a periodic cell in Jmol, but it seems that
> the boundaries of the cell is
> automatically set to be from 0 t
Dear Jennifer
That page
> (http://chemserv.centre.edu/muzyka/spectralzoo/jsmol/supersimple.htm) I see
> the same error
is working fine for me now (Firefox under Win7). No errors.
Caffeine (default) loads ok, and I also entered some other name at the
textbox and it was loaded ok.
Try clearin
Jennifer,
Your page
http://chemserv.centre.edu/muzyka/spectralzoo
is mostly functional for me (at least in Firefox Windows7).
1. JSpecViewer loads, and it loads spectra when I click on the buttons.
2. JSmol aldo loads, althoug it is hidden due to the css rule
#structure { display: none;
Hi all
I'd appreciate any help in diagnosing a problem.
I am saving a state and when I try to restore it later, Jmol hangs
(unresponsive model).
The problem seems to be this line in the state:
structure none ({8909:14655})
Same problem with
structure none ({1.2})
structure none (all)
Thi
I have found a workaround (see below), but I still think this is a bug.
The state saved in this particular case (using "save state" ) can not be
restored (using "restore state" ) or loaded via script file.
Solution to avoid the problem: skip the
structure none {atomexpression}
lines in the sta
Ammending myself, the code should be
change
save state state0
to
~st0 = show("state").replace("structure ","#structure ");
function state0 {
return ~st0;
}
and change
restore state state0
to
state0()
-
Bob, do you mean it is a failure NOT to throw an error?
>From the doc I understand, as Eric said, that chain ID cannot be reassigned
El 22 Jun 2016 a las 12:37, Robert Hanson escribió:
> Yes, sorry, that's a failure to throw an error. Fixed.
>
> On Sun, Jun 19, 2016 at 8:43 PM, Eric Martz wr
Eric,
You could use variables that you assign and then select by those
e.g.
chainA = {chain=A and 1.1}
chainB = {chain=B and 1.1}
chainC = {chain=C and 1.1}
chainG = {chain=A and 2.1}
chainH = {chain=B and 2.1}
chainI = {chain=C and 2.1}
then
select chainG
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