VMD-L Mailing List

From: Anna Modzelewska (amodzelewska_at_iimcb.gov.pl)
Date: Thu Jan 12 2006 - 10:21:07 CST

Hi John,
it works now!

Thank you very much.
Anna

----- Original Message -----
From: "John Stone" <johns_at_ks.uiuc.edu>
To: "Anna Modzelewska" <amodzelewska_at_iimcb.gov.pl>
Cc: "Vlad Cojocaru" <Vlad.Cojocaru_at_eml-r.villa-bosch.de>; "VMD list"
<vmd-l_at_ks.uiuc.edu>
Sent: Thursday, January 12, 2006 5:12 PM
Subject: Re: vmd-l: secondary structure's display - problem

>
> 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