VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 13 2017 - 14:25:15 CST

Hi,
  Most likely this is simply an issue with unrecognized atom or residue naming
conventions in your specific files. STRIDE expects the atoms to follow
PDB naming conventions for the VMD "name" field. You could definitely
rename your atoms to match the PDB conventions that STRIDE is expecting.
You might have other problems also, but I would start out by examining the
atom names in the regions of the structure that you're unable to view with
the ribbon/cartoon type representations. If you can't even draw a "Tube"
representation, then that would indicate that your carbon-alpha atoms are
not named "CA" in the files that you loaded into VMD, so I'd check that
as one of the first things to look at.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Feb 11, 2017 at 09:23:39PM +0800, sunyeping wrote:
> Hi,
>
> The missing part can not be displayed as "tube" or "NewRibbons" either.
> How can I find which atom or residue names are not accepted by STRIDE?
> Could I change these names to what STRIDE accepts?
>
> Best regards.
>
> Yeping
>
> ------------------------------------------------------------------
>
> Hi,
> It is likely that the "unusual structure" warnings are arising due to
> unrecognized atom or residue names, which the STRIDE program likely
> does not accept. Will the affected part of the structure display if
> you use the "Tube" or "NewRibbons" representations, specifically?
>
> Cheers,
> John Stone
>
> ------------------------------------------------------------------
> From:å*ä¸*å¹³ <sunyeping_at_aliyun.com>
> Time:2017 Feb 5 (Sun) 22:17
> To:John Stone <johns_at_ks.uiuc.edu>
> Cc:vmd-l <vmd-l_at_ks.uiuc.edu>
> Subject:vmd-l: Re: vmd-l: vmd cannot display part of the protein in
> gromacs gro/trr file format
> Hi,
>
> This missing part can be displayed by "line" representation when I use
> "all" selection.However, when using ribbon to display it, an error
> message comes out: ribbon code encounters an unusual structure,
> geometry may not look as expected. When using "cartoon" to display it,
> no information is shown in the VMD text console bu it just doesn't
> display.
> Best regards.
> Yeping
> ------------------------------------------------------------------
> From:John Stone <johns_at_ks.uiuc.edu>
> Time:2017 Feb 4 (Sat) 00:31
> To:å*ä¸*å¹³ <sunyeping_at_aliyun.com>
> Cc:vmd-l <vmd-l_at_ks.uiuc.edu>
> Subject:Re: vmd-l: vmd cannot display part of the protein in gromacs
> gro/trr file format
> Hi,
> Is this missing structure still not displayed when you use the "all"
> selection with one of the simple graphical representations such as "lines"?
> Do you get any warnings in the VMD text console when the file is loaded?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Feb 03, 2017 at 04:44:20PM +0800, sunyeping wrote:
> > Dear all,
> > I have a protein coordinate file in gromacs gro format and a MD trajectory
> > of this protein in trr format. When I load the gro/trr file into VMD, I
> > find one of the chains of this protein cannot be displayed. I check the
> > pro coordinate file I confirm the this missing chain in VMD is all right
> > there. Could me tell me how to display this missing chain?
> > Best regards.
> > Yeping Sun
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [1]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [2]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/~johns/
> 2. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/