VMD-L Mailing List

From: $B:,>k(J $B6Q(J (NEJO.Hitoshi_at_nims.go.jp)
Date: Tue Aug 27 2002 - 02:35:49 CDT

 Dear John,
Thanks for your help.

> It appears that your machine is unable to use FTP to
> retrieve structures from the PDB directly. We have updated the
> new VMD 1.8 test versions with code that retrieves these structures
> via the web instead of FTP, as we have found that it is generally
> more reliable than FTP, since many firewalls and proxies allow web
> connections even when they block FTP transfers. If you use the
> direct-download feature from the PDB a lot, then I'd recommend that
> you try one of the new VMD 1.8 pre-release versions which should work
> better for you in this regard. If you prefer to stick with the prodoction
> version of VMD, then we expect to have VMD 1.8 released in the next two
> months or so.
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

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MRS-J Symposium home page opened
www.mrs-j.org/
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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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