[ccp4bb] ideal bond length and bong angel

2008-01-09 Thread yang li
Dear All, I've wonder for a simple problem for a long time, that is: What is the ideal bond length and angel? Every lecture or book says this is a criteria from small organic molecules, but I still donnot know exactly. Like is bond length point to the peptide bond length? Or many other bonds?

Re: [ccp4bb] how to model glycosylated residues?

2008-01-09 Thread Jiamu Du
Dear All, Thank you for your previous response. I have built a 3-mer oligosaccharides in the electron density by using coot. I prefer to refine my structure in CNS due the resolution is only 2.6 Ang. I found there are only topology and parameter files for carbohydrate in CNS but no linkage file for

Re: [ccp4bb] How to refine large moleculars?

2008-01-09 Thread Eleanor Dodson
With such good data you would expect lower R factors I agree. I use all the COOT validation tools - Ramachandran, diff map peaks etc to try to pinpoint errors. Also anomalous difference maps hoping to verify S positions and check the sequence fitting. You could let Arp/Warp rebuild it from t

Re: [ccp4bb] Any programs other than GRASP have a surface scribing function?

2008-01-09 Thread Liz Potterton
James, CCP4mg will allow you select a set of atoms and draw a surface over them in whatever colour scheme that you choose. The tutorial explaining this is at http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/tutorial/surfaces.html Cheers Liz James Thompson wrote: Dear CCP4'ers, Any Window

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread Stuart McNicholas
On 9 Jan 2008, at 10:34, Eleanor Dodson wrote: Bong angels are probably ideal already! There is really no such animal as an ideal bondlength or angle - they depend to some extent on the atomic environment. Not to a complete extent? Stuart

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread Eleanor Dodson
Bong angels are probably ideal already! There is really no such animal as an ideal bondlength or angle - they depend to some extent on the atomic environment. There are papers by Engh and Huber who looked at small molecule highly refined structures to get AVERAGE bond lengths and standard devi

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread Gerard DVD Kleywegt
Can you explain the define of the bond length and bond angel--especially bond angel--here? i leave the definition of angels (be they ideal or not) to clerics, but if you want to find out about bonds and angles, AND YOUR SUPERVISOR IS REALLY UNABLE OR TOO BUSY TO EXPLAIN THESE BASIC CONCEPTS

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread yang li
By the way, I think my bad english embarrassed my meaning. What I want to say is which bond length is used as the standard? the C=N or Ca-N or even the side chains? Or all of them?Which angel is used to compare, the Ca-C'-N or C'-N-Ca or others. At first I suppose the bond length only calc

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread yang li
Dear Prof Gerard: In fact I have read your Model Validation on-line, and I have to say it is youe lecture that made me to think about this problem, though I have used it as a common stand for the quality of the model without understand it for a long time. And the http://en.wikipedia.org/

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread Gerard DVD Kleywegt
them today before I post my mail, but unable to access them. For some reason, wiki is forbiddon here. I really coouldnot find the best answer and have discussed i am shocked. i just checked with one of my 25 chinese students here and indeed even universities in china do not have access to a ba

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread Andreas Förster
Hey Gerard, wikipedia might tell you how to angle for fishes, but I fear it falls short of teaching you how to fish for angels. Andreas Imperial College of Aquatic and Fisheries Sciences London Gerard DVD Kleywegt wrote: Can you explain the define of the bond length and bond angel-

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread David J. Schuller
On Wed, 2008-01-09 at 12:47 +0100, Gerard DVD Kleywegt wrote: > (rhetorical question of the day: just like teaching a person how to fish is > better than to give them a fish, isn't providing the url to google or > wikipedia better than providing an answer to a basic question?) You can read a fe

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread Mischa Machius
Simply use a bong for a while, and you will hear the angels sing :) It's amazing to see how this thread devolved, within two or three posts, into a discussion about drug abuse and totalitarian political regimes... Good way to start the day :) On Jan 9, 2008, at 8:35 AM, Jim Pflugrath wro

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread Jim Pflugrath
Bong angels are probably ideal already! Please explain, so that I can teach this to my students. :) Jim

[ccp4bb] crystallization robot

2008-01-09 Thread Nalam, Madhavi
Hi, Sorry for the non-ccp4 related question. We are planning to buy a crystallization robot. We looked at the 'Mosquito'. We felt it is good for setting 96 well plates (for screening the conditions). Though they say that we can use it for 24 well plates (hanging drop) it didn't seem to be ideal bec

Re: [ccp4bb] how to model glycosylated residues?

2008-01-09 Thread Craig McElroy
In your generate.inp file that generates the input pdb and mtf files for cns there is a section called carbohydrate links which you can use to define the links... see below for an example of a beta link between the C1 and Asn N and a beta link between O4 and C1 of the next sugar. Then just make

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread William Scott
Hi Yang Li: Macromolecular crystal refinement programs use ideal bond lengths and angles. The simplest ones just assume any carbon-carbon single bond (C-C) is the same as any other, and use one average value, and any carbon-carbon double bond (C=C) is the same as any other, and use another averag

Re: [ccp4bb] crystallization robot

2008-01-09 Thread junfeng liu
Douglas Oryx6 or 8. It works well on sitting drop and microbatch in our division. Nalam, Madhavi wrote: Hi, Sorry for the non-ccp4 related question. We are planning to buy a crystallization robot. We looked at the 'Mosquito'. We felt it is good for setting 96 well plates (for screening the condi

Re: [ccp4bb] crystallization robot

2008-01-09 Thread Lisa A Nagy
We chose the Phoenix crystallization robot because: It has no expensive consumables (tips) intrinsic to the machine. This was also a big item for us because we worry about being able to run the machine for more than 3 years. Would the tips for our 2008 machine be available in 2014? It is easy to

Re: [ccp4bb] crystallization robot

2008-01-09 Thread Van Den Berg, Bert
Hi Lisa, is the Phoenix capable of setting up hanging drops? For me that is one of the big plusses of the Mosquito. Are there any other robots out there capable of doing hanging drops? Cheers, Bert Bert van den Berg University of Massachusetts Medical School Program in Molecular Medicine Bi

[ccp4bb] apologize

2008-01-09 Thread yang li
Dear All, I am very sorry to involve you into such insignificance discussion, I have reached agreement with Prof Gerard, please stop talking about things beyond science, thanks! I read a book today, which said "A refined model should exhibit rms deviations of no more than 0.02A for bond

Re: [ccp4bb] crystallization robot

2008-01-09 Thread Lisa A Nagy
It doesn't have a cover slip flipper. We only do sitting drops with our robot- even large volumes (2 ul drops). We don't have the space to store the volume of linbro plates that would be generated by a robot. Also, 24 well linbro plates use a lot of well solution- making them very expensive fo

Re: [ccp4bb] crystallization robot

2008-01-09 Thread Lisa A Nagy
Looking at the mosquito, it doesn't have any cover-slip handling robotics, either. So it's the same thing- rearrange the dispense location and flip the cover- which is either a glass plate or mylar or a tape seal. -- Lisa Nagy University of Alabama-Birmingham [EMAIL PROTECTED]

Re: [ccp4bb] apologize

2008-01-09 Thread William Scott
Dear Yang Li: Happy New Year to you, too, (ahead of Feb. 7th). You certainly owe us no apology; the reverse may not be true. Your question is an important one, as is what you have written below. I'm not certain I have a completely satisfactory answer. The reason is that ideal bond lengths may

Re: [ccp4bb] bond lengths, angles, ideality and refinements

2008-01-09 Thread William Scott
Sorry, that should have read "because the value is established by social consensus, it is thus NOT guaranteed to be perfectly accurate, ..." In other words, one can imagine some source of systematic error in establishing an ideal bond length. For example, the crystal packing environment of small

Re: [ccp4bb] crystallization robot

2008-01-09 Thread Van Den Berg, Bert
The mosquito has special (albeit fairly pricey at $13 each) plastic sheets that allow setup of hanging drops in a 96-well format. It can also do multiple drops per well. As far as I know this is a capability unique to the Mosquito but I may be wrong. Bert van den Berg University of Massachuset

Re: [ccp4bb] bond lengths, angles, ideality and refinements

2008-01-09 Thread Nave, C (Colin)
The latest Acta D shows the "social consensus" is sometimes lacking even (or especially) among very experienced and able crystallographers. Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values Ian J. Tic

Re: [ccp4bb] bond lengths, angles, ideality and refinements

2008-01-09 Thread Gerard DVD Kleywegt
For some current thoughts on bond length and bond angle deviations you may want to look at the following paper: ... but that would be rather a waste of your time (sorry!). if you're only going to read one paper about this subject this year, make it iain tickle's! http://journals.iucr.org/

Re: [ccp4bb] crystallization robot

2008-01-09 Thread Lisa A Nagy
The phoenix can dispense multiple drops per well. You can easily program dispensing on the deck wherever, whatever and whenever, as long as it fits in the plate holder . It can handle at least the 1536 pitch (4 x 384), so if you specify the quadrant of the 384 well cell it will dispense there. Your

Re: [ccp4bb] apologize

2008-01-09 Thread Patrick Loll
Check out the letters in the Dec 2007 edition of Acta D. There is lively discussion even among the experts (and while I recall no mention of angels in this discussion, there IS a reference to Winnie the Pooh). Acta Cryst. (2007). D63, 1274-1281 Acta Cryst. (2007). D63, 1282-1283 Some pe

Re: [ccp4bb] bond lengths, angles, ideality and refinements

2008-01-09 Thread Herbert J. Bernstein
"tables 1" is formally correct but awkward. "table 1s" is confusing. I would suggest that we treat "table 1" like sheep and make the plural the same as the singular. If you don't approve of revising the English language, then a valid way to avoid the need for a plural is to say "each table 1"

Re: [ccp4bb] bond lengths, angles, ideality and refinements

2008-01-09 Thread Todd Holyoak
For some current thoughts on bond length and bond angle deviations you may want to look at the following paper: Acta Cryst. (2007). D63, 611-620 Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them? M.

Re: [ccp4bb] crystallization robot

2008-01-09 Thread Tom Walter
Hi Madhavi In conjunction with a 96-syringe hydra for filling reservoirs, we have been using two Genomic Solutions 8-tip "Cartesian" systems (Called HoneybeeX8 now I believe) for the past 6 years and have been generally very happy with them. They require a bit of looking after in terms of clean

Re: [ccp4bb] bond lengths, angles, ideality and refinements

2008-01-09 Thread Ian Tickle
Hi William & others, Indeed, phenix.refine uses cross-validation to optimise the scaling of the X-ray & B-factor weights. All I did was demonstrate that you can do essentially the same thing as phenix.refine but using Refmac instead. I don't claim to have done anything new, except I modified

Re: [ccp4bb] bond lengths, angles, ideality and refinements

2008-01-09 Thread Anastassis Perrakis
I would only like to iterate a small comment I posted before: Should the cell parameters be inaccurate, optimization of weights by cross-validation (getting the best Rfree) will result in 'higher' RMSD. It is easy to think about it: if in a cell is measured to be 1% larger than in reality, al

Re: [ccp4bb] crystallization robot

2008-01-09 Thread Balaji Bhyravbhatla
All, Just a quick correction on the latest price of the plastic sheets. The new ones cost $5.00, so the overall cost will be much cheaper. Thanks Balaji On Jan 9, 2008, at 11:59 AM, Van Den Berg, Bert wrote: The mosquito has special (albeit fairly pricey at $13 each) plastic sheets that a

[ccp4bb] Principal axes and moment of inertia matrix

2008-01-09 Thread Buz Barstow
Dear All, Does anyone have a python routine that can be used to calculate the moment of inertia matrix and principal axes of a selection of atoms? Thanks! and all the best, --Buz

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread James Stroud
On Jan 9, 2008, at 5:30 AM, Gerard DVD Kleywegt wrote: them today before I post my mail, but unable to access them. For some reason, wiki is forbiddon here. I really coouldnot find the best answer and have discussed i am shocked. i just checked with one of my 25 chinese students here and i

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread Gerard DVD Kleywegt
Be care, you insolence might get someone sent disappear. is the chinese secret service editing my incoming mail already, or are you merely using a microsoft grammar checker? --dvd ** Gerard J. Kleywegt

[ccp4bb] Sulfate ion on 2-fold axis

2008-01-09 Thread Jie Liu
Dear all I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file one S atom with occu=0.5 and two O atoms with occu=1, or should I put one S and four O atoms all with occu=0.5? Thanks for your inputs. Jie

Re: [ccp4bb] crystallization robot

2008-01-09 Thread Janet Newman
The Gilson crystallisation robots (horrible machines: no longer available) were specific for hanging drops - other robots can set them up (using the Mosquito sheets or equivalent), but the flipping will have to be done by hand. The Douglas Instrument machines can basically pipette onto anything yo

[ccp4bb] Malic Acid interferes heavy metal binding?

2008-01-09 Thread JINJIN ZHANG
Dear All, I have got large and nice crystals in a condition that contains 40% glycerol, 75 mM DL-Malic Acid pH7.0, and that's it! No precipitant?! No buffer?! I'm so comfused. As far as from the product website, the Malic Acid has no buffering function. I don't know whether it's a precipitant. The

Re: [ccp4bb] Malic Acid interferes heavy metal binding?

2008-01-09 Thread William Scott
Dear Jinjin: Malic acid, a diprotic acid, has a pKa of about 3.4 for the first dissociation and a second at about 5.1. So it is best as a buffer within a pH range of about 2.4 to 6.1, and it at its best around best in the range of 3.4 to 5.1. If the pH of your solution is indeed 7, then it is

Re: [ccp4bb] Sulfate ion on 2-fold axis

2008-01-09 Thread Charlie Bond
Hi Jie, Depending on your resolution, you may be forced use to use S(0.5) and 4x(0.5) in order to restrain the SO4 to stay tetrahedral in refinement. Cheers, Charlie Jie Liu wrote: > Dear all > > I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file > one S atom with occu=0.5 a

[ccp4bb] unbiased electron density map

2008-01-09 Thread michael nelson
In my understanding, unbiased electron density map usually refers to the Fo-Fc map.But I have seen in some papers sentences like that "The initial, unbiased 2FoFc map is contoured at".I was a bit confused since I was told by my instructor that the 2Fo-Fc was usually biased. Can anyone clear up

Re: [ccp4bb] Sulfate ion on 2-fold axis

2008-01-09 Thread Dale Tronrud
Dear Jie, It also depends on whether you believe the SO4 sits with its internal two-fold along the crystal's two-fold axis. If it does you should probably have a 0.5 occ sulfur and two 1.0 occ oxygen atoms. If the symmetry is not obeyed you will have to have four 0.5 occ oxygen atoms. Be

Re: [ccp4bb] unbiased electron density map

2008-01-09 Thread William Scott
The map will be biased by whatever model is used to generate the phases. If a heavy atom phasing method was used (MIR, MAD, etc) then at least you do not have model bias. A sigma-A weighted 2Fo-Fc map strives to have minimal bias, as does an EDEN map with phase perturbation. However, minimally b

Re: [ccp4bb] Principal axes and moment of inertia matrix

2008-01-09 Thread James Stroud
On Jan 9, 2008, at 11:56 AM, Buz Barstow wrote: Does anyone have a python routine that can be used to calculate the moment of inertia matrix and principal axes of a selection of atoms? I compulsively write python code sometimes--its that fun of a language... If you can get the x, y, z, a

Re: [ccp4bb] unbiased electron density map

2008-01-09 Thread Dale Tronrud
A 2Fo-Fc map is simply an Fc map with two times the Fo-Fc map added to it. ( Fc + 2(Fo-Fc) = Fc + 2Fo - 2Fc = 2Fo - Fc ) The phase comes from the Fc's. The basic formulation is biased toward the model used to calculate the Fc's. You did, after all, start with a pure Fc map! Various tech

[ccp4bb] Crystal imaging system

2008-01-09 Thread Alexander Aleshin
Could anybody also advise about an imaging system for automatic inspection of crystallization plates? Is there a newsgroup dedicated to crystallization robotics? > Hi, > Sorry for the non-ccp4 related question. > We are planning to buy a crystallization robot. We looked at the > 'Mosquito'. We

Re: [ccp4bb] Malic Acid interferes heavy metal binding?

2008-01-09 Thread Artem Evdokimov
Hi, Heavy atoms can be unpredictable. There are rules of thumb regarding their use but these rules are frequently bent and broken. Which heavy atom derivatives have you tried, and at what (approximately) concentrations and exposure times? Does your protein have residues that *can* react wit

Re: [ccp4bb] Crystal imaging system

2008-01-09 Thread Bernhard Rupp
The CrysCam manufactured by Art Robbins is quite versatile at a very competitive price-performance ratio. They also do quick custom mods if you have special tasks, and they always provide a demo. http://www.artrobbinsinstruments.com/cryscam.html Best regards, BR -Original Message- F

Re: [ccp4bb] how to model glycosylated residues?

2008-01-09 Thread Jiamu Du
Thank you for your help. I have make my CNS work on the structure refine successfully. Best Regards. On Jan 10, 2008 4:51 AM, Li Zhijie <[EMAIL PROTECTED]> wrote: > Hi Jiamu, > > I think the glycoside linkages are specified in the generate.inp file. > The text I list in the end of this email is