Biomoo 4/12/97

ClareS turns the ClareS_recorder on.

ClareS says "Welcome everyone"

Mariza [guest] finds its way in.

ClareS says "in this meeting we will be discussing (mostly) sections 2 and 3 of the PPS course material"

ClareS says "does anyone have any particular questions they'd like discussed?"

Ajj says "Clare, In Section III-disulfide bonds the prompt suggests that we view gamma crystallin B with rasmol and "script". Could you explain what "script" is and how we get it?"

Tobias finds his/her way in.

ClareS says "script" refers to a script (!) of commands for use with Rasmol, written to present a particular aspect of protein structure"

ClareS says "it's a simple text file"

Golden-oldie finds his/her way in.

(Domini has disconnected.)

Ajj says "So how do we get the text imported my rasmol brought the image without the text."

ClareS says "you should be able to load the script by double-clicking on a link"

(Valerio has disconnected.)

Ajj says "OK I'll try that thanks."

Pepi says "I had the same problem as Ajj, to view the script, i had to load it separately and then execute it from rasmol"

(Domini has connected.)

Pawel [guest] says "Does the .pdb file contain these 'scripts'....?"

ClareS says "you will need to save the script xzseparately and then run it through Rasmol"

ClareS [to Pawel] that depends on how the particular example has been designed

Pawel [guest] says "OK"

ClareS says "I will find that particular example and check it..."

ClareS says "but you will have to bear with me - the machine I am using is *very slow*"

Tomek finds his way in.

Jola finds her way in.

(Domini has disconnected.)

Tomek says "Halo everybody""

Tobias says "I read the scripts for Rasmol, but I didn'T understand them. What do they tell me ?"

Tomek says " I am sorry ,I am late""

ClareS says "The Rasmol scripts aren't meant to be "understood""

ClareS says "they are instructions for Rasmol"

Tobias says "OK"

ClareS says "basically, each line of a script is a line which could be typed on the Rasmol text window"

ClareS says "so using the script just means that you don't have to remember a long lit of commands"

The housekeeper arrives to cart Domini off to bed.

ClareS says "to demonstrate the particular aspect of protein structure we're interested in"

Tobias says "So it's some kind ofspeech with which the *.pdb files are written in?"

ClareS [to Tobias] not quite...

The housekeeper arrives to cart Valerio off to bed.

Domini finds her way in.

ClareS says "the PDB files just give the atom coordinates"

ClareS says "(together with a lot of other information if they ar standard protein files from the PDB)"

ClareS says "you can, of course just load a molecule into Rasmol with a PDB file only"

ClareS says "(you should all have done that)"

ClareS says "and in that case, the molecule is loaded in a "standard" way: all atoms, coloured by atom type etc"

Pawel [guest] says "The scripts to the .pdb files plays the similar role what the programming of Kinemages....?"

ClareS says "you then apply the script to the molecule, this rotates, translates, labels, changes colours and display options, etc."

ClareS [to Pawel] yes, that's a useful way to look at it

Mariza [guest] says "How can someone save the kinemage files to look off-line?"

ClareS says "you should be able to save them to your hard disk and then load them into Mage in the usual way"

Ajj says "But Clare, my browser asked for a separate viewer for the script file and the plugin finder could not find it."

Golden-oldie use the save option (in file menu) if you are using netscpe and you will be able to save to a disc.

Ajj says "and then I can read it as a text file?"

ClareS says "yes, you should be given the option to save it to disk"

Ajj says "Yes i was given that option."

ClareS says "and then start Rasmol off-line, display the molecule and read the script from the Rasmol command line"

ClareS says "there are full instructions in the Rasmol manual..."

Ajj [to say] OK I'll give that a try.

ClareS says "which is on-line, on Eric Mertz' excellent Rasmol site - have you all found that site?"

ClareS can't remember if she's spelled Eric's surname right

ClareS says "and have you all joined the Rasmol discussion list?"

Tobias says "Not yet. Hoew do I do that?"

Ajj says "at caltech? isn't it mercer?"

Pawel [guest] says "No, I didnt"

Claudia says " Nor I did"

ClareS says "it's well worth it"

Ajj says "I didn't either."

Mariza [guest] says "No,I did not"

Pawel [guest] says "Do you remember what adress has this site ?"

Mariza [guest] says "Where are we supposed to do that?"

Pepi says "i didn't, what is the add"

Jim Pitts says "URL is"

Jim Pitts says "This will help"

ClareS searches through mail archives

Jim Pitts says "Rasmole home page is"

Ajj says "Eric Mercer's site is ""

ClareS says "we seem to have some confusion here..."

ClareS says "there are too many Erics (if you can have too much of a good thing)"

ClareS says "Eric Martz (Univ. Mass.) runs the Rasmol site"

ClareS says "Eric Mercer (Caltech) is a BioMOO wizard"

Ajj says "Thanks for the Clare-ification."

Jim Pitts says "See this An excellent RasMol Homepage/ Resource by Eric Martz and C.F."

Jim Pitts [to getting] installing, and using RasMol.

ClareS grins

Jim Pitts says "See"

Tobias says "Consider it done"

ClareS says "there is a direct link from the Rasmol home page at U. Mass. describing how you subscribe to the list"

Mariza [guest] says "OK, thanks"

Claudia says " Thanks"

Domini (idle 14m) finds her way out.

Mariza [guest] says "What is grins?"

ClareS says "there are many other useful resources on the Rasmol page"

Ajj chuckles

ClareS [to mariza] a grin is somewhere between a smile and a laugh ;)

Mariza [guest] says "Ok!"

ClareS says "how are you all getting on with the scientific material in the course so far: is it making sense to you?"

Ruiz finds his way in.

Ajj says "Clare, what do you think the best way (quickest?) to gain a feeling for phi, psi, and chi angles? "

NickyM says "Sorry I was called on urgent business and missed the last 10 mins. Will catch it on the recorded notes."

Mariza [guest] says "Yes. Chi is the angle of peptide bound, right?"

ClareS ponders

Pepi says "I haven't had problems, with the material, but it is abit difficult to imagine all this angles"

ClareS [to NickyM] don't worry about it

Ajj says "Conceptually it is failrly easy but it is quite difficlt to see it on rasmol or other represetnations of structures."

ClareS says "No - the angles representing the positions of side chain atoms are thermed chi1, chi2 etc..."

ClareS says "the peptide bond angle (whichn is usually close to 180 degrees) is omega"

ClareS says "and (of course ;) the main angles representing the main chain conformation are phi and psi"

ClareS . o O ( it *is* confusing, especially for newcomers )

Ajj says "And can we twist them indiviually on any strucure in rasmol?"

Mariza [guest] says "Thanks! I mixed up."

Patricia finds her way in.

ClareS says "you can't alter individual torsion angles using Rasmol"

Domini finds her way in.

Patricia says "Hello. Just got here"

ClareS says "Rasmol is mainly a visualisation program, bot a modelling program - that's one of its limitations"

ClareS . o O ( bot = not (I can't type) )

Tobias says "Is there any possibility to 'cut off' parts of a molecule in Rasmol.This might facilitate viewing the anfgles"

ClareS says "there should be some Kinemages where you alter torsion angles & examine how the structure changes"

Ajj says "How about MAGE?"

ClareS [to tobisa] you can turn parts of the display on and off

ClareS says "and, of course, if any of you have access to a molecular modelling program such as Insight or Quanta you will be able to manipulate torsion angles using it"

NickyM says "Is that turn molecular parts off in Rasmol"

ClareS says "we can't recommend a particular modelling package as everyone has different hardware"

ClareS [to NickyM] yes

ClareS says "the URL for the rasmol manual is:-"

NickyM says "How is that done?"

Pepi says "what kind of platform do we need to run Insight ot quanta"

ClareS says ""

ClareS [to Pepi] a Silicon Graphics workstation

Antoon (idle 6m) finds his way in.

(Jola has disconnected.)

Patricia says "Are there molecular modeling programs for PC's?"

Claudia says ", Should a workstation Unix be good for molecular modelling?"

(Jola has connected.)

ClareS says "there *are* some modelling programs for PCs. All the most comprehensive modelling packages are for the Silicon Graphics, tho'"

Patricia says "Oh"

ClareS says "there is almost nothing for any other kind of Unix workstation"

Patricia says "Not for PC "Linux" either?"

Tomek says "There are some programs for PC"

ClareS [to Patricia] there are some for linux but there are windows ones which are just as good

Pawel [guest] says "And very useful for me program Alchemy that works on PC ?"

Patricia says "Would you tell me what they may be called? They must be expensive."

ClareS says "my advice is usually: if you are going to buy a computer for modelling and have a decent budget, get a SGI"

Tomek says " For example Hyperchem"

ClareS says "if you can't, don't worry as there is plenty for the PC"

Tobias says "Yes, but Hyperchem only tlet's you view the molecule in two dimension, unless you get yourself some add on"

ClareS [to tomek] yes, Hyperchem is a good modelling program for PCs

Patricia says "I Heard Tomek say "Hyperchem".......ClaireS said an "SGI" system "

Patricia says "but the budget is not......"

ClareS says "Hyperchem is a program.. SGI is a hardware platform"

ClareS says "SGI = Silicon Graphics, Inc."

ClareS . o O ( http//www/ )

Patricia says "Isn't SGI a Sun Graphics computer?"

ClareS [to Patricia] no, it's a separate company

Mariza [guest] [to Clare] Mage does not have the save option.

Patricia says "Oh"

ClareS says "SGI has specialised for years in making computers with very high quality graphics"

Pawel [guest] says "And in very high prices..."

ClareS says "you say Hyperchem doesn't have 3D visualisation: you'll find that it does, but it's very difficult to see tin 3D unless you are using a PC with a *very* good monitor"

ClareS says "that's the problem with SGI machines"

ClareS says "if you have $5K you might be able to get a good 2nd hand one ;)"

ClareS says "and then you have to consider the costs of the software"

Tomek says "In many cases software is more costly than hardware"

Jim Pitts says "URL is not http://www/"

ClareS can't type

Tobias says "OK, but is there any cheap or better Shareware program available for a more common plattform like PCs?"

Ajj says "Where infact we can torsion the angles?"

ClareS says "there are quite a lot of lists of molecular modelling software around on the web"

ClareS [to ajj] I'm not quite sure what you mean

Ajj [to ClareS] Where we can take the phi, psi or chi angles of ana peptide and change them so we can see the effect on structure.

Ajj says "any peptide, that is."

Mariza [guest] [to ajj] May be using mecanical models?

Ajj [to mariza] that's an idea. are there good mechanical models that are cheap?

ClareS says "yes, it might be going against the spirit of this course, but looking at "real-life" models can sometimes help"

Mariza [guest] says "Sorry, I know they exist but I do not know any"

Pawel [guest] says "Can the shareware mol. modelling programs efectively minimize the energy of the e.g. entered peptide sequence ?"

ClareS says "also, there should be some examples in section 3 which you can use with Mage"

ClareS [to Pawel] it depends what you mean by "effectively"...

Claudia says "Is it so important to act and understand the torsion angles?"

ClareS [to claudia] it's important.. if's not *crucial*, and you'll get the hang of it by following examples as you go through the course

(Ruiz has disconnected.)

NickyM says "A small cheap program Molecules 3D can do it to some extent"

ClareS says "everyone needs to "learn" how to think in 3 dimensions, it doesn't come naturally to many people"

Pawel [guest] says "hmmmm... My Alchemy working on PC minimizes the short peptide even 3 days..."

ClareS says "you'll get there in the end - keep working on it ;)"

Ajj says "I think that without twisting these anles around it'll be hard to real unders the Ramachandran Plot."

Claudia says " Oh, I see"

ClareS says "before we go on, I would like to point out that I will be turning the recourder off shortly"

Ajj says "understand, that is"

ClareS says "so if there's anything you'd like to discuss which you think other students would be interested in, speak now..."

Pawel [guest] says "ok"

ClareS says "of course, you can stay and chat for as long as you like ;)"

Mariza [guest] says "So, before that, I could not save the mage files right now."

Mariza [guest] says "I would like to know people that are here after endind the record."

Tobias says "I saved them using the File/Save command from my WWW-Browser"

Golden-oldie says "I have missed bits due to work to do! Will the recording be available and what will it be called?"

Patricia says "About programs like Alchemy,,,,,,or HyperChem.....does ClaireS"

Pawel [guest] says "I will be there for about 1 hour"

ClareS [to golden-oldie] the recording will be mounted on the PPS web site

ClareS [to golden-oldie] and one of us (probbaly Dave) will mail the URL to the list

Patricia says "Let me try that again.....About programs like Alchemy...or HyperChem.....does ClaireS suggest something like this for this course since an SGI is not always available?"

ClareS [to Patricia] you really don't need a modelling program for this course

Patricia says "OK"

ClareS says "of course, you will all find modelling programs very useful if you have access to them"

Claudia says " But should we learn how to try molecular modelling?"

Patricia says "It would be interesting to have access to a modeling program..."

ClareS says "Hyperchem & Alchemy are both good PC based modelling programs"

Claudia says "I agrre with Patricia"

ClareS says "but you will be able to get through the course successfully without even a free PC based one"

The housekeeper arrives to cart Ruiz off to bed.

Patricia says "RasMol and Kinemage show a new dimension about the structures"

Patricia says "At least to this beginner"

ClareS says "if you are having problems understanding torsion angles, and haven't done so, try the kinemage from Brandon & Tooze's book linked from section 3 of the course material"

Patricia says "Isn't each torsion angle based on a constant line along a specific bond?"

(Pepi has disconnected.)

Mariza [guest] [to Tobias] I tried again, Do i have to save as link ..?

ClareS [to Patricia] yes

Patricia says "But, just how is the zero plane determined or described?"

ClareS says "the definition of a torsion angle is really very simple..."

Patricia says "OK"

ClareS says "taking four atoms A-B-C-D, the torsion angle is just the angle you see between A & D when looking along the bond between B & C"

Mariza [guest] says "That's make easier to understand"

Patricia says "I'm writing that down"

Mariza [guest] says "Do they measure how close A & D are?"

Patricia says "I guess then the angle is when the molecule is at it's minimized configuration?"

ClareS [to Patricia] no, the torsion angle just describes the relative position of the atoms, it doesn't say anything about their energy

Patricia says "But the atoms do move a bit, don't they?"

ClareS says "for the definition of "torsion angle" it doesn't matter whether the atoms are moving or even whether they are atoms or just points - it's a geometrical concept"

Patricia says "As geometry.....I can understand......But Mariza asked a question too"

ClareS says "the distance between atoms A & D will depend on the torsion angle - the torsion angle doesn't measure the distance as it also depends on other things like the lengths of the bonds"

Mariza [guest] says "I see, thanks"

Tobias says "Using Netscape there should open a menu which asks to look for an application or to save the file to disk. Choose the later"

The housekeeper arrives to cart Pepi off to bed.

Patricia says "Mariza, I think it's like looking along the C2 - C3 bond in n-butane...the C1 and C4 can be in staggered or eclipsed or gauche positions"

Mariza [guest] [to Tobias] I got it., Thanks

ClareS says "this has been a very interesting discussion (in fact still is) but I will have to go soon..."

ClareS says "I would therefore like to declare the "formal" part of this meeting closed"

ClareS says "thank you all for participating"

Ajj says "thanks Clare, thanks everyone."

ClareS says "and see you at the virtual Christmas party in 2 weeks ;)"

Patricia says "It is an interesting discussion. I'm glad it was finally possible to join in. It's been nice chatting......discussing"

Ajj says "OK! with etoh?"

Mariza [guest] [to Patricia] and Clare, I really got the point know.

ClareS turns the ClareS_recorder off.