Re: [Jmol-users] use of select bonds
Yes, that seems to be our issue. So we need to redo the state scripts. Thanks On 13 Jan 2017 at 18:07, Robert Hanson wrote: Ah, yes! bonds are indexed COMPLETELY differently -- and are not even the same set of bonds -- in PDB, mmCIF, and MMTF. --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] use of select bonds
Ah, yes! bonds are indexed COMPLETELY differently -- and are not even the
same set of bonds -- in PDB, mmCIF, and MMTF.
On Fri, Jan 13, 2017 at 2:29 PM, Robert Hanson wrote:
> This works fine:
>
> load $caffeine
> select bonds ({0 3 4})
> color bonds yellow
>
> so that syntax is fine. What can happen with old files, particularly from
> PDB, is that the underlying file may have changed in such a way that that
> bonds are in different orders. (Or, Jmol is reading the file slightly
> differently.) So that particular command can be a problem.
>
> On Fri, Jan 13, 2017 at 1:21 PM, Robert Hanson wrote:
>
>> Looks like a bug to me. Will get back to you.
>>
>> On Fri, Jan 13, 2017 at 12:29 PM, Kubasik, Matthew A. <
>> mkuba...@fairfield.edu> wrote:
>>
>>> Angel,
>>>
>>> I am unfamiliar with the syntax you are using.
>>>
>>> However, placing the bonds into a variable has worked for me, as in:
>>>
>>> select {oxygen and connected(1) and connected(carbon)} or {carbon and
>>> (connected(oxygen))}
>>> x1={selected}.bonds
>>> select x1
>>> bondorder 2
>>> select none
>>>
>>> I use the above code to make carbonyl bonds “double”. Works for my small
>>> peptides, but will give odd bonding structures to things like carboxylates.
>>>
>>> Matt
>>>
>>> > On Jan 13, 2017, at 11:51 AM, Angel Herráez
>>> wrote:
>>> >
>>> > Hi all
>>> >
>>> > I am not familiar with the use of "select bonds" command, so I am
>>> asking
>>> > here.
>>> >
>>> > We have somewhat old state scripts (saved in Proteopedia scenes) that
>>> > were generated by an older version of Jmol (# Jmol state version
>>> 11.8.24
>>> > 2010-04-26 08:00;).
>>> >
>>> > Right now, Jmol 14.6.0 fails to select the bonds and render their
>>> thickness
>>> > and color.
>>> > The commands in state are of this type:
>>> >
>>> > select BONDS ({5 16 27});
>>> >
>>> > Q: Has this syntax changed, or is it broken?
>>> >
>>> > I've just tried Jmol app 14.6.4 and don't know how to select bonds, my
>>> > simple test is failing
>>> >
>>> > load $caffeine
>>> > select bonds ({2 3})
>>> >
>>> > Should that work as such?
>>> >
>>> > ·
>>> > Dr. Angel Herráez
>>> > Biochemistry and Molecular Biology,
>>> > Dept. of Systems Biology, University of Alcalá
>>> > E-28871 Alcalá de Henares (Madrid), Spain
>>> >
>>> >
>>> >
>>> --
>>> > Developer Access Program for Intel Xeon Phi Processors
>>> > Access to Intel Xeon Phi processor-based developer platforms.
>>> > With one year of Intel Parallel Studio XE.
>>> > Training and support from Colfax.
>>> > Order your platform today. http://sdm.link/xeonphi
>>> > ___
>>> > Jmol-users mailing list
>>> > Jmol-users@lists.sourceforge.net
>>> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>> --
>>> Developer Access Program for Intel Xeon Phi Processors
>>> Access to Intel Xeon Phi processor-based developer platforms.
>>> With one year of Intel Parallel Studio XE.
>>> Training and support from Colfax.
>>> Order your platform today. http://sdm.link/xeonphi
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson 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
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson 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
>
>
--
Robert M. Hanson
Larson-Anderson 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
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
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Re: [Jmol-users] use of select bonds
This works fine:
load $caffeine
select bonds ({0 3 4})
color bonds yellow
so that syntax is fine. What can happen with old files, particularly from
PDB, is that the underlying file may have changed in such a way that that
bonds are in different orders. (Or, Jmol is reading the file slightly
differently.) So that particular command can be a problem.
On Fri, Jan 13, 2017 at 1:21 PM, Robert Hanson wrote:
> Looks like a bug to me. Will get back to you.
>
> On Fri, Jan 13, 2017 at 12:29 PM, Kubasik, Matthew A. <
> mkuba...@fairfield.edu> wrote:
>
>> Angel,
>>
>> I am unfamiliar with the syntax you are using.
>>
>> However, placing the bonds into a variable has worked for me, as in:
>>
>> select {oxygen and connected(1) and connected(carbon)} or {carbon and
>> (connected(oxygen))}
>> x1={selected}.bonds
>> select x1
>> bondorder 2
>> select none
>>
>> I use the above code to make carbonyl bonds “double”. Works for my small
>> peptides, but will give odd bonding structures to things like carboxylates.
>>
>> Matt
>>
>> > On Jan 13, 2017, at 11:51 AM, Angel Herráez
>> wrote:
>> >
>> > Hi all
>> >
>> > I am not familiar with the use of "select bonds" command, so I am asking
>> > here.
>> >
>> > We have somewhat old state scripts (saved in Proteopedia scenes) that
>> > were generated by an older version of Jmol (# Jmol state version 11.8.24
>> > 2010-04-26 08:00;).
>> >
>> > Right now, Jmol 14.6.0 fails to select the bonds and render their
>> thickness
>> > and color.
>> > The commands in state are of this type:
>> >
>> > select BONDS ({5 16 27});
>> >
>> > Q: Has this syntax changed, or is it broken?
>> >
>> > I've just tried Jmol app 14.6.4 and don't know how to select bonds, my
>> > simple test is failing
>> >
>> > load $caffeine
>> > select bonds ({2 3})
>> >
>> > Should that work as such?
>> >
>> > ·
>> > Dr. Angel Herráez
>> > Biochemistry and Molecular Biology,
>> > Dept. of Systems Biology, University of Alcalá
>> > E-28871 Alcalá de Henares (Madrid), Spain
>> >
>> >
>> >
>> --
>> > Developer Access Program for Intel Xeon Phi Processors
>> > Access to Intel Xeon Phi processor-based developer platforms.
>> > With one year of Intel Parallel Studio XE.
>> > Training and support from Colfax.
>> > Order your platform today. http://sdm.link/xeonphi
>> > ___
>> > Jmol-users mailing list
>> > Jmol-users@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>> --
>> Developer Access Program for Intel Xeon Phi Processors
>> Access to Intel Xeon Phi processor-based developer platforms.
>> With one year of Intel Parallel Studio XE.
>> Training and support from Colfax.
>> Order your platform today. http://sdm.link/xeonphi
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson 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
>
>
--
Robert M. Hanson
Larson-Anderson 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
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] use of select bonds
Thank you, Matt Further testing indicates that he command itself is working as it used to be. Suspicion is now on a possible change in the way bonds are indexed, between old PDB files and recent mmCIF files (this is in Proteopedia which changed the source of files last year) --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] use of select bonds
Looks like a bug to me. Will get back to you.
On Fri, Jan 13, 2017 at 12:29 PM, Kubasik, Matthew A. <
mkuba...@fairfield.edu> wrote:
> Angel,
>
> I am unfamiliar with the syntax you are using.
>
> However, placing the bonds into a variable has worked for me, as in:
>
> select {oxygen and connected(1) and connected(carbon)} or {carbon and
> (connected(oxygen))}
> x1={selected}.bonds
> select x1
> bondorder 2
> select none
>
> I use the above code to make carbonyl bonds “double”. Works for my small
> peptides, but will give odd bonding structures to things like carboxylates.
>
> Matt
>
> > On Jan 13, 2017, at 11:51 AM, Angel Herráez
> wrote:
> >
> > Hi all
> >
> > I am not familiar with the use of "select bonds" command, so I am asking
> > here.
> >
> > We have somewhat old state scripts (saved in Proteopedia scenes) that
> > were generated by an older version of Jmol (# Jmol state version 11.8.24
> > 2010-04-26 08:00;).
> >
> > Right now, Jmol 14.6.0 fails to select the bonds and render their
> thickness
> > and color.
> > The commands in state are of this type:
> >
> > select BONDS ({5 16 27});
> >
> > Q: Has this syntax changed, or is it broken?
> >
> > I've just tried Jmol app 14.6.4 and don't know how to select bonds, my
> > simple test is failing
> >
> > load $caffeine
> > select bonds ({2 3})
> >
> > Should that work as such?
> >
> > ·
> > Dr. Angel Herráez
> > Biochemistry and Molecular Biology,
> > Dept. of Systems Biology, University of Alcalá
> > E-28871 Alcalá de Henares (Madrid), Spain
> >
> >
> >
> --
> > Developer Access Program for Intel Xeon Phi Processors
> > Access to Intel Xeon Phi processor-based developer platforms.
> > With one year of Intel Parallel Studio XE.
> > Training and support from Colfax.
> > Order your platform today. http://sdm.link/xeonphi
> > ___
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> --
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today. http://sdm.link/xeonphi
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Larson-Anderson 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
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] use of select bonds
Angel,
I am unfamiliar with the syntax you are using.
However, placing the bonds into a variable has worked for me, as in:
select {oxygen and connected(1) and connected(carbon)} or {carbon and
(connected(oxygen))}
x1={selected}.bonds
select x1
bondorder 2
select none
I use the above code to make carbonyl bonds “double”. Works for my small
peptides, but will give odd bonding structures to things like carboxylates.
Matt
> On Jan 13, 2017, at 11:51 AM, Angel Herráez wrote:
>
> Hi all
>
> I am not familiar with the use of "select bonds" command, so I am asking
> here.
>
> We have somewhat old state scripts (saved in Proteopedia scenes) that
> were generated by an older version of Jmol (# Jmol state version 11.8.24
> 2010-04-26 08:00;).
>
> Right now, Jmol 14.6.0 fails to select the bonds and render their thickness
> and color.
> The commands in state are of this type:
>
> select BONDS ({5 16 27});
>
> Q: Has this syntax changed, or is it broken?
>
> I've just tried Jmol app 14.6.4 and don't know how to select bonds, my
> simple test is failing
>
> load $caffeine
> select bonds ({2 3})
>
> Should that work as such?
>
> ·
> Dr. Angel Herráez
> Biochemistry and Molecular Biology,
> Dept. of Systems Biology, University of Alcalá
> E-28871 Alcalá de Henares (Madrid), Spain
>
>
> --
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today. http://sdm.link/xeonphi
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] use of select bonds
Hi all
I am not familiar with the use of "select bonds" command, so I am asking
here.
We have somewhat old state scripts (saved in Proteopedia scenes) that
were generated by an older version of Jmol (# Jmol state version 11.8.24
2010-04-26 08:00;).
Right now, Jmol 14.6.0 fails to select the bonds and render their thickness
and color.
The commands in state are of this type:
select BONDS ({5 16 27});
Q: Has this syntax changed, or is it broken?
I've just tried Jmol app 14.6.4 and don't know how to select bonds, my
simple test is failing
load $caffeine
select bonds ({2 3})
Should that work as such?
·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871 Alcalá de Henares (Madrid), Spain
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
