VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 08 2017 - 15:38:45 CST
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?
On Sun, Feb 05, 2017 at 10:16:49PM +0800, sunyeping wrote:
> 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.
> 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
> 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?
> John Stone
> 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
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
-- 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/