Transcript of meeting in BioMOO, PPS Base 8th May '96 15:00 GMT: Getting PDB files from Databases

This transcript can currently be found on the tape 'databases_tape' in the PPS Base, but will eventually have to be deleted to save disk space.


jzt turns the C-recorder on.

Jzt says, "Testing database_tape 8th May 1996"

jzt turns the C-recorder off.

jzt turns the C-recorder on.

HorstJS finds his way in.

JohnW says, "ok"

HorstJS says, ""hello everybody"

JohnW says, "Hi"

Jzt [to HorstJS]: Hi Horst, how are you doing?

Jzt [to HorstJS]: Thanks for your comments on the assignment earlier

HorstJS says, ""very well - tanks for the question :-)"

Jzt [to JohnW]: Should we get going, or wait for more people?

JohnW says, "Ok, I think we should begin. Firstly, as I havent seen most of you since last term, welcome back"

JohnW says, "The purpose of this session is to demonstrate how to fetch PDB files from the various databases on the Internet, because some people were still having problems doing this-"

Gayle schulte finds his/her way in.

JohnW says, "-so maybe I should say that if you already know just how to do this, the following might seem a bit boring!"

JohnW smiles

Paulyta finds his/her way in.

Paulyta says, "hi"

Paulyta waves

JohnW says, "so, we can begin with looking at where to get a pdb file, assuming you know what the 4-letter code is."

HorstJS waves

The housekeeper arrives to cart ClareS off to bed.

JohnW says, "When we first mailed all the students with their 'personal' pdb codes in February, we gave a short list of various sites from which they could try to download it."

JohnW says, "There is now a HTML document at the PPS pages: "

JohnW says, "- on which a few more sites have been added"

JohnW says, "Of course the reason for listing several different sites is simply so you can access the one thats nearest to you."

Hrosa finds his/her way in.

Jzt is looking at it now

JohnW says, "Some of these sites are on the WWW, but some others (ftp and gopher) are also listed"

Hrosa says, "hello, sorry for the delay"

JohnW says, "The ftp and gopher sites simply deliver the PDB files themselves, whereas (most of) the WWW URLs are of cgi-scripts which fetch the file, and deliver it in the format that you want (i.e. text, or chemical/mime-stamped)"

HorstJS waves

JohnW says, "For downloading a file, the format that is most convenient is text"

JohnW says, "The chemical/mime-stamped files are the ones which automatically invoke RasMol (or whatever viewer you might have chosen) at the client end (assuming you have your WWW Browser configured appropriately)"

JohnW . o O ( any questions so far? )

JohnW says, "Could I just ask, did anyone here have any particular problems getting hold of their PDB file?"

The counter-ion says, ''The Birkbeck Owl, in the PPS '96 Office (up) will give help if required''.

JohnW vaporizes the counter-ion

Tday finds his/her way in.

Jzt waves to Tday

JohnW welcomes Tday

Tday says, "hi"

HorstJS [to JohnW]: "How brute ;-)

Jzt says, "So did everyone here get their pdb file with no problems, or at least were successful in the end? In that case, would people like to raise related points they'd like to discuss here - something a bit more advanced?"

JohnW [to HorstJS]: I thought I had already chased that thing out the room. I'll be more gentle with it next time

JohnW smiles

Jzt says, "Or are there any more questions on the details of what John said?"

JohnW says, "Well, I will add that there are further details of the URLs of PDB-file-fetching scripts in Section 6 of the course material:"

JohnW says, ".../PPS2/course/section6/chemMIME.html"

JohnW says, "- but this is more aimed at those who may want to use these URLs to include interactive PDB files in their own HTML documents."

ClareS materializes out of thin air.

Jzt says, "John, if no-one has any questions about downloading pdb files, maybe we should discuss the content of pdb files, if people would like to do that?"

ClareS says, "sorry about that... ourt network went totally dead"

JohnW says, "I should also stress that currently the Birkbeck Crystallography server does not run a script to deliver PDB files- to get the files from it, you simply give the URL of the files themselves, which are named in the format pdb****.pdb. The serv

er is currently configured to stamp all .pdb files with the chemical/x-pdb mime-type."

JohnW says, "This will change imminently- i.e. we will have the script format so that you can select either text or chemical mime type-stamped files."

JohnW [to ClareS]: no problem!

JohnW says, "For those who might benefit from a PDB Web-server in central/eastern Europe, I should point out the PDB Browser at the Institute of Biochemistry and Biophysics in Warsaw."

JohnW says, "The URL is of the format:"

JohnW says, "****"

JohnW says, "- but I should stress that that is the chemical/x-pdb mime-stamped copy of the file, i.e. it starts RasMol going."

ClareS says, "There is a problem at the moment with downloading PDB files as text from IBB"

ClareS says, "which we are trying to sort out..."

JohnW says, "In fact I wanted to ask Clare about this (Clare has been helping setting up a PPS mirror in Poznan, Poland- more about this shortly) "

JohnW . o O ( beat me to it )

JohnW nods

SophiaK I have to go. Thanks John

JohnW says, "Ok. The URL to deliver chemical mime PDB files seems to work fine though."

JohnW says, "Thanks for coming Sophia- see you later"

Jzt waves to Sophia

JohnW says, "There is also a WWW server in Halle, Germany :"

JohnW says, "****"

JohnW says, "-will give the text version of the file"

JohnW says, "There is also a PDB server at ExPASy, Geneva."

ClareS [to JohnW]: might it be worth pointing to this as well from the course pages?

SophiaK has disconnected.

JohnW says, "Anyway, the significane of all this for the forthcoming weeks is that the course material for this term deals largely with the nitty-gritty of protein structure, so we will of course be pointing to a large number of PDB files within the hyper


ClareS says, "and (if I've got this right, John) there will be a pointer to each PDB fileat each separate location, so you will be able to choose where to go for your PDB files"

JohnW says, "- so what you will see in each case is a number of links to each PDB file URL (the chemical/x-pdb MIME version, of course)"

JohnW nods

JohnW . o O ( beat me again! )

JohnW smiles

JohnW says, "Yes, thats right: e.g. ' here for duck-billed platypus acetylcholinesterase [Bbk|BNL|Ex|Pz|Hl]'"

Hrosa has disconnected.

JohnW says, "where each of the 5 options is a link to the copy of the file at Birkbeck, Brookhaven, ExPASy, Poznan (actually that should be Warsaw), Halle, etc."

ClareS [to JohnW]: yes, that should be Warsaw (or IBB), we don't have PDB here

JohnW says, "we will also be providing some RasMol scripts to download, which will highlight the relevant structural features (although this wont be appropriate for every single citation of a PDB file, of course)."

The housekeeper arrives to cart SophiaK off to bed.

JohnW says, "Of course, the above system only applies to structures which actually exist in the Protein Data Bank. For others (e.g. model alpha-helices etc), a local copy is stored in the hypertree. So how this file behaves depends on the configuration of

the WWW server which serves the PPS mirror which you are accessing. "

Tday has disconnected.

JohnW says, "E.g. from some of the mirrors, such pdb files may not be chemical-mime stamped, so you will get them as text- in which case simply download them, then load them into RasMol. E.g. next weeks material includes some pdb files like this."

Reissner [guest] waves

Reissner [guest] has disconnected.

The housekeeper arrives to remove reissner [guest].

The housekeeper arrives to cart hrosa off to bed.

ClareS says, "I think that will probably be the case here (Poznan)"

JohnW says, "Ok, well I think I'll have to wind up now."

Jzt says, "There'll be a more general meeting on bioinformatics on 22nd, which Clare has very kindly agreed to lead, when she gets back to UK."

JohnW says, "Did anyone have any questions?"

ClareS says, "What would anyone like me to cover in the meeting on the 22nd, in particular?"

HorstJS says, "not so far"

Jzt says, "Maybe you could give a good definition of what Bioinformatics is, Clare!"

JohnW smiles

The housekeeper arrives to cart tday off to bed.

JohnW says, "Not an easy question, perhaps?!"

ClareS [to JohnW]: Now?

ClareS [to JohnW]: or on the 22nd?

JohnW says, "Well, perhaps we should wait until the Bioinformatics meeting"

ClareS says, "... which gives me the chance to work out a good snappy definition"

Jzt says, "Anyway, please mail in any questions or areas of particular interest and we'll make sure they get discussed then."

jzt turns the C-recorder off.