Re: [ccp4bb] how to convert matrix to angle
To add a bit to what others have already said -- The formula that Kay gave ((a11 + a22 + a33 - 1) / 2) throws out 2/3 of the rotational information. A 3D rotation cannot be described completely by a single angle: minimally three angles are actually required. There are many different ways, of course, to represent a 3D rotation, and what Kay gave is one component of the "axis-angle" representation. However, if you aren't interested per se in the axis of rotation, the angle from that formula will be the minimum possible angle required to rotate one domain/structure onto another -- and in that sense it is somewhat more intuitively apprehensible than the complete rotation. Note that, in general, a translation is also required to completely specify the transformation necessary to superimpose two domains, and thus using just a single angle is ignoring 5/6 of the relevant information. BTW, the corresponding axis of (unnormalized) rotation is given by [a21-a12, a02-a20, a10-102] (ignoring the annoying singularities at 180 degrees). If you use the most recent version of THESEUS to do your superpositions, the angle-axis representation is given in the transformations output file along with the matrix representation of the rotation. And in general the rotation given by the maximum likelihood method used by THESEUS will be different from that of a conventional unweighted least-squares superposition (the ML rotation is much less artifactually biased by regions of a domain, like mobile loops, that differ in conformation between the two domains being superpositioned). http://www.theseus3d.org/ Cheers, Douglas On Jul 8, 2007, at 5:21 AM, Bernhard Rupp wrote: Not that I want to open a can of worms here... but could someone explain what is meant with 'angle between domains'? Thx, br -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Das, Debanu Sent: Saturday, July 07, 2007 7:51 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how to convert matrix to angle Hi, You can also use LSQKAB in CCP4 to get the angle between two similar domains. -Debanu. -Original Message- From: CCP4 bulletin board on behalf of Kay Diederichs Sent: Sat 7/7/2007 7:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how to convert matrix to angle Jiamu Du schrieb: Dear all: I want to calculate the rotation angle between two similar domains. By using Coot, I can superposr the two domain and get the rotation matrix. But how to convert this matrix to an angle. Is there any program can calculate this ? Thanks. Jiamu Du, If you have the rotation matrix a11 a12 a13 a21 a22 a23 a31 a32 a33 then (a11 + a22 + a33 - 1) / 2 is the cosine of the angle you're looking for. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
Re: [ccp4bb] Kay Diederichs Email
S/MIME signed/encrypted messages started crashing my Mail app long ago, after one of the first updates to 10.4. I probably sent in a couple dozen of those crash reports, with absolutely zilch feedback, and of course I still have the problem. From my end of things, those crash feedbacks are worthless, and I don't send them in anymore as I see them as a waste of my time. On Jul 7, 2007, at 10:36 PM, Ian Ollmann wrote: When an app crashes, you should be getting a little dialog box with the option to send a problem report of some kind to Apple. Send in the report. This sends in some diagnostic details about Mail.app state when the crash occurred to Apple. Like crash reports are grouped together in a database and in a few weeks someone inside Apple gets a automated bug report with a title something like "172 crashes in _funcname" along with some crash stack backtraces. If you have the opportunity to do so, please also send in information about what steps you can take to reproduce the crash. Usually, the hardest thing about fixing bugs is reproducing them. If you are a software developer registered with ADC you can short circuit the process and directly file a bug through bugreporter.apple.com. Please attach a crash log and explain how to reproduce the problem. This one sounds serious enough that it might be a candidate for a quick fix for the next MacOS X.4 support update, provided that the right people find out about it soon enough. Ian On Jul 7, 2007, at 1:15 PM, Douglas L. Theobald wrote: Hey, I have the exact same problem. I haven't been able to read SMIME signed/encrypted emails now for some time (Mail just crashes). It is an intel apple bug of some sort. If you find the email in ~/Library/Mail, you can plain text cut out the sig and read the email. [Ick] This is especially annoying since apple Mail used to have such nice native integration of SMIME.
Re: [ccp4bb] Kay Diederichs Email
Hey, I have the exact same problem. I haven't been able to read SMIME signed/encrypted emails now for some time (Mail just crashes). It is an intel apple bug of some sort. If you find the email in ~/Library/Mail, you can plain text cut out the sig and read the email. [Ick] This is especially annoying since apple Mail used to have such nice native integration of SMIME. Cheers, Douglas On Jul 7, 2007, at 6:38 PM, James Stroud wrote: Hello All, I'm not trying to pick on Kay Diederichs here, but is anyone else having trouble with Kay's email? I am using Mac Mail and it seems to be crashing as a result of his cryptographic signature file. This effect is not isolated as it crashes on both of my intel Macs. I am running OS X 10.4.10. Apologies to Kay for the public question, but I was hoping to see if it was just my machines. My guess is that this is a bug from Apple and not any fault of Kay's. Also, I probably wouldn't bother in general, but his emails are usually worth reading. James ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^` Douglas L. Theobald Assistant Professor Department of Biochemistry Mailstop 009 415 South St Brandeis University Waltham, MA 02454-9110 [EMAIL PROTECTED] Office: +1 (781) 736-2303 Cell: +1 (718) 986-4457 Fax:+1 (781) 736-2349 GPG key ID: 38E9EB53 https://www.molevo.org/keys/38E9EB53.gpgkey ^\ /` /^. / /\ / / /`/ / . /` / / ' ' '
Re: [ccp4bb] rmsd calculation
Jenny,
I of course would suggest that you follow Olve's advice, and use
theseus to do a maximum likelihood, simultaneous superposition of all
your structures ( http://www.theseus3d.org ). The variable bits,
like your loop, will be naturally down-weighted in a rigorous
statistical manner. Then you can look at the average structure file
that is output (_ave.pdb at the end of the filename), and the B-
factor column has the overall RMSD for each atom in there. You can
look at the full superposition (the _sup.pdb file) in rasmol or in
pymol with the 'set all_states, on' command.
However, if you really need to do the very analysis that you asked
about, the following bash script will do exactly that with theseus
(you need both awk and theseus in your executable path). It prints
out the average RMSD for the atoms you specify in the loop, after
pairwise least-squares superpositioning on all atoms other than the
loop, for all possible pairwise combinations of your pdb files. (Note
that in this script all backslashes '\' must have a carriage return
immediately after them.) You will need to change the lower and upper
values at the top of the script (inclusive for the loop you want
excluded). You invoke the script something like "karen.sh pdb1.pdb
pdb2.pdb pdb3.pdb" or "karen.sh *.pdb" to do all the .pdbs in one
directory. If you have any problems or have other specific
superpositioning issues I'm glad to help out.
Cheers,
Douglas
karen.sh
#
#!/bin/bash
# everything including and between lower and upper
# is excluded from the superposition
lower=40;
upper=60;
pdbs=($*);
for (( i = 0; i < [EMAIL PROTECTED]; ++i ))
do
for (( j = 0; j < i; ++j ))
do
name="${pdbs[i]%.*}_${pdbs[j]%.*}";
theseus -l -r ${name} -S ${lower}-${upper} ${pdbs[i]} ${pdbs[j]}\
> ${name}.log;
rmsd=$(cut -c 7-11,61-67 ${name}_ave.pdb |\
awk '{if ($1 > lo && $1 < up) {sum += $2; n++}}; END {print sum/
n}'\
lo=${lower} up=${upper});
echo "${name} rmsd = ${rmsd}";
done
done
^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`
Douglas L. Theobald
Department of Biochemistry
Brandeis University
Waltham, MA 02454-9110
[EMAIL PROTECTED]
^\
/` /^. / /\
/ / /`/ / . /`
/ / ' '
'
On May 11, 2007, at 1:58 PM, Olve Peersen wrote:
I would highly recommend Doug Theobald's program Theseus for this -
the pictures at www.theseus3d.org say it all. Theseus does maximum
likely hood superimpositions of multiple structures (i.e. NOT
pairwise against a "master" copy), and the real beauty of it is
that you don't have to pick which residues you want to
superimpose. Places where the whole set of structures show
divergence are effectively down-weighted and don't contribute much
to the final solution vs. least squares where every atom position
has equal weight and the "bad" parts screw up the alignment of the
"good" parts. For this, I would do a Theseus superposition of all
the structures and then analyze the set of superimposed structures
by whatever method you want (e.g. rmsd of variances in important
sections of the structures).
- Olve
---
Olve Peersen
Associate Professor
Dept. of Biochemistry & Molecular Biology
1870 Campus Delivery
Colorado State University
Ft. Collins, CO 80523-1870
---
970.491-0433Office (MRB 279)
970.491-0271Lab (MRB 149)
970.491-0494Fax
[EMAIL PROTECTED]
---
On May 11, 2007, at 11:15 AM, Donnie Berkholz wrote:
Eleanor Dodson wrote:
It is a bit clunky - you can use siperpose molecules - fit
residues to
fit a selected range (1-40; 60-100 say) and write out a complete
fitted
pdb file. Then you could use a VERY old program
compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb)
and it will match all pairs with the same RESIDUE ID and give the
RMSD
distance
There is documentation for it.
There's a nice (non-CCP4) program called ProFit that does a pretty
nice
job of superimposing with a lot of flexibility.
Thanks,
Donnie
On May 10, 2007, at 6:45 PM, Jenny wrote:
Hi, All,
I have a question about rmsd calculation.
I have some pdbs (100 residues ) and these pdbs differ pretty
much only the loop region 40-60. Is there any easy way that I can
superimpose the fixed region ( 1-40,60-100) and then calculate
the rmsd for the loop?I need to calculate for each pair, so if
there is any script or program available to do this quickly, that
would be great.
Thanks.
Jenny
[ccp4bb] Easy proteins to crystallize -- summary
Thanks all who answered, and sorry for the delay -- I was held up having a date with a lovely quasi-species of norovirus. I had asked the list for examples of proteins that are easily crystallizable, especially those that over-express and diffract well, not necessarily well-known. The classics appear to be: lysozyme glucose isomerase thaumatin alpha-lactalbumin catalase ribonuclease S proteinase K trypsin myoglobin ferritin For recipes see the Hampton catalog or http://www.rigaku.com/protein/crystallization.html Some perhaps lesser known proteins, but nice: Concanavalin A CheY RecA RluD, an E. coli pseudouridine synthase Fc portion of antibody bacterial antitoxin HigA, 2ICT glycerol dehydrogenase from the yeast S. pombe tRNA guanine transglycosylase (TGT, e. g. 1n2v) cytochrome C peroxidase (CCP, e.g. 1AC4) Cholesterol oxidase from Streptomyces Beta-lactoglobulin pepsin PepN from E.coli Thanks again! Douglas
Re: [ccp4bb] superpose
Hi Juan, This doesn't directly apply to Superpose -- but THESEUS (which does both conventional least-squares and maximum likelihood superpositions) puts RMSD values by default in the B-factor column of the PDB of the mean structure for a superposition. It is undocumented, but via the THESEUS also will weight the superposition by B-factor, using the B-factors as Bayesian priors for the variances. It can do this two different ways, either (1) by assuming that the B-factors are absolutely known values or (2) by assuming that the B-factors for a structure are only known up to a scale factor (use command line flags -b1 or -b2 respectively). For the latter case, which is most realistic, THESEUS finds the maximum likelihood value for the normalization factor for each structure. http://www.theseus3d.org/ Cheers, Douglas On Mar 12, 2007, at 12:13 PM, Juan Sanchez-Weatherby (UEA) wrote: Dear all I have three questions that might have been answered before but I haven't been able to find them. 1) I was wondering whether anyone could tell me what does (in the Superpose output) "RMS B DISPLACEMENT" stand for? 2) If "B" is B-factor how meaningful is it if the haven't been normalised prior to the comparison? 3) Lastly I was wondering if there is a way of putting RMS deviation values in the B-factor column of a PDB file so it can coloured according to RMS instead of B-factor. Thank you very much Juan Juan Sanchez-Weatherby School of Biological Sciences University of East Anglia Norwich NR4 7TJ United Kingdom ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^` Douglas L. Theobald Department of Biochemistry Brandeis University Waltham, MA 02454-9110 [EMAIL PROTECTED] GPG key ID: 38E9EB53 https://www.molevo.org/keys/38E9EB53.gpgkey ^\ /` /^. / /\ / / /`/ / . /` / / ' ' '
Re: [ccp4bb] Easy proteins to crystallize
Thanks to all who have responded. Any last minute suggestions before I summarize? On Mar 1, 2007, at 7:40 PM, [EMAIL PROTECTED] wrote: I really like to use glucose isomerase, for sale from for example Hampton. It is a crystalline suspension when you buy it and it is trivial to get crystals with almost any precipitant - we have managed to crystallize it from water with temperature variation :-). Some precipitants give multiple crystal habits (and spacegroups). There is a clear correlation between recipe and quality. For example, you can grow beautiful crystals with ammonium sulfate but those are next-to-impossibe to cryo-cool, while others are much easier. Protein is a lot bigger than lysozyme and insulin, so perhaps more representative of a 'typical protein'. The crystals diffract like rocks. When I get to setting up a class to teach, I think that is what I will use. Mark Mark van der Woerd, PhD Research Scientist Dept. of Biochemistry and Molecular Biology Colorado State University Fort Collins, CO 80523 Phone (970) 491-0469 -Original Message- From: [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Thu, 22 Feb 2007 11:23 AM Subject: [ccp4bb] Easy proteins to crystallize Hi all, I'd like to pick the collective brain of crystallographers on this list -- what are some of the most easily crystallizable proteins? I'm especially interested in those that over-express and diffract well, and in ones that might be less well-known than, say, lysozyme (but nearly as nice). Douglas ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^` Douglas L. Theobald Department of Biochemistry Brandeis University Waltham, MA 02454-9110 [EMAIL PROTECTED] ^\ /` /^. / /\ / / /`/ / . /` / / ' ' ' Check Out the new free AIM(R) Mail -- 2 GB of storage and industry- leading spam and email virus protection.
Re: [ccp4bb] Easy proteins to crystallize
On Feb 22, 2007, at 2:35 PM, Nat Echols wrote: I take it you're only interested in well-characterized and well- known proteins? Actually no -- well-characterized is good, but well-known is unnecessary. I have a receiver domain that expresses at >100mg/L and forms crystals right out of most screens that diffract to atomic/ subatomic resolution, but it's still being functionally characterized and the system it's a part of is of limited interest outside of a specific field of microbiology. Experimentally, though, I can't imagine an easier protein to work with. On Thu, 22 Feb 2007, Douglas L. Theobald wrote: Hi all, I'd like to pick the collective brain of crystallographers on this list -- what are some of the most easily crystallizable proteins? I'm especially interested in those that over-express and diffract well, and in ones that might be less well-known than, say, lysozyme (but nearly as nice). Douglas ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^` Douglas L. Theobald Department of Biochemistry Brandeis University Waltham, MA 02454-9110 [EMAIL PROTECTED] ^\ /` /^. / /\ / / /`/ / . /` / / ' ' '
Re: [ccp4bb] Easy proteins to crystallize
Yes, but I was wanting to compile something more like a specific list of "classic" proteins, similar to lysozyme. On Feb 22, 2007, at 1:33 PM, Iain Kerr wrote: Proteins extracted from hyperthermophiles are sometimes easier to crystallise than homologues from more temperate environmentsthe purification protocol often involves a "boiling step" that denatures/degrades everything else in the prep...the resulting incredibly high purity and homogeneity may be a contributing factor... HTH, Iain Douglas L. Theobald wrote: Hi all, I'd like to pick the collective brain of crystallographers on this list -- what are some of the most easily crystallizable proteins? I'm especially interested in those that over-express and diffract well, and in ones that might be less well-known than, say, lysozyme (but nearly as nice). Douglas ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^` Douglas L. Theobald Department of Biochemistry Brandeis University Waltham, MA 02454-9110 [EMAIL PROTECTED] ^\ /` /^. / /\ / / /`/ / . /` / / ' ' '
[ccp4bb] Easy proteins to crystallize
Hi all, I'd like to pick the collective brain of crystallographers on this list -- what are some of the most easily crystallizable proteins? I'm especially interested in those that over-express and diffract well, and in ones that might be less well-known than, say, lysozyme (but nearly as nice). Douglas ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^` Douglas L. Theobald Department of Biochemistry Brandeis University Waltham, MA 02454-9110 [EMAIL PROTECTED] ^\ /` /^. / /\ / / /`/ / . /` / / ' ' '
Re: ccp4bb on new site
On Jan 19, 2007, at 4:20 PM, Steve Lane wrote: Agreed. If at all possible, please resume use of the [ccp4bb] Subject: tag. I'll add another vote for the [ccp4bb] tag. -- Steve Lane System, Network and Security Administrator Doudna Lab Biomolecular Structure and Mechanism Group UC Berkeley On Fri, Jan 19, 2007 at 04:02:20PM -0500, [EMAIL PROTECTED] wrote: On 19 Jan, Andy Purkiss wrote: I know that it is an easy fix :) However, nearly all of the lists that I am on use the [listname] notation and this makes it a bit easier to sort out the lists from the personal mail. I'm more likely to look at something with [ccp4bb] and not just skip over it. I agree with this. Messages are often forwarded to friends or other lists, and it is good to know where they are coming from. It also helps to address the cross-posting issue, because the cross-posted replies are easily identified. Prefixing the Subject line with [listname] is the best way to do this in my opinion. Regards, Michael L. Love Ph.D
