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 <hans...@stolaf.edu> 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 <hans...@stolaf.edu> 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 <angel.herr...@uah.es>
>>> 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
https://lists.sourceforge.net/lists/listinfo/jmol-users
