Dear All,
I have two models 1PRG.PDB and 4HHB.PDB,
My probelm is , i want to create bond between suppose ,
SER A 123 (1PRG) <=> PRO B 34 (4HHB)
So how to give the command with atomno and chain to build bond
2008/5/7 <[EMAIL PROTECTED]>:
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> Today's Topics:
>
> 1. Re: line missing when using
> jmolGetPropertyAsString("stateInfo") and getState() (Bob Hanson)
> 2. jmolApplet0 inside div (Mark Halling-Brown)
> 3. Re: jmolApplet0 inside div (Bob Hanson)
> 4. Executing commands from the GUI (Andrew R Turner)
> 5. Re: Executing commands from the GUI (Bob Hanson)
> 6. [ jmol-Bugs-1959402 ] Select chain Command does not work
> anymore (SourceForge.net)
> 7. [ jmol-Bugs-1959402 ] Select chain Command does not work
> anymore (SourceForge.net)
> 8. [ jmol-Bugs-1959402 ] Select chain Command does not work
> anymore (SourceForge.net)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 08 Apr 2008 18:28:46 -0500
> From: Bob Hanson <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-developers] line missing when using
> jmolGetPropertyAsString("stateInfo") and getState()
> To: jmol-developers@lists.sourceforge.net
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> This bug is fixed for Jmol 11.5.27. In the mean time, just make sure you
> add a space character to the beginning of any file data starting with \n
> or \r.
>
> Bob
>
>
> Angel Herr?ez wrote:
>
> >Sorry if that wasn't clear enough.
> >
> >I'm reading the state from the original window using
> > var x = jmolGetPropertyAsString("stateInfo")
> >and then applying it to the new window using
> > script javascript:x
> >
> >On 8 Apr 2008 at 21:56, Angel Herr?ez wrote:
> >
> >
> >
> >>For MOLfiles witout content in the first line (mine is generated as
> inline model by reading a
> >>textarea), the call to
> >> jmolGetPropertyAsString("stateInfo")
> >>returns a string that has
> >> data "model inline"
> >>followed by a line break and the second line of the MOLfile. It seems
> that this is due to the
> >>first data line (empty here) being appended after "model inline" without
> any new line.
> >>
> >>So then, when I feed that string into Jmol (resizable popup) using
> >> getState()
> >>there is an error -format not recognized.
> >>
> >>This is fixed if I manually enter any text -even a space- into the first
> line or if I replace the
> >>first \n with \n \n
> >>
> >>Could this detail be fixed in stateInfo?
> >>
> >>
> >
> >
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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: 2
> Date: Tue, 22 Apr 2008 10:30:00 +0100
> From: Mark Halling-Brown <[EMAIL PROTECTED]>
> Subject: [Jmol-developers] jmolApplet0 inside div
> To: jmol-developers@lists.sourceforge.net
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear jmol_developers
>
> Just a quick question.
> I am developing a website with embedded jmol applets.
> I am loading the jmol applet with an ajax call using the code below (N/B
> this is all working fine)
>
> ########Javascript########
> jmolSetDocument(0);
> jmolInitialize("jmol")
> jmolSetAppletColor("#FFFFFF");
> document.getElementById("datadiv").innerHTML = jmolApplet(500, jmoltext,
> 'jmolApplet0');
>
> #######HTML##########
> <div id='datadiv'></div>
>
> I would like to colour certain residues on a onmouseover event like this:
> onmouseover="this.style.backgroundColor='#66FF00'; jmolScript('select
> resno = 150; color green;');"
>
> However this reports the error: "could not find applet jmolApplet0".
> I assume this is because it is inside a div.
> Has anyone got ideas how I tell jmolScript where to look??
>
> Cheers
> Mark
>
>
>
> --
>
> ---------------------------------------------------------------------------
> Mark Halling-Brown | Tel: +44-20-7631-6839
> Research Associate |
> Room 359 | Fax: +44-20-7631-6803
> School of Crystallography |
> Birkbeck College | Email:
> Malet Street | [EMAIL PROTECTED]
> London WC1E 7HX | [EMAIL PROTECTED]
> UK |
>
> http://people.cryst.bbk.ac.uk/~ghall04<http://people.cryst.bbk.ac.uk/%7Eghall04>
>
> ---------------------------------------------------------------------------
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 22 Apr 2008 06:04:34 -0500
> From: Bob Hanson <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-developers] jmolApplet0 inside div
> To: jmol-developers@lists.sourceforge.net
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> In the jmolApplet call, don't use the full tag -- jmolApplet0 -- use
> just an extension, and don't use "0", because that might be
> misinterpreted by some browsers as 0.
>
> document.getElementById("datadiv").innerHTML = jmolApplet(500, jmoltext,
> "1");
>
>
> then, in your call to jmolScript, refer to that same extension.
>
> onmouseover="this.style.backgroundColor='#66FF00'; jmolScript('select
> resno = 150; color green;', '1');"
>
>
> (You could use "jmolApplet0" above, but then the real id is
> jmolAppletjmolApplet0.)
>
> That should do it.
>
>
> Mark Halling-Brown wrote:
>
> >Dear jmol_developers
> >
> >Just a quick question.
> >I am developing a website with embedded jmol applets.
> >I am loading the jmol applet with an ajax call using the code below (N/B
> >this is all working fine)
> >
> >########Javascript########
> >jmolSetDocument(0);
> >jmolInitialize("jmol")
> >jmolSetAppletColor("#FFFFFF");
> >document.getElementById("datadiv").innerHTML = jmolApplet(500, jmoltext,
> >'jmolApplet0');
> >
> >#######HTML##########
> ><div id='datadiv'></div>
> >
> >I would like to colour certain residues on a onmouseover event like this:
> >onmouseover="this.style.backgroundColor='#66FF00'; jmolScript('select
> >resno = 150; color green;');"
> >
> >However this reports the error: "could not find applet jmolApplet0".
> >I assume this is because it is inside a div.
> >Has anyone got ideas how I tell jmolScript where to look??
> >
> >Cheers
> >Mark
> >
> >
> >
> >
> >
>
>
> --
> 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: Thu, 01 May 2008 15:27:54 +0100
> From: Andrew R Turner <[EMAIL PROTECTED]>
> Subject: [Jmol-developers] Executing commands from the GUI
> To: Jmol Developers <jmol-developers@lists.sourceforge.net>
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Hi,
>
> Now that my teaching commitments are finished for the moment I have a
> chance to get on with working on the dialogs in Jmol. I have had a
> look around the code and I have a question: how do you execute a jmol
> command using the GUI?
>
> I know how to create buttons and add action listeners etc. but I
> cannot seem to see the method to call to actually execute a command. I
> have tried the following (as a test) and it just gives errors:
>
> viewer.evalString("cpk 75%");
>
> (viewer is associated with the instance of the Viewer class.)
>
> Sorry if my question is obvious but I am still getting to grips with
> the structure of the package!
>
> Best regards
>
> Andy
>
> ==================================
> Dr Andrew R. Turner
> Research Computing Officer
> e: [EMAIL PROTECTED]
> t: +44 (0)131 650 7748
> w: http://www.eastchem.ac.uk/rcf
> icq: 370-899-715
> p: School of Chemistry
> University of Edinburgh
> EH9 3JJ
> ==================================
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 01 May 2008 11:27:30 -0500
> From: Bob Hanson <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-developers] Executing commands from the GUI
> To: jmol-developers@lists.sourceforge.net
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Andrew R Turner wrote:
>
> >Hi,
> >
> >Now that my teaching commitments are finished for the moment I have a
> >chance to get on with working on the dialogs in Jmol. I have had a
> >look around the code and I have a question: how do you execute a jmol
> >command using the GUI?
> >
> >I know how to create buttons and add action listeners etc. but I
> >cannot seem to see the method to call to actually execute a command. I
> >have tried the following (as a test) and it just gives errors:
> >
> >viewer.evalString("cpk 75%");
> >
> >(viewer is associated with the instance of the Viewer class.)
> >
> >Sorry if my question is obvious but I am still getting to grips with
> >the structure of the package!
> >
> >
> >
> No, no. Don't be shy. It takes some getting used to.
>
> Check org.openscience.jmol.DisplayPanel. In there you will see actions
> that call
>
> viewer.evalStringQuiet(action);
>
> "Quiet" is what you want, because otherwise messages are sent to the
> command console.
>
> Bob
>
>
>
>
>
> >Best regards
> >
> >Andy
> >
> >==================================
> > Dr Andrew R. Turner
> > Research Computing Officer
> > e: [EMAIL PROTECTED]
> > t: +44 (0)131 650 7748
> > w: http://www.eastchem.ac.uk/rcf
> >icq: 370-899-715
> > p: School of Chemistry
> > University of Edinburgh
> > EH9 3JJ
> >==================================
> >
> >
> >
>
>
> --
> 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: Wed, 07 May 2008 03:39:57 -0700
> From: "SourceForge.net" <[EMAIL PROTECTED]>
> Subject: [Jmol-developers] [ jmol-Bugs-1959402 ] Select chain Command
> does not work anymore
> To: [EMAIL PROTECTED]
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset="UTF-8"
>
> Bugs item #1959402, was opened at 2008-05-07 12:39
> Message generated for change (Tracker Item Submitted) made by Item
> Submitter
> You can respond by visiting:
>
> https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1959402&group_id=23629
>
> Please note that this message will contain a full copy of the comment
> thread,
> including the initial issue submission, for this request,
> not just the latest update.
> Category: None
> Group: None
> Status: Open
> Resolution: None
> Priority: 5
> Private: No
> Submitted By: bob morane (bobmorane84)
> Assigned to: Nobody/Anonymous (nobody)
> Summary: Select chain Command does not work anymore
>
> Initial Comment:
> With "select :A" or "select *:A" it should be possible to select Chain A
> in a PDB File.
> It's not working but it works with older versions (11.4.0).
> Tested with PDB files 1qsf and 1hla.
> Also tested JMol Applet on PDB website.
>
> ----------------------------------------------------------------------
>
> You can respond by visiting:
>
> https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1959402&group_id=23629
>
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 07 May 2008 05:30:20 -0700
> From: "SourceForge.net" <[EMAIL PROTECTED]>
> Subject: [Jmol-developers] [ jmol-Bugs-1959402 ] Select chain Command
> does not work anymore
> To: [EMAIL PROTECTED]
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset="UTF-8"
>
> Bugs item #1959402, was opened at 2008-05-07 05:39
> Message generated for change (Comment added) made by hansonr
> You can respond by visiting:
>
> https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1959402&group_id=23629
>
> Please note that this message will contain a full copy of the comment
> thread,
> including the initial issue submission, for this request,
> not just the latest update.
> Category: None
> Group: None
> Status: Open
> Resolution: None
> Priority: 5
> Private: No
> Submitted By: bob morane (bobmorane84)
> >Assigned to: Bob Hanson (hansonr)
> Summary: Select chain Command does not work anymore
>
> Initial Comment:
> With "select :A" or "select *:A" it should be possible to select Chain A
> in a PDB File.
> It's not working but it works with older versions (11.4.0).
> Tested with PDB files 1qsf and 1hla.
> Also tested JMol Applet on PDB website.
>
> ----------------------------------------------------------------------
>
> >Comment By: Bob Hanson (hansonr)
> Date: 2008-05-07 07:30
>
> Message:
> Logged In: YES
> user_id=1082841
> Originator: NO
>
> I cannot reproduce this problem. Certainly with 11.5.35 I get:
>
> $ load =1qsf
> $ select *:A
> 2179 atoms selected
> $ select *:B
> 837 atoms selected
> $ select :A
> 2179 atoms selected
>
>
> Nothing has been done in the chain selection area for some time. Please
> try the latest 11.5.x version and let us know if the problem persists. If
> it does, please send a state file (from WRITE STATE "chainselect.spt") to
> [EMAIL PROTECTED] illustrating the problem.
>
>
> ----------------------------------------------------------------------
>
> You can respond by visiting:
>
> https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1959402&group_id=23629
>
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 07 May 2008 10:34:36 -0700
> From: "SourceForge.net" <[EMAIL PROTECTED]>
> Subject: [Jmol-developers] [ jmol-Bugs-1959402 ] Select chain Command
> does not work anymore
> To: [EMAIL PROTECTED]
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset="UTF-8"
>
> Bugs item #1959402, was opened at 2008-05-07 12:39
> Message generated for change (Comment added) made by bobmorane84
> You can respond by visiting:
>
> https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1959402&group_id=23629
>
> Please note that this message will contain a full copy of the comment
> thread,
> including the initial issue submission, for this request,
> not just the latest update.
> Category: None
> Group: None
> Status: Open
> >Resolution: Fixed
> Priority: 5
> Private: No
> Submitted By: bob morane (bobmorane84)
> Assigned to: Bob Hanson (hansonr)
> Summary: Select chain Command does not work anymore
>
> Initial Comment:
> With "select :A" or "select *:A" it should be possible to select Chain A
> in a PDB File.
> It's not working but it works with older versions (11.4.0).
> Tested with PDB files 1qsf and 1hla.
> Also tested JMol Applet on PDB website.
>
> ----------------------------------------------------------------------
>
> >Comment By: bob morane (bobmorane84)
> Date: 2008-05-07 19:34
>
> Message:
> Logged In: YES
> user_id=1996704
> Originator: YES
>
> Ok your right it works with the newest version stable and prerelease.
> It's only a problem with the RSCB PDB website so I wrote to them. They are
> using a old version of Jmol 10.2.0.
> We were only shocked and thought that the bug is in the current version of
> jmol.
>
> ----------------------------------------------------------------------
>
> Comment By: Bob Hanson (hansonr)
> Date: 2008-05-07 14:30
>
> Message:
> Logged In: YES
> user_id=1082841
> Originator: NO
>
> I cannot reproduce this problem. Certainly with 11.5.35 I get:
>
> $ load =1qsf
> $ select *:A
> 2179 atoms selected
> $ select *:B
> 837 atoms selected
> $ select :A
> 2179 atoms selected
>
>
> Nothing has been done in the chain selection area for some time. Please
> try the latest 11.5.x version and let us know if the problem persists. If
> it does, please send a state file (from WRITE STATE "chainselect.spt") to
> [EMAIL PROTECTED] illustrating the problem.
>
>
> ----------------------------------------------------------------------
>
> You can respond by visiting:
>
> https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1959402&group_id=23629
>
>
>
> ------------------------------
>
> -------------------------------------------------------------------------
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