Re: [ccp4bb] DNA/RNA modeling

[jens j birktoft]

and if everything else fails including kicking the trash can one could
indeed read the manual/FAQ - thanks  Paul


On Wed, May 23, 2012 at 4:27 PM, Paul Emsley wrote:

>
> On Wed, May 23, 2012 at 12:54 PM, Mark J van Raaij  > wrote:
> even more flexible than COOT?
> - the only thing I can think of that I haven't worked out how to do in
> COOT is grabbing and moving one atom at a time.
>
>
> On 23/05/12 19:50, jens j birktoft wrote:
>
> Thanks Mark.
>
>  As a matter of fact that is what I am really looking for.  The ability
> to move one or a few selected atoms/fragments at a time.
>
>
> And you thought that Coot was not flexible enough to do that?
>
> :-(
>
> Coot FAQ 4.23
>
>
> http://www.biop.ox.ac.uk/coot/doc/coot-faq.html#How-do-I-_0022grab_0022-just-one-atom-in-Real-Space-Refinement_002fRegularization_003f
>
> Also:
>
> If you don't want regularization/refinement, use the Rotate/Translate tool
> and Ctrl-click the atom(s) to move them one at a time.
>
> If you want "on the fly" regularization/refinement of fragments that
> include atoms that don't move when you "drop" them you need to fix them
> with the Fix Atom tool before regularization/refinement.
>
> HTH,
>
> Paul.
>
>


-- 
Jens J. Birktoft
e-mail: jens.kn...@gmail.com
slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025
Phone: 212-749-5057

Re: [ccp4bb] DNA/RNA modeling

[Paul Emsley]

On Wed, May 23, 2012 at 12:54 PM, Mark J van Raaij 
mailto:mjvanra...@cnb.csic.es>> wrote:

even more flexible than COOT?
- the only thing I can think of that I haven't worked out how to do in 
COOT is grabbing and moving one atom at a time.



On 23/05/12 19:50, jens j birktoft wrote:

Thanks Mark.

As a matter of fact that is what I am really looking for.  The 
ability to move one or a few selected atoms/fragments at a time.




And you thought that Coot was not flexible enough to do that?

:-(

Coot FAQ 4.23

http://www.biop.ox.ac.uk/coot/doc/coot-faq.html#How-do-I-_0022grab_0022-just-one-atom-in-Real-Space-Refinement_002fRegularization_003f

Also:

If you don't want regularization/refinement, use the Rotate/Translate 
tool and Ctrl-click the atom(s) to move them one at a time.


If you want "on the fly" regularization/refinement of fragments that 
include atoms that don't move when you "drop" them you need to fix them 
with the Fix Atom tool before regularization/refinement.


HTH,

Paul.

Re: [ccp4bb] DNA/RNA modeling

[Francis E Reyes]

For the RNA I recommend Eric Westhof's Assemble. 

F

On May 23, 2012, at 9:32 AM, jens j birktoft wrote:

> Hi everybody,
> 
> Does anyone know of a (non-commercial) software  that are suitable for 
> modeling DNA/RNA structures.  Coot is great, however I am looking something 
> that allows more flexibility
> 
> Thanks
> 
> 
> -- 
> Jens J. Birktoft
> e-mail: jens.birkt...@nyu.edu
> 
> slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025
> Phone: 212-749-5057

Re: [ccp4bb] DNA/RNA modeling

[Tuhin Bhowmick]

Hi Jens,
You can try NAMOT (Nucleic Acid MOdelling Tool), from the links below.

http://namot.sourceforge.net/
http://sourceforge.net/projects/namot/

Best,

Tuhin.

Tuhin Bhowmick
Prof. S. Ramakumar’s Lab
Biocrystallography and Computation
Department of Physics
Indian Institute of Science
Bangalore, 560012
India





On Wed, May 23, 2012 at 10:18 PM, Francisco Hernandez-Guzman <
francisco.hernan...@accelrys.com> wrote:

> Hi Jens,
>
> ** **
>
> You can try the free DS Visualizer:
> http://accelrys.com/products/discovery-studio/visualization-download.php**
> **
>
> ** **
>
> It comes with a free molecular builder for proteins, dna/rna and ligands.
> Please note that if you do need to make anything more interesting (energy
> calculations, minimizations, md, etc) will then need a license.
>
> ** **
>
> I hope this helps.
>
> ** **
>
> Francisco
>
> ** **
>
> Full Disclaimer: I do work for Accelrys. 
>
> ** **
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *jens
> j birktoft
> *Sent:* Wednesday, May 23, 2012 9:32 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] DNA/RNA modeling
>
> ** **
>
> Hi everybody,
>
> ** **
>
> Does anyone know of a (non-commercial) software  that are suitable for
> modeling DNA/RNA structures.  Coot is great, however I am looking something
> that allows more flexibility
>
> ** **
>
> Thanks
>
> ** **
>
> ** **
>
> --
> Jens J. Birktoft
> e-mail: jens.birkt...@nyu.edu 
>
>
> slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025
> Phone: 212-749-5057
>

Re: [ccp4bb] DNA/RNA modeling

[Francisco Hernandez-Guzman]

Hi Jens,

You can try the free DS Visualizer: 
http://accelrys.com/products/discovery-studio/visualization-download.php

It comes with a free molecular builder for proteins, dna/rna and ligands. 
Please note that if you do need to make anything more interesting (energy 
calculations, minimizations, md, etc) will then need a license.

I hope this helps.

Francisco

Full Disclaimer: I do work for Accelrys.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of jens j 
birktoft
Sent: Wednesday, May 23, 2012 9:32 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] DNA/RNA modeling

Hi everybody,

Does anyone know of a (non-commercial) software  that are suitable for modeling 
DNA/RNA structures.  Coot is great, however I am looking something that allows 
more flexibility

Thanks


--
Jens J. Birktoft
e-mail: jens.birkt...@nyu.edu

slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025
Phone: 212-749-5057