VMD-L Mailing List

From: Vyom Sharma (vysharma_at_MIT.EDU)
Date: Thu Jun 01 2006 - 21:19:19 CDT

Is it possible to make a movie out of different reps??

Vyom

On Jun 1, 2006, at 7:01 PM, John Stone wrote:

>
> Hi,
> Did you send us the same sphere.pqr you loaded below? I'm not
> getting
> any of the bonding errors your message below was showing.
> If you can upload the DX file to the VMD Public project area on
> BioCoRE, I'd
> like to have a look:
> http://www.ks.uiuc.edu/Research/vmd/alpha/
>
> Most likely you just need to create an Isosurface representation after
> the data is loaded. Also, although the APBS home page directs people
> to use their my_functions.tcl script for loading DX files (in
> particular
> for older versions of VMD), the built-in DX reader plugin in VMD 1.8.4
> is MUCH faster. (just load the DX file using the File menu as for
> other
> files...)
>
> To keep things simple to start with, try loading just the DX file into
> VMD (using the built-in DX reader, rather than the load_pot script
> routine..)
> and see if you see the potential surface. Once you get that far, we
> can
> move on to the next questions..
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jun 01, 2006 at 06:34:04PM -0400, Vyom Sharma wrote:
>> I am getting a very strange problem for quite sometime now.
>> I use a "PQR" file that i generate and run it on APBS to give me the
>> potential data.
>> VMD is able to show the molecule nicely but it is not able to
>> visualize
>> the potential data at all. Infact it does not show anything when I try
>> to load the potential data.
>>
>> I am using the "my_functions" script to sort and load the potential
>> data into VMD.
>> Also I am attaching the "PQR" file (I can send the "pot.dx" file which
>> contains the potential data , if required- its 27 MB big)
>>
>> While loading the potential using "load_pot" command, I get these
>> messages:
>>
>> ---------------------
>> nfo) VMD for MACOSX, version 1.8.4 (April 17, 2006)
>> Info) http://www.ks.uiuc.edu/Research/vmd/
>> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
>> Info) Please include this reference in published work using VMD:
>> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
>> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
>> Info) -------------------------------------------------------------
>> Info) Multithreading available, 1 CPU detected.
>> Info) OpenGL renderer: ATI Radeon 9200 OpenGL Engine
>> Info) Features: STENCIL MTX
>> Info) Textures: 2-D (2048x2048), 3-D (128x128x128), Multitexture (6)
>> vmd > source my_functions
>> vmd > load_pot
>> Info) Using plugin pdb for structure file sphere.pqr
>> Info) Using plugin pdb for coordinates from file sphere.pqr
>> Info) Determining bond structure from distance search ...
>> ERROR) MolAtom 131: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 173: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 285: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 423: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 79: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 310: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 147: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 475: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 140: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 331: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 140: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 331: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 292: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 263: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 177: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 196: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 222: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 256: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 263: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 177: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 196: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 222: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 263: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 210: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 110: Exceeded maximum number of bonds (8).
>> ERROR) BaseMolecule: Excessive bonding errors encountered, perhaps
>> atom
>> coordinates are in the wrong units?
>> ERROR) BaseMolecule: Silencing bonding error messages.
>> Info) Finished with coordinate file sphere.pqr.
>> Info) Analyzing structure ...
>> Info) Atoms: 501
>> Info) Bonds: 1112
>> Info) Residues: 53
>> Info) Waters: 0
>> ---------------------------------------
>>
>>
>> I would immensely appreciate any repsonse.
>>
>> Thanks
>> Vyom
>>
>
>
>
>>
>
>
> --
> 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