[Jmol-users] Thickness to double bond and single bonds

[Hoelzer, Mark]

Morning Jmol users,



I'm wondering if there is a way to set the wireframe thickness of all single 
bonds in a small molecule to one thickness, and all double bonds to a different 
thickness.  I anticipate this may not be possible, since most atoms that 
connect with a double bond will also have single bonds - but maybe I'm wrong?


Thanks as always, Jmol community!



- Mark Hoelzer



PS: 5-cheers to Bob and anyone else that helped get the STL exporter feature 
into Jmol.  We've been hoping for that for a while (we and even coded a Ruby on 
Rails converter that ran online). But having it directly in the program is a 
definite improvement.





MSOE Center for BioMolecular Modeling - http://cbm.msoe.edu
3D Molecular Designs - 
www.3dmoleculardesigns.com
hoel...@msoe.edu
office: 414-277-4554
cell: 414-640-8668
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Re: [Jmol-users] Jmol 14.4.4_2016.03.21

[Hoelzer, Mark]

Hmm - I've also been seeing this same error for a number of our pages over the 
past week or two (for example, see the email below that I just received from a 
teacher).  It looks like if I host the PDB file on our site, it loads just 
fine. But if I try to use the "load=" command to grab it directly from the 
RCSB, it throws this "unrecognized file format" error.

Doesn't seem to be consistent across browsers either - works on some but not 
others.  I'll try to run some more tests and figure out what the "load=" 
command is and isn't working on here.

- Mark


MSOE Center for BioMolecular Modeling - http://cbm.msoe.edu
3D Molecular Designs - www.3dmoleculardesigns.com
hoel...@msoe.edu
office: 414-277-4554
cell: 414-640-8668


-

Afternoon Mark,

I am wondering if you can help me.  The page at 
http://www.3dmoleculardesigns.com/jmol/aask/zincfinger.html is not loading. my 
class was able to use it 2 weeks ago, but now it has this message "unrecogized 
file format"

-




From: Philip Bays 
Sent: Monday, March 21, 2016 4:34 PM
To: Jmol Jmol
Subject: Re: [Jmol-users] Jmol 14.4.4_2016.03.21

And I am seeing on the campus website using the 0228 release.

Possible that RCSB is down??


> On Mar 21, 2016, at 5:13 PM, Robert Hanson  wrote:
>
> I am not seeing that. Others?
> ​
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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu



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Re: [Jmol-users] connecting atoms in two different models of a pdb file

[Hoelzer, Mark]

Margaret,


Could you try something like "select atomno=XXX and model=1" to get the 
specific atom in just one of the biological units?  I think I remember being 
able to select just one of the models in an assembly using that "model=" 
command.


I'm not by my CPU right now or I'd try it myself - but if I get a chance later, 
I will!


-Mark



MSOE Center for BioMolecular Modeling - http://cbm.msoe.edu
3D Molecular Designs - 
www.3dmoleculardesigns.com
hoel...@msoe.edu
office: 414-277-4554
cell: 414-640-8668



From: Franzen, Dr. Margaret 
Sent: Friday, September 25, 2015 5:55 PM
To: Angel Herráez; jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] connecting atoms in two different models of a pdb file


Since the goal is to show the interaction between atoms that are contained in 
two different models, the command to select two atoms in the same model doesn't 
work.



I loaded the biological assembly; selected all models, and then tried to show 
interactions between models.



Although we have a workaround for creating physical models of the proteins, I 
haven't found a way to display these types of interactions on the screen for 
educational purposes.



Margaret



From: Angel Herráez [mailto:angel.herr...@uah.es]
Sent: Friday, September 25, 2015 5:19 PM
To: Franzen, Dr. Margaret; jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] connecting atoms in two different models of a pdb file



On 25 Sep 2015 at 20:15, Franzen, Dr. Margaret wrote:

> I am using Jmol Jmol 14.3.16_2015.08.11 (2015-08-11 16:13)



Wow!

It seems that "select" is not recognized, neither in my version 
14.3.16_2015.09.15



$ select atomno=3

ERROR en guión: no se reconoce la instrucción



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