VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 18 2004 - 19:29:30 CDT

Dan,
  I think that psfgen wants you to use residue names that its familiar with,
and that are listed in the charmm forcefield, though Jim Phillips can probably
give you more information on this since he wrote psfgen. I'm CCing him on
my reply in case he has other suggestions.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 15, 2004 at 01:18:14PM +0300, Dr. Daniel James White PhD wrote:
> Hi John,
>
> Just got back from easter in england and tried the script
>
> but I get an error: unknown residue type CA......... what am I doing
> wrong,
> the pdb file in use is the biological unit file for 1c8d
>
> cheers
>
> Dan
>
> vmd > source mergemultiframepdb.tcl
> vmd > merge_multi_frame_structure top /tmp /cpv60
> reading topology file /Applications/VMD/VMD
> 1.8.2.app/Contents/vmd/plugins/noarch/tcl/membrane1.0/
> top_all27_prot_lipid.inp
>
> >>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
> >>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
> from
> >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
> >>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
> >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
> and
> \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
> \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
> Alexander D. MacKerell Jr.
> August 1999
> All comments to ADM jr. email: alex,mmiris.ab.umd.edu
> telephone: 410-706-7442
>
> Created by CHARMM version 27 1
> aliasing residue HIS to HSD
> PDB: /tmp/merge0000.A.pdb V1
> building segment V1
> setting patch for first residue to NONE
> setting patch for last residue to NONE
> reading residues from pdb file /tmp/merge0000.A.pdb
> unknown residue type CA
> extracted 549 residues from pdb file
> Info: generating structure...
> unknown residue type CA
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> vmd >
>
>
>
> On 6 Apr 2004, at 17:59, John Stone wrote:
>
> >
> >Daniel,
> > I didn't realize you were working with the biological unit files,
> >that being the case, I've already written a script to process these
> >with psfgen, adding missing hydrogens, and merging them into a single
> >structure file. I guess you hadn't seen my previous posts of this
> >script? Anyway, here it is, try it out and let me know if you need
> >help using it.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >##
> >## A simple VMD/psfgen script to merge multi-frame PDB files into a
> >single PDB
> >## structure, as in the case of the large multi-frame Virus capsids
> >provided
> >## at the RCSB PDB site.
> >##
> >## Usage:
> >## source mergemultiframepdb.tcl
> >## mol new myfavoritemultiframepdb.pdb
> >## merge_multi_frame_structure top /tmp/myworkarea /my/final/filename
> >##
> >## Results will be written to /my/final/filename.psf and
> >/my/final/filename.pdb
> >##
> >## This script was tested with the following file from the RCSB PDB
> >site:
> >##
> >ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/divided/k4/
> >1k4r.pdb1.gz
> >##
> >package require psfgen
> >
> ># this is a hack, just to get the topology file
> >package require membrane
> >
> >proc writeallframes { whichmol workdir } {
> > set allsel [atomselect $whichmol "all"]
> > for {set i 0} {$i < [molinfo $whichmol get numframes]} {incr i} {
> > foreach chain [lsort -unique [$allsel get chain]] {
> > set sel [atomselect $whichmol "chain $chain"]
> > $sel frame $i
> > set filename [format "%s/merge%04d.%s.pdb" $workdir $i $chain]
> > file delete $filename
> > $sel writepdb $filename
> > $sel delete
> > }
> > }
> > $allsel delete
> >}
> >
> >proc deleteworkarea { whichmol workdir } {
> > set allsel [atomselect $whichmol "all"]
> > for {set i 0} {$i < [molinfo $whichmol get numframes]} {incr i} {
> > foreach chain [lsort -unique [$allsel get chain]] {
> > set filename [format "%s/merge%04d.%s.pdb" $workdir $i $chain]
> > file delete $filename
> > }
> > }
> > $allsel delete
> >}
> >
> >proc mergeallframes { workdir filename } {
> > global env
> >
> > # this next line is a total hack, needs a permanent place to get
> >this from
> > set topologyfile [format
> >"%s/plugins/noarch/tcl/membrane1.0/top_all27_prot_lipid.inp"
> >$env(VMDDIR)]
> >
> > psfcontext new
> > resetpsf
> > topology $topologyfile
> > pdbalias residue HIS HSD
> >
> > set nseg 1
> > foreach pdb [lsort [glob $workdir/merge*.pdb]] {
> > set segid V$nseg
> > puts stdout "PDB: $pdb $segid"
> > segment $segid {
> > first NONE
> > last NONE
> > pdb $pdb
> > }
> > coordpdb $pdb $segid
> > incr nseg
> > }
> >
> > guesscoord
> >
> > set psffilename [format "%s.psf" $filename]
> > set pdbfilename [format "%s.pdb" $filename]
> > writepsf $psffilename
> > writepdb $pdbfilename
> >}
> >
> >proc merge_multi_frame_structure { whichmol workdir filename } {
> > writeallframes $whichmol $workdir
> > mergeallframes $workdir $filename
> > deleteworkarea $whichmol $workdir
> >}
> >
> >
> >
> >
> >
> >
> >On Tue, Apr 06, 2004 at 12:12:58PM +0300, Dr. Daniel James White PhD
> >wrote:
> >>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
> >>
> >
> >--
> >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
> ><mergemultiframepdb.tcl>
> 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