From: tiago sobreira (tiagosobreira_at_yahoo.com.br)
Date: Mon Apr 18 2011 - 10:00:13 CDT

Thanks John I will try to fix this in the webpdb plugin too. Cheers, Tiago ________________________________ De: John Stone <johns_at_ks.uiuc.edu> Para: tiago sobreira <tiagosobreira_at_yahoo.com.br> Cc: vmd-l_at_ks.uiuc.edu Enviadas: Sexta-feira, 15 de Abril de 2011 17:51:38 Assunto: Re: Res: vmd-l: webpdb load problem Tiago, I'm guessing that for some reason, your http::config settings are not affecting the webpdb download the way I had expected. I'll have to investigate the reason for this and get back to you. I don't think that the problem has to do with too short of a timeout, most likely it's just not using the proxy as we had hoped it would. If I come up with a solution for this, I'll let you know. In the short term, you can use a short script to download the structures yourself until the webpdb plugin has been made to cooperate. I may have to create a modified version of the webpdb plugin for you in order to get around this problem. Cheers, John Stone vmd_at_ks.uiuc.edu On Thu, Apr 14, 2011 at 07:25:02AM -0700, tiago sobreira wrote: > Hi John > The http::config fix part of the problem. Now I can download a PDB with > the command like that: > puts [http::data [http::geturl > >http://www.rcsb.org/pdb/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1fmo]] > > But I still can not load a molecule directly with mol new > vmd > mol new 1fmo > Error loading PDB: couldn't open socket: connection timed out > ERROR) Could not read file 1fmo > Unable to load file '1fmo' using file type 'webpdb'. > Is it possible to increase timeout ? > Thanks > Tiago > > ---------------------------------------------------------------------- > > De: John Stone <johns_at_ks.uiuc.edu> > Para: tiago sobreira <tiagosobreira_at_yahoo.com.br> > Cc: vmd-l_at_ks.uiuc.edu > Enviadas: Terc,a-feira, 12 de Abril de 2011 16:09:33 > Assunto: Re: vmd-l: webpdb load problem > > Hi, > Try adding Tcl ::http::config calls to your .vmdrc file, to setup > your local web proxy: > http://www.tcl.tk/man/tcl8.5/TclCmd/http.htm > http://www.tcl.tk/man/tcl8.5/TclCmd/http.htm#M6 > > Cheers, > John Stone > vmd_at_ks.uiuc.edu > > On Tue, Apr 12, 2011 at 11:48:29AM -0700, tiago sobreira wrote: > > Hi > > I am trying to load a molecule direct from internet and I get the > > following error menssagem: > > vmd > mol new 1bxs > > Error loading PDB: couldn't open socket: connection timed out > > ERROR) Could not read file 1bxs > > Unable to load file '1bxs' using file type 'webpdb'. > > I am inside of network with proxy. Is it necessary open some door? > > Thanks for the attention, > > Tiago Jose Paschoal Sobreira > > Pesquisador em Biologia Computacional > > Laboratorio Nacional de Biociencias (LNBio) > > -- > 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 -- 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