VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 12 2006 - 10:12:47 CST

Hi,
  I've compiled both a Linux and Windows build of Stride with increased
residue atom count limits for you and placed the binaries here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/stridehack/

Please grab those and let me know if they solve your problem.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 12, 2006 at 01:23:56PM +0100, Anna Modzelewska wrote:
> Great!
> My ligand has 173 atoms defined with ATOM cards.
> I use VMD mainly on Windows, but we have installed it also on Linux
> computer. So your help with Stride on Linux will be very apreciated too.
>
> Thank you!
> Anna
>
> ----- Original Message -----
> From: "John Stone" <johns_at_ks.uiuc.edu>
> To: "Vlad Cojocaru" <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
> Cc: "Anna Modzelewska" <amodzelewska_at_iimcb.gov.pl>; "VMD list"
> <vmd-l_at_ks.uiuc.edu>
> Sent: Wednesday, January 11, 2006 4:58 PM
> Subject: Re: vmd-l: secondary structure's display - problem
>
>
> >
> >Hi,
> > I can certainly compile a Windows Stride with the increased limit if that
> >will solve Anna's problem...
> >
> > John
> >
> >On Wed, Jan 11, 2006 at 04:25:01PM +0100, Vlad Cojocaru wrote:
> >>Dear Anna,
> >> So, I was right in guessing your problem ... However I am afraid that
> >>I have no experience whatsoever with compiling in Windows .... On linux
> >>I could help you to fix this ... but on Windows maybe somebody else can
> >>give you a hint .... But the problem is clear .. you need to increase
> >>the maximum number of atoms in standard or non-standard (depending
> >>whether your ligand comes with ATOM or HETATM cards) residues in
> >>stride.h. For linux I believe those numbers are set to 75 and 200
> >>respectively in the stride.h used for compiling the stride executable
> >>delievered with vmd, but again no idea about windows.... sorry
> >>
> >>vlad
> >>
> >>Anna Modzelewska wrote:
> >>
> >>> Dear Vlad,
> >>> thank you for the answer.
> >>> The error that I get is "to many atoms in residue (ligand name)", my
> >>> ligand is not linked to the protein and it is defined with ATOM cards.
> >>> I use VMD on Windows XP.
> >>> I'm not familiar with compiling. Could you please tell me where can I
> >>> find the stride.h file and how to compile it?
> >>> I guess after compiling the program, I just have to overwrite the
> >>> stride_win32.exe file in the vmd directory?
> >>>
> >>> Anna
> >>>
> >>> ----- Original Message ----- From: "Vlad Cojocaru"
> >>> <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
> >>> To: "Anna Modzelewska" <amodzelewska_at_iimcb.gov.pl>
> >>> Cc: "VMD list" <vmd-l_at_ks.uiuc.edu>
> >>> Sent: Tuesday, January 10, 2006 6:08 PM
> >>> Subject: Re: vmd-l: secondary structure's display - problem
> >>>
> >>>
> >>>> Dear Anna,
> >>>> What error do you get in the console upon running STRIDE? Is the
> >>>> ligand defined with ATOM cards or with HETATM cards??? Is your ligand
> >>>> coordinated anyhow to one of the protein residues?
> >>>> Just trying to guess ... if your ligand is defined with ATOM cards
> >>>> and
> >>>> if you get an error message that sounds like "to many atoms in residue
> >>>> ...." then you should just compile STRIDE yourself with increasing the
> >>>> number of maximum atoms in a standard residue (standard means defined
> >>>> with ATOM cards) by changing the line 43 of stride.h file prior to
> >>>> compilation...
> >>>> But first .. tell us the error that you get and then maybe we can
> >>>> help more ...
> >>>>
> >>>> vlad
> >>>>
> >>>>
> >>>> Anna Modzelewska wrote:
> >>>>
> >>>>> Hi,
> >>>>> I have problem with STRIDE. In my model I have two proteins and a
> >>>>> ligand. When I load the whole model into the VMD it doesn't recognize
> >>>>> the secondary structure. However when I load the proteins and the
> >>>>> ligand as two separate files it does. The same behavior I observed in
> >>>>> the model containing 5 proteins, and ATP. It's strange because STRIDE
> >>>>> recognize the sec. str. even when protein has non-standard residues
> >>>>> for which I had to define the topology by myself. Once it finds in
> >>>>> the
> >>>>> pdb file a residue that is not a part of protein or membrane it
> >>>>> doesn't do anything.
> >>>>> It's not funny to cut the files and load them separately each time
> >>>>> when I need to see the secondary structure or to use the new-cartoon
> >>>>> graphic representation.
> >>>>> Is there any way to resolve this problem?
> >>>>>
> >>>>> Thanks for any advises
> >>>>> Anna
> >>>>>
> >>>>>
> >>>>>
> >>************************************************************************
> >>>>>
> >>>>> Anna Modzelewska, M.Sc. amodzelewska_at_iimcb.gov.pl
> >>>>> <mailto:amodzelewska_at_iimcb.gov.pl>
> >>>>> International Institute of Molecular and Cell Biology
> >>>>> http://www.iimcb.gov.pl/
> >>>>> Trojdena 4, 02-109 Warsaw, Poland
> >>>>> phone: +48 22 5970721 fax: +48 22 5970715
> >>>>>
> >>************************************************************************
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>> --
> >>>> Dr. Vlad Cojocaru
> >>>> EML Research gGmbH
> >>>> Molecular and Cellular Modeling Group
> >>>> Schloss-Wolfsbrunnenweg 33
> >>>> 69118 Heidelberg, Germany
> >>>> Phone: +49-6221-533266
> >>>> Fax: +49-6221-533298
> >>>> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> >>>> http://projects.villa-bosch.de/mcm/people/cojocaru/
> >>>>
> >>>
> >>>
> >>
> >>--
> >>Dr. Vlad Cojocaru
> >>EML Research gGmbH
> >>Molecular and Cellular Modeling Group
> >>Schloss-Wolfsbrunnenweg 33
> >>69118 Heidelberg, Germany
> >>Phone: +49-6221-533266
> >>Fax: +49-6221-533298
> >>e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> >>http://projects.villa-bosch.de/mcm/people/cojocaru/
> >>
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078