VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Jan 12 2006 - 06:43:06 CST

Dear Anna,
  Ok... that is clear the problem and if John can give you a Windows
executable compiled with something like 200 max atoms in standard
residues should be solving the problem ... As for Linux ... I will send
you the stride zipped archive (see next email addressed only to you).
After you copy the file on your Linux machine, you should type in a
terminal "tar xzvf stride.tar.gz". You will get a directory which stores
all the files necessary for compilation. If you "cd" to that directory
and edit the "stride.h" file you will see at line 43 and 44 the following:

#define MAX_AT_IN_RES 100
#define MAX_AT_IN_HETERORES 200

First line is for standard residues (provided with ATOM cards) and
second is for residues provided with HETATM cards... Before compilation
you should change the numbers according to your needs .. (for example
200 in the first line .. anyhow > 173). After you did that, type "make"
in the directory and this should give you an executable "stride" in this
directory. On a standard Linux you should not get any errors upon
"make". To make this executable available for vmd you have to copy it in
your vmd installation directory (for ex: /usr/local/lib/vmd .. might be
different for you!!) and change the name to "stride_LINUX" (there should
already be a file like that present). After you complete this
steps...you should be able to use stride with you ligand on Linux...

If you have any problems with the compilation ... I can compile one here
for you or maybe John can do it if you tell him the exact Linux
distribution that you have (just to avoid any distribution
incompatibilities ).

Hope this helps
vlad

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
>
>
> 

-- 
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/