VMD-L Mailing List

From: Dr. Daniel James White PhD (dan_at_chalkie.org.uk)
Date: Tue Apr 06 2004 - 04:12:58 CDT

Hi John,

just got a reply from Warren the pymol man

the easiest way to achieve what I wanted, was this:

download the "biological unit" version of the pdb file containing the
60 molecule positions as 60 different "models" in 1 file.

pymol leads this file as 60 different "states"...

then do
split_states object-name

as below.

VMD could have something like this?

now I have all 60 molecules as different pymol objects and can show and
hide and do whatever to them individually.
I'm modelling and making pretty pictures, so this works for me.

cheers

Dan

  Message: 10
From: "Warren DeLano" <warren_at_delanoscientific.com>
To: "'Todd Geders'" <geders_at_purdue.edu>,
        "'Ann Mullin'" <amullin_at_tulane.edu>
Cc: <pymol-users_at_lists.sourceforge.net>
Subject: RE: [PyMOL] biological unit question
Date: Mon, 5 Apr 2004 13:07:13 -0700

Todd,

Try MacPyMOL for the full PYMOL effect. http://delsci.com/macpymol

There is also a new command in the 0.95 series:

    split_states object-name

which will spread a PDB "biological unit" (or any multi-state object --
including SD files) over a series of independent objects. This makes it
possible to interact with such objects more naturally than with
"all_states
= 1".

    load 1c8e.pdb1, 1c8e
    split_states 1c8e
    delete 1c8e
    zoom
    spectrum b
    hide lines
    set cartoon_sampling,3
    show cartoon
    bg_color grey70
    set hash_max, 150
    ray
...
    orient
    zoom complete=1
    ray

image & screen-shot at:

   http://delsci.com/img/1c8e.jpg
   http://delsci.com/img/1c8e-screen.jpg

Note that looking at large systems such as this (255300 atoms) may take
some
extra RAM -- 1.5 GB is recommended for this task, and it still takes a
dual
2 Ghz G5 85 seconds to render...

Cheers,
Warren

On 5 Apr 2004, at 22:11, John Stone wrote:

>
> Hi,
> Try using something like this (replacing the upper left 3x3 matrix
> elements
> as appropriate of course):
>
> set sel [atomselect top "all"]
> $sel move {{1.0 0.0 0.0 0.0}
> {0.0 1.0 0.0 0.0}
> {0.0 0.0 1.0 0.0}
> {0.0 0.0 0.0 1.0}}
> $sel writepdb /tmp/myfile.pdb
>
> While it would be great to automatically parse PDB files and read
> these transformation matrices in a script, as far as I know there is
> not standard method of storing them. The transformation matrices
> are just included in the comments section of the file and don't have
> any guaranteed formatting or ordering to my knowledge. If someone
> knows
> otherwise however, and they can supply a spec, it would be fairly
> simple
> to write a Tcl script that does this automatically if formatting is
> known and guaranteeably consistent.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Apr 05, 2004 at 06:35:06PM +0300, Dr. Daniel James White PhD
> wrote:
>> Hi,
>>
>> I have a virus envelope protein structure pdb entry,
>> and I want to rebuild the whole virus protein shell
>> using the symmetry transformations given in the 180 (60 trimers)
>>
>> REMARK 350 BIOMT1 1 1.00000 0.00000 0.00000
>> REMARK 350 BIOMT2 1 0.00000 1.00000 0.00000
>> REMARK 350 BIOMT3 1 0.00000 0.00000 1.00000
>> REMARK 350 BIOMT1 2 0.80900 0.30900 0.50000
>> REMARK 350 BIOMT2 2 etc...
>> REMARK 350 BIOMT3 2 etc...
>> etc......
>>
>> lines of the pdb file. These lines give the transformations to give
>> the
>> complete protein spherical capsid structure.
>>
>> can I use some vmd
>> command to do this?
>>
>> I did manage to do this in SwissPDBViewer, but it is very boring doing
>> it 1 by 1 and I cant save the complete capsid structure as a file that
>> Bodil reads properly.
>>
>> can vmd do this,
>> if not, anyone know how I can?
>>
>> cheers
>>
>> Dan
>>
>> Dr. Daniel James White BSc. (Hons.) PhD
>> Cell Biology
>> Department of biological and environmental science
>> PO Box 35
>> University of Jyväskylä
>> Jyväskylä FIN 40014
>> Finland
>> +358 14 260 4183 (work)
>> +358 468102840 (new mobile)
>> NEW PHONE NUMBER!!!
>>
>> http://www.chalkie.org.uk
>> dan_at_chalkie.org.uk
>> white_at_cc.jyu.fi
>
> --
> 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. Daniel James White BSc. (Hons.) PhD
Cell Biology
Department of biological and environmental science
PO Box 35
University of Jyväskylä
Jyväskylä FIN 40014
Finland
+358 14 260 4183 (work)
+358 468102840 (new mobile)
NEW PHONE NUMBER!!!

http://www.chalkie.org.uk
dan_at_chalkie.org.uk
white_at_cc.jyu.fi