hi all,
I got a small but a big problem, i had embedded the jmol applet
in a interface and tried to access it through net. even though the
jmol console is showing the protein is not loading on the console
I had got 2GB ram in my system.
i had used this command
<script>
jmolInitialize("jmol",1);
jmolApplet(420, "load PDB/2CSW.pdb; select all; color green; select
38-70;color red; select all; spacefill off; wireframe
off;cartoon;spin:off;");
</script>
Can you please help me out on this
On Sat, Feb 2, 2008 at 6:38 PM, <[EMAIL PROTECTED]>wrote:
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> Today's Topics:
>
> 1. set shadow (S?rgio Ceroni da Silva)
> 2. Re: new site launched (Bob Hanson)
> 3. Re: High-resolution graphics output? (Bob Hanson)
> 4. Re: Publishing enhanced figures in IUCr journals (Bob Hanson)
> 5. Re: set shadow (Bob Hanson)
> 6. Re: changing font size according to zoom (Bob Hanson)
> 7. Re: set shadow (S?rgio Ceroni da Silva)
> 8. Re: set shadow (Bob Hanson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 01 Feb 2008 23:48:00 -0200
> From: S?rgio Ceroni da Silva <[EMAIL PROTECTED]>
> Subject: [Jmol-users] set shadow
> To: [email protected]
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi everybody
>
> Today I found out that some old scripts were misbehaving with the latest
> (11.4.RC2) Jmol (can't tell when it started).
> The command "set shadow off" was the culprit (many commands stop
> responding after a "set shadow").
> It appears that this Rasmol/Chime command was never implemented (could
> find only a few discussions dating back to 2004 on the mailing lists).
> Strangely, only recent Jmol versions started to show this behaviour.
> Regards
> S?rgio
>
> --
> Dr. S?rgio Ceroni da Silva
> Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
> Av. Bento Gon?alves, 9500 - Pr?dio 43421 - Campus do Vale - Caixa Postal
> 15005
> Porto Alegre, RS - Brasil - 91501-970
> ==================================================
> Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309
> http://www6.ufrgs.br/bioquimica
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 01 Feb 2008 22:02:49 -0600
> From: Bob Hanson <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] new site launched
> To: [email protected]
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Angel Herr?ez wrote:
>
> > Hi Steve
> >
> > Congratulations! The site looks very interesting. I will come back to
> > you when I have some time to play with it.
> > I find some very interesting approaches there.
> >
> > At first look, resizing the browser window below 1024x768 is not very
> > well managed; Jmol resizes, but the text panels don't show their
> > scrollbars in a visible place; you should fine- tune your CSS setup.
> > You may find help in my resizable templates for Jmol.
> >
> >> This does not: jmolScript("set echo atmsize top left; echo test?);
> >
> "top" is essentially a special reserved name, so "atmsize" and "top" are
> not both allowed to be present.
>
> >------------------------------------------------------------------------
> >
> >-------------------------------------------------------------------------
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> >_______________________________________________
> >Jmol-users mailing list
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> >
> >
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 01 Feb 2008 22:13:18 -0600
> From: Bob Hanson <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] High-resolution graphics output?
> To: [email protected]
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Brian McMahon wrote:
>
> >Would it be possible for Jmol to emit images scaled to any arbitrary
> >user-requested factor? Alternatively, are there internal variables that
> >can be accessed to allow scaling of font sizes, line widths etc?
> >
> >
> >
> This will take some thinking. Bounding boxes and unit-cell axes should
> not be a problem if defined in terms of Angstroms, but that is not the
> default. Fonts in particular could be difficult. Let me see if I can do
> it specifically for images first.
>
> Bob
>
>
> >Thanks
> >Brian
> >_________________________________________________________________________
> >Brian McMahon tel: +44 1244 342878
> >Research and Development Officer fax: +44 1244 314888
> >International Union of Crystallography e-mail: [EMAIL PROTECTED]
> >5 Abbey Square, Chester CH1 2HU, England
> >
> >-------------------------------------------------------------------------
> >This SF.net email is sponsored by: Microsoft
> >Defy all challenges. Microsoft(R) Visual Studio 2005.
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> >_______________________________________________
> >Jmol-users mailing list
> >[email protected]
> >https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 01 Feb 2008 22:16:51 -0600
> From: Bob Hanson <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] Publishing enhanced figures in IUCr journals
> To: [email protected]
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Brian McMahon wrote:
>
> >>>>Q: How did you solve the font scaling problem?
> >>>>
> >>>>
> >>Definitely more than half an hour's work. Perhaps what we are going to
> >>need is some sort of font size expressed in percent -- which would use
> the
> >>Jmol default font size and offsets and some sort of default applet size
> >>(height? width? 400?), and then calculate the font sizes on the fly from
> >>that. Or what we will need is some sort of setting such as
> >>
> >> set fontScaleAutomatic 400
> >>
> >>that would take whatever font sizes and offsets are present and apply the
> >>ratio of this number to the zoom-determining dimension (height or width).
> >>Might work....
> >>
> >>
> >
> >Would it be possible just to introduce a dimensioned measure of size.
> >let us say pt, with an internal setting
> > set pixelsPerPoint 4.2
> >or whatever? Then the user who is concerned about such things would
> >have the responsibility of specifying dimensions in pt.
> >
> >
> >
> I don't think that's the issue. The issue is that when you zoom the
> drawing change the size of the image the fonts, since they are defined
> in terms of pixels, don't scale. I think all fonts should scale
> properly, not just the ones users have somehow set to do so.
>
> Bob
>
> >Brian
> >
> >-------------------------------------------------------------------------
> >This SF.net email is sponsored by: Microsoft
> >Defy all challenges. Microsoft(R) Visual Studio 2008.
> >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> >_______________________________________________
> >Jmol-users mailing list
> >[email protected]
> >https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 01 Feb 2008 22:28:38 -0600
> From: Bob Hanson <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] set shadow
> To: [EMAIL PROTECTED], [email protected]
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> S?rgio Ceroni da Silva wrote:
>
> >Hi everybody
> >
> >Today I found out that some old scripts were misbehaving with the latest
> >(11.4.RC2) Jmol (can't tell when it started).
> >The command "set shadow off" was the culprit (many commands stop
> >responding after a "set shadow").
> >It appears that this Rasmol/Chime command was never implemented (could
> >find only a few discussions dating back to 2004 on the mailing lists).
> >Strangely, only recent Jmol versions started to show this behaviour.
> >Regards
> >S?rgio
> >
> >
> >
> That's because we made "set" function only with implemented Jmol
> parameters. So really this is a GOOD thing -- that it is indicating
> properly that "set shadow" doesn't exist.
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 01 Feb 2008 23:13:35 -0600
> From: Bob Hanson <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] changing font size according to zoom
> To: [email protected]
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Xavier Prat-Resina wrote:
>
> > Dear Jmol users,
> >
> > so far I've specified the font size of my labels using the following
> > command
> > font label 40 sanserif bold
> > The problem is that when zooming in and out, the font size does not
> > change
> > accordingly to the size of the molecule. I have some labels "inside"
> > some atom spheres of a CPK model, but they become too big when I zoom
> out.
> >
> > I was wondering if there is any way to set a "dynamic" font size
> > according to the size of the molecule.
> >
> I'm working on it....
>
> > Thanks
> >
> > Xavier
> >
> >
> >
> >
> > --
> > Xavier Prat-Resina
> > Research Associate
> > Journal of Chemical Education and University of Wisconsin
> > 209 N. Brooks St. Madison, WI 53715-1116
> >
> > Tel: 608 2627917 // Fax: 608 2627145
> > e-mail: [EMAIL PROTECTED]
> > <mailto:[EMAIL PROTECTED]>; skype: xavierprat
> > http://x.prat.resina.googlepages.com
> >
> >------------------------------------------------------------------------
> >
> >-------------------------------------------------------------------------
> >This SF.net email is sponsored by: Microsoft
> >Defy all challenges. Microsoft(R) Visual Studio 2008.
> >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> >
> >------------------------------------------------------------------------
> >
> >_______________________________________________
> >Jmol-users mailing list
> >[email protected]
> >https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Sat, 02 Feb 2008 10:32:28 -0200
> From: S?rgio Ceroni da Silva <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] set shadow
> To: [email protected]
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Bob Hanson escreveu:
> > S?rgio Ceroni da Silva wrote:
> > Hi everybody
> > Today I found out that some old scripts were misbehaving with the latest
> (11.4.RC2) Jmol (can't tell when it started). The command "set shadow off"
> was the culprit (many commands stop responding after a "set shadow"). It
> appears that this Rasmol/Chime command was never implemented (could find
> only a few discussions dating back to 2004 on the mailing lists). Strangely,
> only recent Jmol versions started to show this behaviour.
> > Regards
> > S?rgio
> >
> >
> >> That's because we made "set" function only with implemented Jmol
> >> parameters. So really this is a GOOD thing -- that it is indicating
> >> properly that "set shadow" doesn't exist
>
> I'm deeply sorry if I didn't make myself clear. I wasn't complaining
> about the missing "set shadow". I was just reporting that I would expect
> for Jmol to ignore it and carry on with the remaining valid instructions
> in the script instead of the odd behaviour I've seen. Thought could be a
> symptom worth reporting, since an invalid command is affecting several
> other valid ones that follow in the script. Should this really be expected?
>
> --
> Dr. S?rgio Ceroni da Silva
> Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
> Av. Bento Gon?alves, 9500 - Pr?dio 43421 - Campus do Vale - Caixa Postal
> 15005
> Porto Alegre, RS - Brasil - 91501-970
> ==================================================
> Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309
> http://www6.ufrgs.br/bioquimica
>
>
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Sat, 02 Feb 2008 07:07:58 -0600
> From: Bob Hanson <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] set shadow
> To: [EMAIL PROTECTED], [email protected]
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> S?rgio Ceroni da Silva wrote:
>
> >Bob Hanson escreveu:
> >
> >
> >>S?rgio Ceroni da Silva wrote:
> >>Hi everybody
> >>Today I found out that some old scripts were misbehaving with the latest
> (11.4.RC2) Jmol (can't tell when it started). The command "set shadow off"
> was the culprit (many commands stop responding after a "set shadow"). It
> appears that this Rasmol/Chime command was never implemented (could find
> only a few discussions dating back to 2004 on the mailing lists). Strangely,
> only recent Jmol versions started to show this behaviour.
> >>Regards
> >>S?rgio
> >>
> >>
> >>
> >>
> >>>That's because we made "set" function only with implemented Jmol
> >>>parameters. So really this is a GOOD thing -- that it is indicating
> >>>properly that "set shadow" doesn't exist
> >>>
> >>>
> >I was just reporting that I would expect
> >for Jmol to ignore it and carry on with the remaining valid instructions
> >in the script instead of the odd behaviour I've seen. Thought could be a
> >symptom worth reporting, since an invalid command is affecting several
> >other valid ones that follow in the script. Should this really be
> expected?
> >
> >
> Whether or not it is expected, I'm just saying that the current behavior
> is probably better than the previous in that now you can find the points
> in your old Chime scripts that should be modified to run properly in
> Jmol. "set shadow" is fairly superficial, but there could be other Chime
> settings that are more critical. As it was, your script might silently
> malfunction; now you get to find out exactly what in Chime is not
> implemented in Jmol.
>
> If you would like to have a setting that ignores SET variable errors,
> that would be easy to implement.
>
> Bob
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
>
>
> ------------------------------
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>
> ------------------------------
>
> _______________________________________________
> Jmol-users mailing list
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>
>
> End of Jmol-users Digest, Vol 21, Issue 2
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