On 3 Feb 2006 at 0:58, Tamas Horvath wrote:
> Indeed they are aligned. So u say that e.g. I can make jmol render model 0 as
> static, and all the
> others animated?
I think Jmol cannot do this; you can see all models superimposed, or you
can choose one, or you can get an animation with one at
On Feb 2, 2006, at 5:58 p, Tamas Horvath wrote:
hi Tamas,
are all of your models aligned to your reference structure? if so,
you could just add your reference as a separate model in your multi-
model file - no need to add it as a chain to every model. Jmol has
decent tools to manipulate model
hi Tamas,are all of your models aligned to your reference structure? if so,
you could just add your reference as a separate model in your multi-model file - no need to add it as a chain to every model. Jmol hasdecent tools to manipulate models. (there are several tools availablefor aligning model
On Feb 2, 2006, at 5:02 p, Tamas Horvath wrote:
well.. before I run the simulation, I have a pdb file which
contains my reference structure. After md, I create another pdb
file with multiple models.
Of course I can merge the 2 files, but that would mean I would need
to copy my reference s
Cannot be done.If you are going to load both chains at the same time, and they are
logically associated, then it seems to me that they *should* be in thesame file.
well.. before I run the simulation, I have a pdb file which contains my
reference structure. After md, I create another pdb file with m
Programmers are too busy improving and implementing our suggestions for
the program. That's why the doc's are behind desirable state.
I don't know either about all files, but yes fro some.
We could collaborate on this documentation through the Wiki. I have just
opened a page for it:
http://wiki.
> ok... Let me explain:
> I've got a structure at time point 0. This is the reference. I want to
> see,
> how it changes through time, so I want it to be rendered throughout the
> animation.
OK, I understand.
> I have a simulation, and from that I create a pdb file, that contains many
> models,
De: [EMAIL PROTECTED]
>Oh, I would have already if I knew what they all were. :-)
>
>But other than Jmol.js and Jmol.jar and Jmol.sh I haven't very much of a
>clue :-)
Ok, I have done a first version.
I am committing it under CVS.
It's not complete, I hope someone else will modify it
Nico
-
On Thu, February 2, 2006 2:12 pm, [EMAIL PROTECTED] said:
>
>
> De: [EMAIL PROTECTED]
>>
>>I'd like to see this file expanded to have, even a brief, description of
>>each of the files in the distribution.
>
> Would you be willing to write the descriptions ?
Oh, I would have already if I knew what
De: [EMAIL PROTECTED]
>
>I'd like to see this file expanded to have, even a brief, description of
>each of the files in the distribution.
Would you be willing to write the descriptions ?
Nico
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I'd like to see this file expanded to have, even a brief, description of
each of the files in the distribution.
Rich
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On Feb 2, 2006, at 12:00 p, Miguel wrote:
On Feb 2, 2006, at 11:32 a, Angel Herraez wrote:
1.- I still think "connect" is more intuitive for changing bond
order, but I am not thinking much in terms of distance as Bob, just
on selecting the atoms I want to connect-disconect-change.
2.- Apart fr
Can Jmol read a zipped/jar-ed pdb file?
> so it is not possible to read and render multiple structures at the same
> time?
No, reading multiple structures into the same window is not supported.
Miguel
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how can ı do it.
thanks
ok... Let me explain:I've got a structure at time point 0. This is the reference. I want to see, how it changes through time, so I want it to be rendered throughout the animation.I have a simulation, and from that I create a pdb file, that contains many models, each representing a timepoint. And wh
> Sorry, at this time I really cannot follow all this traffic.
> I started the digression about "connect double" etc. in a post (30
> Jan) that seemingly went unnoticed (maybe becuase I changed the
> subject line to something more significant).
>
> To be brief:
>
> 1.- I still think "connect" is m
> If I would like to do something like that, where should I start looking in
> the source code?
Supporting the general case of loading more than one molecular model file
is a *huge* job that would impact the entire system.
If it were straightforward then it would already have been done.
> what
This command already exists in RasMol/Chime and Jmol.
set bonds off
Will display all bonds as single order.
The command name was poorly chosen in RasMol.
carried over to Jmol:
set bonds ON/OFF
In some file formats (.mol files, for example) the connection data may
indicate the bond
Sorry, at this time I really cannot follow all this traffic.
I started the digression about "connect double" etc. in a post (30
Jan) that seemingly went unnoticed (maybe becuase I changed the
subject line to something more significant).
To be brief:
1.- I still think "connect" is more intuitive
A gzipped file yes, but not a zipped file (I just tested it)
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If I would like to do something like that, where should I start looking in the source code?what I want to do is the following:I have a structure, which I run through a molecular dynamics simulation.I want to render the initial structure as a reference, and watch how the structure changes in course
De: Egon Willighagen <[EMAIL PROTECTED]>
>A: jmol-users@lists.sourceforge.net
>Sujet: Re: [Jmol-users] Re: compressed PDB
>Date: Thu, 2 Feb 2006 17:01:37 +0100
>
>On Thursday 02 February 2006 16:56, Tamas Horvath wrote:
>> or gzipped of course
>>
>> On 2/2/06, Tamas Horvath <[EMAIL PROTECTED]> wro
On Thursday 02 February 2006 17:20, Tamas Horvath wrote:
> so it is not possible to read and render multiple structures at the same
> time?
Yes, but that's something else... but at least Jmol does not support a zip
file with more than one PDB file... see also below.
> On 2/2/06, [EMAIL PROTECTED
Bob, I think it would be a good idea for you to coordinate with others on
the list to determine what the commands should be.
I'd like to do that. Let's bat around a few possibilities. I know my own
proposition is a moving target. The issue for me came up as I was
rewriting the documentatio
so it is not possible to read and render multiple structures at the same time?On 2/2/06, [EMAIL PROTECTED]
<[EMAIL PROTECTED]> wrote:
De: Egon Willighagen <[EMAIL PROTECTED]>>A: jmol-users@lists.sourceforge.net>Sujet: Re: [Jmol-users] Re: compressed PDB
>Date: Thu, 2 Feb 2006 17:01:37 +0100>>On Th
> or gzipped of course
gzip: yes ... gzip is designed for compressing individual files. Jmol can
read any file in gzip format.
zip: no ... zip is not designed for compressing individual files. Rather,
it is designed for compressing directory structures. Jmol would not know
which file to choose t
thanksOn 2/2/06, Egon Willighagen <[EMAIL PROTECTED]> wrote:
On Thursday 02 February 2006 16:56, Tamas Horvath wrote:> or gzipped of course>> On 2/2/06, Tamas Horvath <[EMAIL PROTECTED]> wrote:> > Can Jmol read a zipped/jar-ed pdb file?
Yes, just like an unziped/unjared PDF file. Jmol detects this
On Thursday 02 February 2006 16:56, Tamas Horvath wrote:
> or gzipped of course
>
> On 2/2/06, Tamas Horvath <[EMAIL PROTECTED]> wrote:
> > Can Jmol read a zipped/jar-ed pdb file?
Yes, just like an unziped/unjared PDF file. Jmol detects this on the fly.
Egon
--
[EMAIL PROTECTED]
PhD student on
> I disagree. From a user perspective, "single" and "double" are just
> rendering issues of wireframe.
> I know, programmatically they are more akin to connect,
Actually, I think that they are closer to wireframe. That is why I
initially put them with wireframe.
But, then again, I thought that '
> on the other hand, it would be nice to be able to tell the wireframe
> command whether or not to display the bond order. perhaps an
> addition to the set command (e.g., set bondorder on|off)?
This command already exists in RasMol/Chime and Jmol.
set bonds off
Will display all bonds as singl
Timothy Driscoll wrote:
a) both connect and wireframe have a dependence upon the set
bondmode setting.
b) the sequence:
select carbon
connect 1.5 (hydrogen)
adds C-H bonds, but then, right after it,
connect double
is unpredictable. One then needs to specify
set bondmode OR
first to do t
> About connect/wireframe. Maybe I wasn't clear.
>
> wireframe SINGLE, DOUBLE, AROMATIC, etc.
>
> makes good sense.
Feedback from others indicated that they thought that bond order should
also be part of the 'connect' command.
> Just like wireframe ON/OFF, we aren't defining bonds,
> just
> tweak
or gzipped of courseOn 2/2/06, Tamas Horvath <[EMAIL PROTECTED]> wrote:
Can Jmol read a zipped/jar-ed pdb file?
Tim, et al.
Let's have more of a discussion about this.
Maybe it is best to have SINGLE,DOUBLE, etc. in connect instead of
wireframe.
But the way this is being implemented is a problem.
Here's a suggestion:
Option 1 (current 00.48)
connect:
creates single bonds based on distance, regardless
On Feb 2, 2006, at 10:20 a, Bob Hanson wrote:
I disagree. From a user perspective, "single" and "double" are just
rendering issues of wireframe.
bond color and diameter are display issues, but I think bond order
implies something much more inherent, and it should not be considered
a renderi
On Thu, February 2, 2006 10:20 am, Bob Hanson said:
> I disagree. From a user perspective, "single" and "double" are just
> rendering issues of wireframe.
Wireframe should be allowed to respect or not respect the underlying
connect type. If atoms are connected using a double bond then that *is*
th
I disagree. From a user perspective, "single" and "double" are just
rendering issues of wireframe.
I know, programmatically they are more akin to connect, but here's the
problem:
If you propose
connect DOUBLE
instead of
wireframe DOUBLE
then,
a) both connect and wireframe have a dependence
On Feb 2, 2006, at 9:58 a, Bob Hanson wrote:
Thanks, Miguel, especially for the ZIP option.
About connect/wireframe. Maybe I wasn't clear.
wireframe SINGLE, DOUBLE, AROMATIC, etc.
makes good sense. Just like wireframe ON/OFF, we aren't defining
bonds, just
tweaking how they are displayed (
I think we need a welcome message for the mailing list reminding users
that there is a difference between a public mailing list like this one
and personal email. Which to me and many people on the net means that
mailers should exercise discipline in keeping mail messages small.
* Restict data
Thanks, Miguel, especially for the ZIP option.
About connect/wireframe. Maybe I wasn't clear.
wireframe SINGLE, DOUBLE, AROMATIC, etc.
makes good sense. Just like wireframe ON/OFF, we aren't defining bonds, just
tweaking how they are displayed (at least from a user perspective).
I was only sug
Miguel wrote:
Jmol prerelease 10.00.48 is now available for download from:
www.jmol.org/files
This version includes the following:
- Support for Catalan localization
(Thanks to Toni for the translation and Nico for integration)
- change of some commands from WIREFRAME -> CONNECT (see below
On Feb 1, 2006, at 9:56 p, Miguel wrote:
Bob wrote:
To me it would seem more logical to have
connect DELETE
rather than
wireframe DELETE
Bob feels that the commnd for deleting bond should be
connect delete;
rather than
wireframe delete;
hi Miguel,
I agree with this as well.
t
On Feb 2, 2006, at 9:30 AM, Miguel wrote:The problem is the last HELIX record.There needs to be a space character after the sequence number ... tospecify the insertion code.All of the other records have this.Thank you, thank you, thank you! This is a beautiful thing, it works with this change, of c
Jmol prerelease 10.00.48 is now available for download from:
www.jmol.org/files
This version includes the following:
- Support for Catalan localization
(Thanks to Toni for the translation and Nico for integration)
- change of some commands from WIREFRAME -> CONNECT (see below)
- binary d
>
> On Feb 2, 2006, at 8:51 AM, [EMAIL PROTECTED] wrote:
>>
>>
>> Could you send the pdb files so that we can try to open it and see
>> where the exception happens ?
>
> I am attaching the file at this point because I realize that my
> method of looking at character length may be unreliable--I am
On Feb 2, 2006, at 9:06 AM, Miguel wrote:Q: The file is bad ... Can't you pull a valid file from the PDB?I am in my usual situation of converting someone else's Chime tutorial to Jmol. They have a script that uses atomnos that are specific to this pdb file, not the same as the original pdb file. So
On Thursday 02 February 2006 15:03, Frieda Reichsman wrote:
> On Feb 2, 2006, at 8:55 AM, Miguel wrote:
> > file format is invalid.
> >
> > PDB files must have records (lines) that are 80 characters long.
> >
> > You have a record that is short.
>
> It looks to me like every line in the file is sho
>
> On Feb 2, 2006, at 8:55 AM, Miguel wrote:
>>
>> file format is invalid.
>>
>> PDB files must have records (lines) that are 80 characters long.
>>
>> You have a record that is short.
>
> It looks to me like every line in the file is short, and the header
> has varying degrees of "shortness". So
On Feb 2, 2006, at 8:55 AM, Miguel wrote:file format is invalid.PDB files must have records (lines) that are 80 characters long.You have a record that is short.It looks to me like every line in the file is short, and the header has varying degrees of "shortness". Some as short as 67, and the atom r
> Hi,
>
> I am getting the following error message in the Java console, on Mac
> OSX10.4, can someone tell me what it means? I suspect I am doing
> something simple wrong, but cannot seem to find my error.
>
> error opening file:/Users/friedar/Sites/minm/scitech/boyer/animations/
> enzyme/cox2.pdb
De: Frieda Reichsman <[EMAIL PROTECTED]>
>
>Hi,
>
>I am getting the following error message in the Java console, on Mac
>OSX10.4, can someone tell me what it means? I suspect I am doing
>something simple wrong, but cannot seem to find my error.
>
>error opening file:/Users/friedar/Sites/minm/
Hi,I am getting the following error message in the Java console, on Mac OSX10.4, can someone tell me what it means? I suspect I am doing something simple wrong, but cannot seem to find my error.error opening file:/Users/friedar/Sites/minm/scitech/boyer/animations/enzyme/cox2.pdbjava.lang.StringInde
>> I think there are two concepts:
>> - the connections/bond -> connect
>> - the visualisation of the connections/bonds -> wireframe
>
> As I have posted before, I also think it makes more sense to have
> display-rendering under WIREFRAME and bonding under CONNECT
> and this will mean not only
> "
> I think there are two concepts:
> - the connections/bond -> connect
> - the visualisation of the connections/bonds -> wireframe
As I have posted before, I also think it makes more sense to have
display-rendering under WIREFRAME and bonding under CONNECT
and this will mean not only
"connect del
On Thursday 02 February 2006 03:56, Miguel wrote:
> Bob wrote:
> > To me it would seem more logical to have
> >
> > connect DELETE
> >
> > rather than
> >
> > wireframe DELETE
>
> Bob feels that the commnd for deleting bond should be
>
> connect delete;
>
> rather than
>
> wireframe delete;
>
>
On Thursday 02 February 2006 00:32, EXTEIDE (sent by Nabble.com) wrote:
> Did you hear about EXTEIDE?
>
> If you're working on Windows, visit once this site. http://www.exteide.com
>
> I think that will be referenced to your development.
Is this some kind of SPAM? What's the deal with it? It does
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