t might be helpful.
Thanks,
--Chuck
- Original Message -
From: Robert Hanson
To: Charles Shubert ; jmol-users@lists.sourceforge.net
Sent: Monday, January 30, 2012 11:16 AM
Subject: Re: [Jmol-users] JmolViewer
Chuck, question: JmolViewer extends JmolSimpleViewer, so how is it
Hi Lochana,
We embed Jmol and redistribute Jmol.jar in our free StarBiochem application
(http://web.mit.edu/star/biochem/). The StarBiochem app has a user interface
that drives Jmol with scripts through the JmolViewer interface. Although the
scripting interface works and does most things we w
On Mon, Aug 9, 2010 at 6:00 AM, Charles Shubert wrote:
Hi Bob,
Sounds like the conference was a success.
As I noted in an earlier email, I'm generating the script and I don't
exactly know when a particular script will be generated, so I then to sprinkle
extr
Hi Bob,
Sounds like the conference was a success.
As I noted in an earlier email, I'm generating the script and I don't exactly
know when a particular script will be generated, so I then to sprinkle extra
"subset"s and "select"s around to make sure that I know the selection state
when I send a
On Fri, Jul 2, 2010 at 1:56 PM, Charles Shubert wrote:
Between RC18 and RC19, rendering of parallel isosurfaces stopped working.
You really don't need "parallel" to show this bug, but "parallel" is really
cool and I like it.
--Chuck
Here is the script:
Between RC18 and RC19, rendering of parallel isosurfaces stopped working. You
really don't need "parallel" to show this bug, but "parallel" is really cool
and I like it.
--Chuck
Here is the script:
load "1crn.pdb"
parallel makeIsos{process{ subset; select {A and PROTEIN}; isoSurface surfaceA
#Bug: spacefill for residue with missing N not working
#Jmol 12.0.RC22 2010-06-24 21:45
load "2KTQ.pdb"
subset; select PROTEIN; spacefill 0 %; color bonds TRANSLUCENT 1.0;
subset; select WATER; spacefill 0 %;
#Notice the hanging residue below the DNA.
#This is [GLU]634:A
#In the 2KTQ.pdb file RE
. That is why we were interested
in the isosurface generation performance. We really appreciate the work you
did with Ivan on that.
Many thanks,
--Chuck
- Original Message -
From: Robert Hanson
To: Charles Shubert ; jmol-users@lists.sourceforge.net
Sent: Saturday, June 26, 2010
in(chain,*:A)) ignore
(not within(chain,*:A)) VDW 90 % color TRANSLUCENT 230.4 [192,208,255] NOFILL
molecular;
}}; set multiProcessor true; show mulitProcessor; makeIsos;
Bob
On Fri, Jun 25, 2010 at 11:38 AM, Charles Shubert wrote:
Bug or Feature? "display WITHIN(2.0, select
Bug or Feature? "display WITHIN(2.0, selected)" does not hide isosurface.
Script below.
Thanks,
--Chuck
# Test script
load http://pdb.rcsb.org/pdb/files/1CRN.pdb;
# Show the helices
subset; select {[ILE]7:A or [VAL]8:A or [ALA]9:A or [ARG]10:A or [SER]11:A or
[ASN]12:A or [PHE]13:A or [ASN]1
Hi Bob,
The off by 1 bug on bond transparency (with or without my typo for 38) in RC6,
seems to be fixed in RC8.
Thanks,
--Chuck
On Apr 23, 2010, at 4:49 PM, Robert Hanson wrote:
> 38 is ALA not ARG.
>
> On Fri, Apr 23, 2010 at 3:41 PM, Charles Shubert wrote:
> In RC6 Bond
In RC6 Bond Transparency appears to be applied to the wrong residues:
load "1crn.pdb";
subset; spacefill 0 %;
subset {[PRO]36:A or [GLY]37:A or [ARG]38:A}; select PROTEIN; spacefill 32 %
color bonds TRANSLUCENT 1.0;
--Chuck
---
>> On Wed, Apr 7, 2010 at 8:26 AM, Charles Shubert wrote:
>>
>>> I'm confused by the 2400% CPU usage claimed below. Does this imply
>>> that
>>> 24 cores of a multicore machine are running at 100%?
>>>
>>> I have not been able to get Jmol
code.
--Chuck
- Original Message -----
From: Robert Hanson
To: Charles Shubert ; jmol-users@lists.sourceforge.net
Sent: Wednesday, April 07, 2010 11:37 AM
Subject: Re: [Jmol-users] Jmol -- two major advances
On Wed, Apr 7, 2010 at 8:26 AM, Charles Shubert wrote:
I&#
I'm confused by the 2400% CPU usage claimed below. Does this imply that 24
cores of a multicore machine are running at 100%?
I have not been able to get Jmol to run on more than one core of my Mac 8 core
machine. In looking at the source code for Jmol 11.8.not_too_long_ago there
seems to be a
ob
On Tue, Mar 23, 2010 at 4:03 PM, Charles Shubert wrote:
I have size and translucency on sliders and that works pretty well. I
think that allowing changes of color might not work very well. In
talking with a few folks who are color blind, it seems like ambient,
diffuse, and
command:
calculate backbone
that will fill in the backbone (C, O, N) given just CA positions.
Anyone know if there is already an algorithm for this?
Bob
On Mon, Mar 22, 2010 at 2:15 PM, Charles Shubert wrote:
I should have seen that. Thanks.
On Mar 19, 2010, at 4:11 PM
I have size and translucency on sliders and that works pretty well. I
think that allowing changes of color might not work very well. In
talking with a few folks who are color blind, it seems like ambient,
diffuse, and some combination of specular values are closer to what
they can detect
Thank you!
On Mar 23, 2010, at 2:14 PM, Angel Herráez wrote:
>> 1. select an atom in a pdb file and make it the center of rotation
>
> see Scrpting Documentation, commands "select" and "center"
>
>
>> 2. restrict rendering to only those atoms or structure at a given
>> radius away from the se
Feature request: atom expression for set (lighting)
I realize that lighting attributes are globals, but it would be
helpful the set these attributes on an atom expression basis. I'd
like to use this feature to help color blind students manipulate how
atoms/structures appear in my applicati
What is the preferred way to do the following:
1. select an atom in a pdb file and make it the center of rotation
2. restrict rendering to only those atoms or structure at a given
radius away from the selected atom (center of rotation)
3. increase/decrease the radius to increase o
I should have seen that. Thanks.
On Mar 19, 2010, at 4:11 PM, Angel Herráez wrote:
> Robert Hanson wrote:
>> was there a question here?
>
> The question is in the email subject line, Bob.
>
> Charles, that PDB file only has alpha carbons for the Y chain. Not
> Jmol's fault.
>
> The model has j
load 2b64.pdb;
select *:Y.*;
spacefill 50 %;
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See
Thanks, Bob! I was going to have to write some interesting user documentation
to explain this feature. This particular thing is fairly easy to do with the
user interface for my app.
--Chuck
- Original Message -
From: Robert Hanson
To: jmol-users@lists.sourceforge.net
Sent: W
Feb 9, 2010, at 10:57 AM, Robert Hanson wrote:
Can you just give me the commands, please?
Maybe show history after that.
On Tue, Feb 9, 2010 at 9:31 AM, Charles Shubert
wrote:
Thanks for getting back to me so quickly, Bob!
Here is an app that demonstrates the bug. Put 1crn.pdb in the same
Thanks, Angel!
On Feb 24, 2010, at 12:29 PM, Angel Herráez wrote:
> Ah. numeric chain IDs! They are not common, so this passes
> unnoticed.
> Charles, that's probably a bug, but I guess you can safely remove the
> dot asterisk part and get the same result you are expecting
>
> select {[GLY]100:
script compiler ERROR: unrecognized expression token: 2.0
subset {[GLY]100:V.* or [THR]1:2.*}
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
PM, Robert Hanson
wrote:
We'll need a file and a set of script commands - certainly doesn't
do it with:
load =1crn
select helix
cartoons on
select 12-16
cartoons on
Bob
On Mon, Feb 8, 2010 at 2:17 PM, Charles Shubert
wrote:
This is a bug that has been in Jmol for a while.
Ste
This is a bug that has been in Jmol for a while.
Steps to reproduce the bug:
1. Select a set of residues from a helix
2. Render cartoons (See the set of residues from a helix as a cartoon.)
3. Select a small subset of residues of the initial set of residues
4. Render cartoons (See the small subse
It seems to me that there is a small problem with parsing pdb files
that contain hydrogen atoms. I don't see this problem with most pdb
files.
--Chuck
Using 1GXX this code snippet produces the output below:
private String[] getMoleculeElements(String script)
{
asing may be "bonds on" which I gather is a
global setting too.
BTW, Jmol 11.6+ does not accept "bonds on" any longer (a remnant
from RasMol/Chime compatibility), requiring either "set bonds on" or
the recommended "set showMultipleBonds on"
Charles Sh
I'd like to ask a slightly more general question about unique visualization
properties.
Would I be correct in saying the following?
The following visualization properties can be applied to a selected set of
atoms:
select ;
color atoms TRANSLUCENT ;
bonds on; color bond TRANSLUCENT ;
color hbon
nson
To: Charles Shubert ; jmol-users@lists.sourceforge.net
Sent: Tuesday, August 11, 2009 3:16 PM
Subject: Re: [Jmol-users] Getting list of protein secondary structures
fromJmolViewer
Charles, the information from show structure isn't exactly what is in the
header. For example, f
structures
fromJmolViewer
Sure, so in your case you want to process the header yourself and not rely
upon Jmol's processing.
On Mon, Aug 10, 2009 at 2:41 PM, Charles Shubert wrote:
Hi Bob,
In looking at the return from viewer.getProperty(null, "PolymerInfo", "*"
SHEET 10 S10 2 MET A 180 ALA A 183
SHEET 11 S11 2 PRO A 198 CYS A 201
SHEET 12 S12 2 LYS A 204 TRP A 215
SHEET 13 S13 2 GLY A 226 THR A 229
Bob Hanson
On Thu, Aug 6, 2009 at 11:17 AM, Charles Shubert
wrote:
How does my Java application get a list of secondary structure
U A 67
SHEET6 S6 2 GLN A 81 VAL A 90
SHEET7 S7 2 MET A 104 LEU A 108
SHEET8 S8 2 GLN A 135 GLY A 140
SHEET9 S9 2 LYS A 156 PRO A 161
SHEET 10 S10 2 MET A 180 ALA A 183
SHEET 11 S11 2 PRO A 198 CYS A 201
SHEET 12 S12 2 LYS A 204 TRP A 215
SHEET 13 S13 2 GLY A 22
How does my Java application get a list of secondary structures from
JmolViewer that duplicates the information in a pdb file?
For a HELIX this would be: the helix id, init residue, end residue.
For a SHEET STRAND this would be: the strand#, sheet id, number of
strands, init residue, end resi
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