VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Wed Jul 20 2011 - 05:28:48 CDT

Hi

Thank you all for the suggestions. Axel, I am attaching a link below below.

http://i56.tinypic.com/mwrym8.jpg

the middle panel is the most desired, where i have changed the carbon color
to pink, and have only a single representation using Mark's
suggestion. Mark's solution thus works very well, except that it is possible
that someone wants to color 5 different residues with carbons in different
colors, in which case, the solution can become quite complicated. Secondly,
one can alter the vdw radii as per Axel's suggestion, but this would again
be a global change? Even if it is possible to change vdw radii for each
selection, the solution will not be as good as the middle panel. Axel, the
bonds representation does not seem as good as the licorice in your
suggestion? [right panel vs. left panel]

by god, i hope the above link to the image works,

Maria

On Tue, Jul 19, 2011 at 10:24 PM, Hurt, Darrell (NIH/NIAID) [E] <
darrellh_at_niaid.nih.gov> wrote:

> Great answer, Mark. Thanks!
>
>
>
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
>
> 31 Center Drive, Room 3B62G, MSC 2135
> Bethesda, MD 20892-2135
> Office 301-402-0095
> Mobile 301-758-3559
> http://bioinformatics.niaid.nih.gov (Within NIH)
> http://exon.niaid.nih.gov (Public)
>
> Disclaimer: The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be used
> by anyone who is not the original intended recipient. If you have received
> this e-mail in error please inform the sender and delete it from your
> mailbox or any other storage devices. National Institute of Allergy and
> Infectious Diseases shall not accept liability for any statements made
> that are sender's own and not expressly made on behalf of the NIAID by one
> of its representatives.
>
>
>
>
> On 7/19/11 4:19 PM, "Mark Cunningham" <cunningham_at_utpa.edu> wrote:
>
> >Darrell:
> >
> >You can assign different carbon colors to Name and to Type and to Element.
> >You can then color different selections according to Coloring Method:
> >Name or Type or Element.
> >This will give you at least three different representations that color
> >most atoms by
> >their "normal" colors and carbon differently. You can also hijack the
> >other
> >Coloring Methods if you need more than three different colors of carbon
> >but those
> >may require more work to put the other atom colors back to their "normal"
> >colors.
> >
> >Mark
> >________________________________________
> >From: Hurt, Darrell (NIH/NIAID) [E] [darrellh_at_niaid.nih.gov]
> >Sent: Tuesday, July 19, 2011 2:24 PM
> >To: Mark Cunningham; maria goranovic
> >Cc: vmd-l_at_ks.uiuc.edu
> >Subject: Re: vmd-l: shades of licorice representation
> >
> >Hi everyone,
> >
> >Mark's answer is exactly what Maria was asking for and provides a "look
> >and feel" of PyMOL to VMD. However, I wonder if Maria also wants the
> >"PyMOL-like" ability to have different molecules (structures) colored
> >differently in the scheme she has described. I think that Mark's answer
> >will color every "C" name in every molecule the same color (whether the
> >default cyan or some other color), which will make distinguishing
> >different molecules difficult if they are overlaid. Is there some way to
> >color the carbon atoms of one molecule differently than the carbon atoms
> >of another molecule while keeping ALL of the oxygen, nitrogen, sulfur,
> >etc. atoms in every molecule colored in their traditional, default colors?
> >
> >Thanks,
> >Darrell
> >
> >
> >
> >Darrell Hurt, Ph.D.
> >Section Head, Computational Biology
> >Bioinformatics and Computational Biosciences Branch (BCBB)
> >OCICB/OSMO/OD/NIAID/NIH
> >
> >31 Center Drive, Room 3B62G, MSC 2135
> >Bethesda, MD 20892-2135
> >Office 301-402-0095
> >Mobile 301-758-3559
> >http://bioinformatics.niaid.nih.gov (Within NIH)
> >http://exon.niaid.nih.gov (Public)
> >
> >Disclaimer: The information in this e-mail and any of its attachments is
> >confidential and may contain sensitive information. It should not be used
> >by anyone who is not the original intended recipient. If you have
> >received this e-mail in error please inform the sender and delete it from
> >your mailbox or any other storage devices. National Institute of Allergy
> >and Infectious Diseases shall not accept liability for any statements
> >made that are sender's own and not expressly made on behalf of the NIAID
> >by one of its representatives.
> >
> >From: Mark Cunningham <cunningham_at_utpa.edu<mailto:cunningham_at_utpa.edu>>
> >Date: Tue, 19 Jul 2011 12:53:54 -0400
> >To: maria goranovic
> ><mariagoranovic_at_gmail.com<mailto:mariagoranovic_at_gmail.com>>
> >Cc: "vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>"
> ><vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
> >Subject: RE: vmd-l: shades of licorice representation
> >
> > Maria:
> >
> >The VMD licorice representation does exactly what you want, or at least
> >exactly what is shown in the figure you sent. To change the carbon color,
> >go to the Graphics..Colors menu. Select the Category Name and Name C,
> >then choose the color you want for carbon. If you select pink for carbon,
> >then VMD will draw a bond that is half pink and half blue (if connected to
> >nitrogen). If it is still somehow cyan, then you have TWO representations
> >that are drawing the bond. Delete the other representation.
> >
> >Mark
> >________________________________
> >From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>
> >[owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>] on behalf of
> >maria goranovic
> >[mariagoranovic_at_gmail.com<mailto:mariagoranovic_at_gmail.com>]
> >Sent: Tuesday, July 19, 2011 7:53 AM
> >To: VMD list
> >Subject: vmd-l: shades of licorice representation
> >
> >Hi
> >
> >I am wondering if this feature is already present in VMD?
> >
> >In Pymol, it is possible to color an amino acid residue represented as
> >licorice in say, orange, and yet one can distinguish between different
> >atoms of the residue. For example, all bonds will become pink, but a
> >nitrogen will still appear blue and an oxygen red. If I try to color all
> >carbons in VMD pink, a C-N bond still appears in the cyan color, and the
> >effect is not the same.
> >
> >Such a representation can be very useful in visualization. for example:
> >
> >http://hwmaint.jbc.org/cgi/content/full/285/34/26245/F4
> >
> >--
> >Maria G.
> >Technical University of Denmark
> >Copenhagen
>
>
> 

-- 
Maria G.
Technical University of Denmark
Copenhagen