Re: [Jmol-users] Set hydrogen on/off using script editor

[Manish Agrawal <manish@st...>]

Hi,

Thanks everyone for quick response. the commad "set showHydrogens
on/off" is working fine. 

"restrict" command also served the purpose but whenever I have to turn
on hydrogen display I have to call commands for cpk, bond etc, whereas
"set showHydrogens" is much simpler.

Thanks & Regards
Manish Agrawal
manish@...
http://www.strandgenomics.com
Phone: (080) 2361 1349-52/2361 8992-95

> 
> timothy driscoll wrote
> > On 2005-03-22 (10:25) Manish Agrawal wrote:
> >>
> >>I am trying this command to turn off display of hydrogen atoms: "set
> >>hydrogens off". It's not doing anything. Do I need to change any
> >>other display settings?
> > 
> > I don't think that syntax is correct.  try "restrict not hydrogen"
instead.
> > 
> > btw, script commands are well-documented by Bob Hanson here:
> > <http://www.stolaf.edu/people/hansonr/jmol/docs/>;
> 
> Hi Manish,
> 
> I guess what you're really looking for is:
> 
>   set showHydrogens on/off
> 
> This is the script-command called by "Options/Show Hydrogens" in the 
> context menu.
> 
> 
> @Bob: It seems that your Documentation isn't up to date in that point.
> (see section: "set (visibility)")
> 
> ...Oliver
> -- 
> Oliver Stueker
> =======================================================================
> = University of Paderborn                Office: W1.111               =
> = Faculty of Science/Dep. of Chemistry    phone: +49 (5251) 60-5466   =
> = Warburger Str. 100                        fax: +49 (5251) 60-3245   =
> = D-33098 Paderborn                                                   =
> = Germany                                                             =
> =======================================================================
> 
> 
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> 

Re: [Jmol-users] Set hydrogen on/off using script editor

[Manish Agrawal <manish@st...>]

Hi Tim,

Thank you very much for your help. "restrict not hydrogen" works fine
for turning hydrogen off, but I am not able to find reverse command to
turn hydrogen on in the document. Could you please help me with this.



Thanks & Regards
Manish Agrawal
manish@...
http://www.strandgenomics.com
Phone: (080) 2361 1349-52/2361 8992-95

> On 2005-03-22 (10:25) Manish Agrawal wrote:
> 
> >Hi,
> >
> >I am trying this command to turn off display of hydrogen atoms: "set
> >hydrogens off". It's not doing anything. Do I need to change any
> >other display settings?
> >
> >The reason I am executing this command is, when I am displaying a
> >molecule I want to display it without hydrogen.
> >
> 
> hi Manish,
> 
> I don't think that syntax is correct.  try "restrict not hydrogen"
instead.
> 
> 
> btw, script commands are well-documented by Bob Hanson here:
> 
> <http://www.stolaf.edu/people/hansonr/jmol/docs/>;
> 
> 
> 
> regards,
> 
> 
> tim
> -- 
> Timothy Driscoll
> molvisions - see, grasp, learn.
> <http://www.molvisions.com/>;
> usa:north carolina:raleigh
> 
> "Everything should be made a simple as possible, but not simpler." -
Albert Einstein
> 
> 
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> 
> 

RE: [Jmol-users] Set hydrogen on/off using script editor

[Herraez Sanchez Angel <angel.herraez@ua...>]

Hi Manish
To make hydrogens appear again, you have to select them and then tell =
the
program how to render them:=20
     select hydrogen
     spacefill=20
or=20
     select hydrogen
     wireframe 35
etc.

Not too intuitive, but this goes back to RasMol.

Re: [Jmol-users] Set hydrogen on/off using script editor

[Manish Agrawal <manish@st...>]

Hi,

Thanks everyone for quick response. the commad "set showHydrogens
on/off" is working fine. 

"restrict" command also served the purpose but whenever I have to turn
on hydrogen display I have to call commands for cpk, bond etc, whereas
"set showHydrogens" is much simpler.

Thanks & Regards
Manish Agrawal
manish@...
http://www.strandgenomics.com
Phone: (080) 2361 1349-52/2361 8992-95

> 
> timothy driscoll wrote
> > On 2005-03-22 (10:25) Manish Agrawal wrote:
> >>
> >>I am trying this command to turn off display of hydrogen atoms: "set
> >>hydrogens off". It's not doing anything. Do I need to change any
> >>other display settings?
> > 
> > I don't think that syntax is correct.  try "restrict not hydrogen"
instead.
> > 
> > btw, script commands are well-documented by Bob Hanson here:
> > <http://www.stolaf.edu/people/hansonr/jmol/docs/>;
> 
> Hi Manish,
> 
> I guess what you're really looking for is:
> 
>   set showHydrogens on/off
> 
> This is the script-command called by "Options/Show Hydrogens" in the 
> context menu.
> 
> 
> @Bob: It seems that your Documentation isn't up to date in that point.
> (see section: "set (visibility)")
> 
> ...Oliver
> -- 
> Oliver Stueker
> =======================================================================
> = University of Paderborn                Office: W1.111               =
> = Faculty of Science/Dep. of Chemistry    phone: +49 (5251) 60-5466   =
> = Warburger Str. 100                        fax: +49 (5251) 60-3245   =
> = D-33098 Paderborn                                                   =
> = Germany                                                             =
> =======================================================================
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: 2005 Windows Mobile Application Contest
> Submit applications for Windows Mobile(tm)-based Pocket PCs or Smartphones
> for the chance to win $25,000 and application distribution. Enter today at
> http://ads.osdn.com/?ad_id=6882&alloc_id=15148&op=click
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> 

Re: [Jmol-users] Set hydrogen on/off using script editor

[Frieda S. Reichsman <friedar@ns...>]

Manish,

First use the select command as detailed at the page Tim referred you=20
to:
>> http://www.stolaf.edu/people/hansonr/jmol/docs/

Then follow it with a rendering command such as spacefill, also=20
detailed at the URL above.

It might be a good idea to take a look at the examples at the jmol=20
demonstration page to see how the scripting language works:
http://jmol.sourceforge.net/demo/

Frieda

On Mar 22, 2005, at 12:59 AM, Manish Agrawal wrote:

>
> Hi Tim,
>
> Thank you very much for your help. "restrict not hydrogen" works fine
> for turning hydrogen off, but I am not able to find reverse command to
> turn hydrogen on in the document. Could you please help me with this.
>
>
>
> Thanks & Regards
> Manish Agrawal
> manish@...
> http://www.strandgenomics.com
> Phone: (080) 2361 1349-52/2361 8992-95
>
>> On 2005-03-22 (10:25) Manish Agrawal wrote:
>>
>>> Hi,
>>>
>>> I am trying this command to turn off display of hydrogen atoms: "set
>>> hydrogens off". It's not doing anything. Do I need to change any
>>> other display settings?
>>>
>>> The reason I am executing this command is, when I am displaying a
>>> molecule I want to display it without hydrogen.
>>>
>>
>> hi Manish,
>>
>> I don't think that syntax is correct.  try "restrict not hydrogen"
> instead.
>>
>>
>> btw, script commands are well-documented by Bob Hanson here:
>>
>> <http://www.stolaf.edu/people/hansonr/jmol/docs/>;
>>
>>
>>
>> regards,
>>
>>
>> tim
>> --=20
>> Timothy Driscoll
>> molvisions - see, grasp, learn.
>> <http://www.molvisions.com/>;
>> usa:north carolina:raleigh
>>
>> "Everything should be made a simple as possible, but not simpler." -
> Albert Einstein
>>
>>
>> -------------------------------------------------------
>> SF email is sponsored by - The IT Product Guide
>> Read honest & candid reviews on hundreds of IT Products from real=20
>> users.
>> Discover which products truly live up to the hype. Start reading now.
>> http://ads.osdn.com/?ad_ide95&alloc_id=14396&op=3Dclick
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@...
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real=20
> users.
> Discover which products truly live up to the hype. Start reading now.
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> _______________________________________________
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*************************************
Frieda S. Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.MoleculesInMotion.com
Shutesbury, MA
*************************************