Re: [Jmol-users] writing .mol files
exactly.
You should be able to test it using
print write("coord", "mol")
and then check the console.
On Thu, Apr 14, 2011 at 5:01 PM, wrote:
> If I have selected just the "good" atoms of an interesting molecule in a
> binding pocket will "write file.mol" or "write coords file.mol" give me
> just those atoms in the file?
>
> I can't actually test this since the server, at the moment, has neither a
> current version of Jmol nor the signed applet on it.
>
> Rich
>
>
>
> --
> Benefiting from Server Virtualization: Beyond Initial Workload
> Consolidation -- Increasing the use of server virtualization is a top
> priority.Virtualization can reduce costs, simplify management, and improve
> application availability and disaster protection. Learn more about boosting
> the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
--
Benefiting from Server Virtualization: Beyond Initial Workload
Consolidation -- Increasing the use of server virtualization is a top
priority.Virtualization can reduce costs, simplify management, and improve
application availability and disaster protection. Learn more about boosting
the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] writing .mol files
If I have selected just the "good" atoms of an interesting molecule in a binding pocket will "write file.mol" or "write coords file.mol" give me just those atoms in the file? I can't actually test this since the server, at the moment, has neither a current version of Jmol nor the signed applet on it. Rich -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Select ssbonds and hbonds
Dear Jaim, After dislaying a protein in FirstGlance in Jmol: click "More Views", then "Disulfide Bonds: Show All". This also shows cysteines (not in SS bonds) and labels all cys residues. To see met sulfurs, use "Find" and enter "sulfur and met". Please recall that scenes generated in FirstGlance can be installed in Proteopedia: http://www.proteopedia.org/wiki/index.php/Help:Copying_FirstGlance_Scenes_into_Proteopedia Reminder: "cystine" means a pair of ssbonded cys residues. "cysteine" strictly speaking means cys residues not engaged in ssbonding (I think -- maybe someone can correct me?) but is sometimes used loosely to include all cys residues regardless of whether ssbonded. "cys" in Jmol selection includes both cystine and cysteine. A convenient example with cysteines, cystines, and methionines is 3kwb. Consider the following script options: select cys select cystine select sulfur and cystine select sulfur and cys select sulfur and cys and not cystine (Hbonds seem complicated to me and I can't help with them.) Regards, -Eric At 4/14/11, jaime.prilu...@weizmann.ac.il wrote: >A question just came out from a chemistry teachers workshop: >"Can you place a label pointing to an ssbond?" They wanted to >make it evident for students where hbonds and ssbonds are. > >My question: how do I select a particular (or all) ssbond/hbond ? >The idea is not to select neither of the atoms that the >bond is connecting to, but to the bond line itself. >If possible, then, can I attach a label to the selection? > >Thanks in advance, >Jaim >-- > Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il > Head Bioinformatics| > R&D Bioinformatics and Data Management | > Department of Biological Services | > Weizmann Institute of Science | fax: 972-8-9344113 > 76100 Rehovot - Israel | tel: 972-8-9344959 > > OCA, http://oca.weizmann.ac.il (the protein structure/function database) > Proteopedia, http://proteopedia.org (because life has more than 2D) > > >-- >Benefiting from Server Virtualization: Beyond Initial Workload >Consolidation -- Increasing the use of server virtualization is a top >priority.Virtualization can reduce costs, simplify management, and improve >application availability and disaster protection. Learn more about boosting >the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] An Old Paper and Jmol/Resolver
I was thinking just a little FOR loop that moves the atoms explicitly in a linear fashion. Nothing fancier than that. You want the "morph" command now, I suppose :) Bob On Thu, Apr 14, 2011 at 8:31 AM, Wayne Decatur wrote: > Hi Bob, > I was curious what commands you had in mind to use to "morph the model back > to setB"? The 'compare' command? 'minimize'? 'translateSelected'? > Thanks, > Wayne > > > Message: 1 > Date: Wed, 13 Apr 2011 14:41:51 -0500 > > From: Robert Hanson > Subject: Re: [Jmol-users] An Old Paper and Jmol/Resolver > To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > > 1) save the blown up atom positions (setA). > 2) reload the model, and save the atoms positions (setB). > 3) set the atom positions to setA. (bonds will be there) > 4) morph the model back to setB. > > Bob > > On Wed, Apr 13, 2011 at 2:24 PM, Otis Rothenberger >wrote: > > > Bob, > > > > I really want to do that in the worst way. I mean animate it back > together > > rather than just reload it. Do you have any ideas? > > > > Hmm... I wonder if reloading it with connect delete, followed by a delay > > loop reconnecting bonds, followed by a proper load to correct multiple > bonds > > would make it look like a reverse animation? > > > > > > Otis > > > > -- > > Otis Rothenberger > > Department of Chemistry > > Illinois State University Normal, IL 61790-4160 > > http://chemagic.org > > > > -- > > *From*: "Robert Hanson" > > *Sent*: Wednesday, April 13, 2011 2:50 PM > > > > > *To*: osrot...@chemagic.com, jmol-users@lists.sourceforge.net > > *Subject*: Re: [Jmol-users] An Old Paper and Jmol/Resolver > > > > > > Great -- > > > > -- I suggest a "put it back together" link. > > > > > > -- > Benefiting from Server Virtualization: Beyond Initial Workload > Consolidation -- Increasing the use of server virtualization is a top > priority.Virtualization can reduce costs, simplify management, and improve > application availability and disaster protection. Learn more about boosting > the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Select ssbonds and hbonds
You would attach a 3D echo rather than a label.
use a SMARTS search for SS:
Var ssBondAtoms = {*}.find("SMARTS","SS")
Then get those bonds:
Var ssBonds = ssBondAtoms.bonds
Now go through those, pinpointing the centers:
for (Var i = 1; i <= ssBonds.length; i++) {
Var bondCenter = ssBonds[i].xyz
script inline @{"set echo ssbond" + i +" " + bondCenter + ";echo
WHATEVER"}
}
[The script inline business is necessary because I have not gotten set echo
going with variables yet .]
Bob
On Thu, Apr 14, 2011 at 3:00 AM, wrote:
>
> A question just came out from a chemistry teachers workshop:
> "Can you place a label pointing to an ssbond?" They wanted to
> make it evident for students where hbonds and ssbonds are.
>
> My question: how do I select a particular (or all) ssbond/hbond ?
> The idea is not to select neither of the atoms that the
> bond is connecting to, but to the bond line itself.
> If possible, then, can I attach a label to the selection?
>
> Thanks in advance,
> Jaim
> --
> Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
> Head Bioinformatics|
> R&D Bioinformatics and Data Management |
> Department of Biological Services |
> Weizmann Institute of Science | fax: 972-8-9344113
> 76100 Rehovot - Israel | tel: 972-8-9344959
>
> OCA, http://oca.weizmann.ac.il (the protein structure/function database)
> Proteopedia, http://proteopedia.org (because life has more than 2D)
>
>
>
> --
> Benefiting from Server Virtualization: Beyond Initial Workload
> Consolidation -- Increasing the use of server virtualization is a top
> priority.Virtualization can reduce costs, simplify management, and improve
> application availability and disaster protection. Learn more about boosting
> the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
--
Benefiting from Server Virtualization: Beyond Initial Workload
Consolidation -- Increasing the use of server virtualization is a top
priority.Virtualization can reduce costs, simplify management, and improve
application availability and disaster protection. Learn more about boosting
the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please evaluate: Jmol and 3D-alignment
> Jmol, not JMol, please! I support that, and it is stressed in the website, but -for the record- actually Will York's JMol vanished into thin air time ago. There is no way to find it on the web. -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Select ssbonds and hbonds
According to "=?ISO-8859-1?Q?Angel_Herr=E1ez?=" :
> I would suggest something like
>
> select _S and connected(_S)
> # this works is there is only one SSbond
> set echo myBondOne {selected}
> echo " <-- This is a disulphide bond"
>
> select connected(hbond)
> # here you will need to work by pairs
Thank you Angel for a useful suggestion,
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
R&D Bioinformatics and Data Management |
Department of Biological Services |
Weizmann Institute of Science | fax: 972-8-9344113
76100 Rehovot - Israel | tel: 972-8-9344959
OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)
--
Benefiting from Server Virtualization: Beyond Initial Workload
Consolidation -- Increasing the use of server virtualization is a top
priority.Virtualization can reduce costs, simplify management, and improve
application availability and disaster protection. Learn more about boosting
the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] An Old Paper and Jmol/Resolver
Hi Bob, I was curious what commands you had in mind to use to "morph the model back to setB"? The 'compare' command? 'minimize'? 'translateSelected'? Thanks, Wayne Message: 1 Date: Wed, 13 Apr 2011 14:41:51 -0500 From: Robert Hanson Subject: Re: [Jmol-users] An Old Paper and Jmol/Resolver To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net Message-ID: Content-Type: text/plain; charset="iso-8859-1" 1) save the blown up atom positions (setA). 2) reload the model, and save the atoms positions (setB). 3) set the atom positions to setA. (bonds will be there) 4) morph the model back to setB. Bob On Wed, Apr 13, 2011 at 2:24 PM, Otis Rothenberger wrote: > Bob, > > I really want to do that in the worst way. I mean animate it back together > rather than just reload it. Do you have any ideas? > > Hmm... I wonder if reloading it with connect delete, followed by a delay > loop reconnecting bonds, followed by a proper load to correct multiple bonds > would make it look like a reverse animation? > > > Otis > > -- > Otis Rothenberger > Department of Chemistry > Illinois State University Normal, IL 61790-4160 > http://chemagic.org > > -- > *From*: "Robert Hanson" > *Sent*: Wednesday, April 13, 2011 2:50 PM > > *To*: osrot...@chemagic.com, jmol-users@lists.sourceforge.net > *Subject*: Re: [Jmol-users] An Old Paper and Jmol/Resolver > > > Great -- > > -- I suggest a "put it back together" link. >-- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please evaluate: Jmol and 3D-alignment
just for reference: Jmol, not JMol, please! :) -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Please evaluate: Jmol and 3D-alignment
Dear users, JMol has been tightly integrated into the protein alignment program supporting 3D-superposition and multiple 3D sequence alignments of peptide chains or even entire multiprotein complexes. Please evaluate the system by clicking the following demo: http://www.bioinformatics.org/strap/strap.php?script=http%3A%2F%2Fwww.bioinformatics.org%2Fstrap%2FPDF%2F2003%2FPMID12595256%2F6.txt&v3d=jmol&aligner=neobio It will launch an interactive Web-start application with JMol. Running it for the first time, the view will slowly build up. The delay is because large amounts of data (4MB) are loaded from several resources. First you will see three Uniprot sequences since these small protein files are quickly downloaded from the Uniprot repository. Once the large PDB files have been downloaded, you will see three 3D-superimposed peptide chains in JMol. The 3D- and sequence alignments are based on 3D-superposition of cAlpha atoms. Strap is driven by Drag-and-drop: you can insert further 3d-models into the view by dragging protein objects or files into the Jmol view with the mouse. You can also drag sequence features into Jmol to observe the 3D-location of mutations, phosphorylation, glycosylation ... sites. These sequence features are indicated by underlining of residues. Do not get confused with the application menu-ba. In fact there are two alternative menu-bars which can be distinguished: the one for the 3D-view has a black background, whereas the one for the multiple sequence alignment has a standard white background. The native JMol menu is still available by right-click the JMol pane. It provides all specific JMol functions. Rarely, models vanish from the JMol view. To get them back use the first menu item of the Jmol context menu. It should work on Linux, Windows, Mac and Solaris. It even copes with a fire wall of an intranet (Web proxy). Please enjoy and share your ideas and suggestions. Christoph -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Select ssbonds and hbonds
Bob, it seems that "connected" and "connect" do not accept "ssbond" as a parameter. Would that be too dificult to implement? e.g. I can do select all; hbond calculate; select connected(hbond,cys); but cannot do select connected(ssbond,cys); Hey! I forgot we have select cystine Jaime, maybe that's useful for you -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Select ssbonds and hbonds
Hello, Jaime
I'd say you cannot use labels, but you can use echos with 3D
coordinates. Also, you can draw an arrow pointing to the bond
midpoint.
Regarding selecting bonds, I'm not sure. You really select atoms
always I think. But it makes no difference.
More difficult will be to aim at all ssbonds at a time.
For a single bond, if you know the atom IDs there is no problem. For
all bonds, you probably have to find out how to extract them one by
one, maybe from the array of atom pairs.
I would suggest something like
select _S and connected(_S)
# this works is there is only one SSbond
set echo myBondOne {selected}
echo " <-- This is a disulphide bond"
select connected(hbond)
# here you will need to work by pairs
--
Benefiting from Server Virtualization: Beyond Initial Workload
Consolidation -- Increasing the use of server virtualization is a top
priority.Virtualization can reduce costs, simplify management, and improve
application availability and disaster protection. Learn more about boosting
the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Select ssbonds and hbonds
A question just came out from a chemistry teachers workshop: "Can you place a label pointing to an ssbond?" They wanted to make it evident for students where hbonds and ssbonds are. My question: how do I select a particular (or all) ssbond/hbond ? The idea is not to select neither of the atoms that the bond is connecting to, but to the bond line itself. If possible, then, can I attach a label to the selection? Thanks in advance, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| R&D Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
