VMD-L Mailing List

From: $B:,>k(J $B6Q(J (NEJO.Hitoshi_at_nims.go.jp)
Date: Thu Aug 29 2002 - 03:21:12 CDT

 Hi John,
Thanks.
I have sent a query message to the mailing list of PDB.
Another question which you may answer is;
I have downloaded a file with extension .ent from PDB.
This file should be read by VMD but
VMD gave me an error message that VMD cannot recognize this file type.
I assume that if the file is downloaded by VMD,
VMD recognizes and handles this file type automatically.
How I can make VMD to recognize this file type?
Thanks in advance.
Hitoshi

> 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

----------------------------------------------------------
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
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