VMD-L Mailing List

From: sunyeping (sunyeping_at_aliyun.com)
Date: Sat Feb 11 2017 - 07:23:39 CST

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:孙业平 <sunyeping_at_aliyun.com>Time:2017 Feb 5 (Sun) 22:17To: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) 00:31To:孙业平 <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
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/