bioMoo Held on the 22nd April 1998

ClareS turns the ClareS_recorder on.

ClareS says "Hi, welcome to this PPS meeting in which we will be discussing molecular forces"

ClareS says "Before we start, I would like to emphasise that this is one of the hardest sections of the course"

ClareS says "the material is quite complex and mathematical"

ClareS says "although we are not using a (very) mathematical treatment in this course"


ClareS is looking through the section material (slowly)

ClareS says "How have you found this section: any particular problems?"

JudyH says "I found difficulty unserstanding the terminology inthe section on types of inetractions"

ClareS is looking at that section now

Jim Pitts says "Ditto"

ClareS [to JudyH] what in particular didn't understand

JudyH says "finally I figured it out this morning, does for eg Lys NZ mean N-zeta?"

ClareS [to JudyH] I meant, didn't you understand - sorry

ClareS [to JudyH] Yes - that's right

Jim Pitts [to JudyH] You count from the alpha carbon out through the side chain for the amino acid. Next beta carbon and so on

JudyH says "good! I know it was a bit stupid but it wasn't obvious to me that the letters stood for the greek!"

ClareS says "it's harder to remember this when you're typing everything so you can't use the greek letters - but you still have to remember the order"

ClareS says "and in thr greek alphabet, G comes between B and D and so on..."

ClareS apologises for typo (again)

Ruiz says "I would like to know if it is possible to have all the interactions wich exists in a structure from a PDB file"

ClareS [to Ruiz] do you mean to list the interactions?

JudyH says "I am still not sure about his , how does the order go?"

ClareS [to JudyH] the order of the greek alphabet?

Ruiz says "yes and the aminoacids which interacts"

JudyH says "no, the numbering when there is a cyclical sidechain; sorry my lack of chemistry shows,"

ClareS says "there are even problems when the side chain is branched rather than cyclic"

ClareS says "you count the heavy atoms from the alpha carbon by the shortest route and name them starting from C-beta for the first atom in the chain (the only side chain heavy atom in alanine is C-beta)"

Jim Pitts says " If you look at you can see the numbering"

ClareS says "if there are two atoms in the same position then you give them a number as welll"

ClareS [to Jim Pitts] thanks very much - I was looking for it too, you got there first

Jim Pitts says " And on this one you can see the way it works."

ClareS says "the first of those URLs even has a beginner's guide to the Greek alphabet"

ClareS says "but as E has been used for Epsilon, Eta is missed out...."

Jim Pitts says "So you need the atom type the greek letter and if it is a ring whether it is 1 or 2."

ClareS says "so the atoms in the side chain are labelled B(eta), G(amma), D(elta), E(psilon), Z(eta), (t)Heta"

ClareS says "I don't know why H is used for theta rather than T - does anyone?"

ClareS says "By the way there is no difference between e.g. OE1 and OE2 (in Glu): they're interchangeable and might just as easily have been labelled the other way round"

ClareS [to JudyH] does this make it clearer?

JudyH says "yes, thank you"

ClareS [to JudyH] good - happy to be able to help ;)

ClareS [to Ruiz] could you repeat your last question please?

Ruiz says "it is possible to have the list of interactions and aminoacids which interact for a PDB file?"

ClareS [to Ruiz] thanks very much - sorry, it went offscreen & I can't scroll on this machine

ClareS [to Ruiz] it's very difficult to say what is an "interaction" and what isn't

(Jim Pitts has disconnected.)

ClareS says "some are quite easy (such as hydrogen bonds)"

ClareS says "if you have a modelling program you should be able to get it to list all the H bonds in a protein"

ClareS says "some of them just list donors and acceptors which are less than a given distance apart"

ClareS says "others also include an angle criterion if hydrogen atoms are present"

(Jim Pitts has connected.)

Jim Pitts says "Lost the connection"

ClareS [to Jim Pitts] don't worry - it often happens to me too

ClareS is trying to remember whether Rasmol will list hydrogen bonds

JudyH says "we have seen h bonds in Rasmol in some of the course material"

ClareS . o O ( it will certainly label all hydrogen bonds )

ClareS says "with some other types of interaction, such as van der Waals interactions, it's much less well defined"

ClareS says "two atoms will always be interacting, it's just that if they are more than a certain distance apart their interaction will be abeolutely negligible"

ClareS . o O ( absolutely )

ClareS says "Some other types such as aromatic-aromatic interactions are clear-cut but I don't know of a way of estimating them except by looking closely at the PDB file"

ClareS says "(with a molecular viewing program, not a text editor ;)"

ClareS [to Ruiz] is this helpful at all?

ClareS says "and does anyone know of a program you can use to e.g. list all aromatic-aromatic intractions in a protein?"

Jim Pitts says "I have just been checking my other PC."

Ruiz says "thank you"

Jim Pitts says "the command line in RASMOL has the option of hbonds"

Jim Pitts says "if you then say hbonds on you will display them"

ClareS [to Jim Pitts] can you also get a listing of H bonds as text?

Jim Pitts says "the first time it tells you the number, then when ON is set they are displayed"

ClareS doesn't have rasmol on this PC for some unknown reason (

ClareS says "with Insight (Biosym/MSI) you can ask for a listing of all H bonds"

ClareS says "you get the information as a table of donor, acceptor and distance"

ClareS says "almost certainly any comparable program will give you the same information"

Ruiz says "are there free software which give the same information? "

Jim Pitts says "i do not know if you can list the h-bonds in RASMOL. I think it unlikely!"

ClareS says "has anyone here used Chime 2?"

ClareS says "I haven't but I have been told that it has many of the features of Rasmol not in the first version of Chime"

ClareS says "it just might have this one as well..."

ClareS will investigate a few free software lists

Jim Pitts says "Also in the command line you can set colour hbonds blue for example to see them all in blue"

Jim Pitts says "I assume you can all find the command line window"

ClareS says "The EBI has a "BioCatalog" of software on the Web but it's almost all for bioinformatics"

ClareS says "there is a molecular graphics and modelling section"

(Ruiz has disconnected.)

ClareS has been searching (unsuccessfully so far)

ClareS has been looking up PDBsum

ClareS says "this is very useful: the URL is"

ClareS says "unfortunately it doesn't list all H bonds, but it *does* plot a nice picture of all interactions between a protein and its inhibitor or other ligand, and give a lot of other useful information"

ClareS says "does anyone have any other questions.. on this section or anything else?"

ClareS says "if I find a free program which will list all H bonds in a protein (or other information on interactions) I'll post the list"

The housekeeper arrives to cart Ruiz off to bed.

ClareS says "I think, if no-one has any further questions or comments, we should close the meeting now"

ClareS says "Thank you very much for coming and for your questions"

ClareS turns the ClareS_recorder off.