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
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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
According to =?ISO-8859-1?Q?Angel_Herr=E1ez?= angel.herr...@uah.es:
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|
RD 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)
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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, 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|
RD 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)
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If nature does not answer first what we want,
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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| RD 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
