VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 28 2002 - 15:28:00 CDT

Hi,
  Sounds like those PDB entries aren't actually available yet.
If you try to download an accession code that fails within VMD,
the next thing to do is look it up on their web site www.rcsb.org,
if you are not able to download it from there via their web interface,
then VMD won't be able to download it either. I'm guessing that
"on hold" means that these structures are not being made available yet,
but since I'm not an expert PDB user (I'm a programmer after all..) I
can't be sure what the exact meaning is. I suspect that the PDB web
site has details on what the real meaning of "on hold" is. They also
have an email support line that you could send a note to if you are
having trouble finding a structure that should be there.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 27, 2002 at 04:35:49PM +0900, ?$B:,>k?(J ?$B6Q?(J wrote:
> Dear John,
> Thanks for your help.
> I gave query of the term "Actin" and got 12 matches at Protein Data Bank.
> When I tried to get data pdbxxxx.ent.Z, I could not find any of these files.
> The status code of most of them is HPUB.
> Or they are all "on hold" at "Structurs" column
> and this means that the data is not valable?
> Thanks in advance.
>
> Hitoshi
>
> >
> > Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Fri, Aug 23, 2002 at 04:14:23PM +0900, Hitoshi Nejo wrote:
> > > Hi,
> > > I tried to get four-chracter accesion code
> > > from pdb databeck but failed.
> > > Below please find the error message which VMD creates.
> > > It seems that ftp failed. How I can retrive data?
> > > Thanks.
> > > Hitoshi
> > >
> > > VMD Win32 FTP Client
> > > ftp.rcsb.org:/pub/pdb/data/structures/all/pdb/pdb1kqm.ent.Z:
> > > C:\DOCUME~1\nejo~1\LOCALS~1\Temp\urlload2
> > >
> > > abnormal program termination
> > > ERROR) Cannot open file 'C:\DOCUME~1\nejo~1\LOCALS~1\Temp\urlload'
> > > ERROR) Cannot creat new molecule
> > >
> >
> > --
> > 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
>
> ----------------------------------------------------------
> MRS-J Symposium home page opened
> www.mrs-j.org/
> ----------------------------------------------------------
> Hitoshi Nejo $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!:,>k!!6Q(J
> National Institute for Materials Science$B!!J*<A!&:`NA8&5f5!9=(J
> 1-2-1 Sengen, Tsukuba 305-0047 Japan$B$D$/$P;T_at_i8=#1!]#2!<#1(J
> NEJO.Hitoshi_at_nims.go.jp
> http://www.nims.go.jp/nano-elec/
> TEL:+81 298 59 2847
> FAX:+81 298 59 2801
> --------------------------------------------------- 

-- 
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