Re: [ccp4bb] rmsd calculation. .
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Jenny and Iain, But my understanding is that Iain's procedure gives the rmsds of the _aligned_ C-alphas, whereas Jenny actually seems to be more interested in those that she excludes from the alignment. I may be wrong, but in these cases, I use lsqman (from DVD) or lsqkab (from ccp4) to superpose the proteins (using one as reference) according to a particular scheme (Jenny's 1-40,60-100) and then write a script to calculate the rmsds for the interesting 41-59 residues. There may be an easier way, which I'll be interested to learn about. Cheers, M. Kerr, Iain escribió: Hi Jenny, You can do this in LSQMAN (if I’m understanding your question correctly…) You’d first superimpose the residues in the “fixed region” to give a superimposed core using the ‘EXplicit’ command, eg: *LSQMAN ex m1* * Range 1 ? (A1-10) a4-10 a19-23 a28-36 a44-51 a53-66 a91-97 a106-111 a123:126* * Mol 2 ? (M1) m2* * Range 2 ? (A1) a4 a19 a28 a44 a53 a91 a106 a123* * Explicit fit of M1 A4-10 A19-23 A28-36 A44-51 A53-66 A91-97 A106-111 A123:126* * And M2 A4 A19 A28 A44 A53 A91 A106 A123* * Atom types | CA | N | C | O | CB |* * Nr of atoms to match : (295)* * The295 atoms have an RMS distance of0.892 A* * Rotation: -0.956932 0.127723 -0.260706* * 0.170532 -0.479456 -0.860837* *-0.234946 -0.868222 0.437026* * Translation : 13.78726.80038.541* Then use the “IMProve” command to iteratively improve the fit over all CAs…this only works for two molecules at a time though…I guess choose a fixed standard to align all the others against. Remember to write out the coordinates for the rotated (ie. “m2”) molecules: Ø apply m1 m2 Ø wr m2 blah_rotated.pdb Then to calculate the RMSDs for just the loop regions compare the superimposed molecules to the fixed standard (ie. “m1” is the fixed standard, “m2” is your blah_rotated.pdb), explicitly using just the loop atoms this time in “m1” and “m2” ranges. I’m sure there is an easier way to do this, but works for me. HTH, Iain *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Jenny *Sent:* Thursday, May 10, 2007 5:46 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] rmsd calculation. . 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 - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGRAwlF6oOrDvhbQIRAjmEAJ9UvAWXfIZU7bR1idcVqn8hE5zPwQCfc8Ko JkvZQL9IHdB+ENi92nVVUmI= =3HO2 -END PGP SIGNATURE-
Re: [ccp4bb] CCP4 GUI
On Thu, May 10, 2007 at 02:46:44PM +0100, Kolstoe S.E. wrote: The most useful aspect of the ccp4i GUI is its automatic generation of com files. However, I would prefer the GUI to output a .com file into my working directory (rather than the obscure location they are saved to now) every time I run a program so that I can then tinker with it and add any extra keywords I want to. I often use the GUI to get a 'second opinion' about good default values and options for a given CCP4 program - especially if the documentation is a bit confusing. Kind of double-checking if I understood the documentation correctly. One thing I found very confusing though, is that the com-files created by the CCP4i will often have (nearly) all possible keywords set, even if I haven't changed any of the defaults in the gui. Often, a CCP4 program has defaults itself and only requires keywords if one wants to change things - which is nice, since it leads e.g. to a very short SCALA comand-file. I'm not always convinced that the settings done by the CCP4i interface (when keeping all edfaults) correspond to the defaults as implemented in the program itself. Maybe any parameter setting unchanged from the values in the $CCP4/ccp4i/tasks/*.def file should be internally flagged as being at the 'default value' - resulting in them _not_ being written to the com-file? This way any potential change in defaults inside the actual program would have immediate effect, even if the CCP4i hasn't been updated yet. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Molecular Replacement issues with a WD-40 7-bladed beta propeller
Hello Scott, hmmm - it is quite difficult to do a good analysis of your problem, remotely. You've tried the enantiomorphic space group I4(3), just to be sure? In principle, the molecular replacement solution given by Phaser sounds good, but this is no proof of whether it's correct. What sounds good is, that you have high Z-scores, the packing looks good to you and the starting R-factor is quite low, not high! For a first model, the working-R and Free-R are usually very close (the initial unrefined model explains the whole set and a random subset equally well), and it is normal, that the Free-R rises in the first xyzB refinement cycles (the free set decouples from the working set, so to say). You don't say how much it rises, but make sure that you use _very_ tight geometry restraints at this resolution to reduce overfitting. I suggest a starting weight of 0.01 or even 0.005 for the X-ray term, resulting in final RMSD values for the bonds of ~0.010-0.012 (there is no exact rule). Your could also use tight NCS restraints for the two molecules to even further reduce any potential overfitting. In contrast, you can leave the B-factor restraints as they are, or even loosen their restraints (I use always values of 2.0, 3.0, 4.5, 6.0 - you can find them in REFMAC under the Geometrical Parameters tab)! On one hand, this gives the model more freedom which could potentially result in more overfitting, on the other hand, however, this additional freedom, at least in my experience, effectively _reduces_ model bias by allowing wrongly placed atoms to vanish. In general, for molecular replacement, never believe any solution until you see the resulting electron density maps. For a true solution, the electron densities should tell you, which parts are wrong and which are missing. At 2.9 A, resolution, this might be difficult. I would suggest that you look at the NCS-averaged electron density map in Coot. However, there could be a lot of other problems ... I would suggest that you could find a local crystallographer at Berkeley that helps you on site. I hope that helps a little bit. Good luck, Dirk. Scott Coyle wrote: Hello, I'm an undergraduate and recently crystallized and obtained 2.9A diffraction data for a protein which is predicted to fold into a WD40 7-bladed beta-propeller structure (which has been crudely verified by cryo-EM by another lab). The space group appears to be I4(1) with unit cell parameters 118.936 118.93685.45690.00090.000 90.000. Using a number of different search models (which I trimmed and aligned to my protein's sequence using Chainsaw) I have obtained a number of MR solutions placing 2 molecules in the AU with Phaser with high Z-scores (ranging from Z=9 to 12) that seem to pack together nicely, so I was hoping to use this technique to solve my structure. However, the initial Rfree for my best solution is relatively high (0.49) and all attempts to refine the structure result in the Rfree blowing up almost immediately. This makes me worry that the maps I'm generating may be too model-biased to use to generate a solution. I've tried using Prime and Switch to remove model bias but the resulting map looks worse than the starting map. As the predicted structure possesses so much radial symmetry (7-fold), I'm worried that my MR solutions will never be oriented correctly enough for me to be able to build a model. If anyone has any suggestions for tackling this kind of molecular replacement woe, I would greatly appreciate it. Otherwise I guess I'll just plan to collect experimental phasing information sometime in the near future. I'm not sure if this is the right place to be asking this question, perhaps you guys could direct me elsewhere. Thanks! -Scott -- Dirk Kostrewa Paul Scherrer Institut Biomolecular Research, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: [EMAIL PROTECTED] http://sb.web.psi.ch
Re: [ccp4bb] CCP4 GUI
Hi Maybe any parameter setting unchanged from the values in the $CCP4/ccp4i/tasks/*.def file should be internally flagged as being at the 'default value' - resulting in them _not_ being written to the com-file? This way any potential change in defaults inside the actual program would have immediate effect, even if the CCP4i hasn't been updated yet. This is a _really_ good idea for another reason. There are programs which determine processing parameter values dyamically, based on what they have actually been presented with - UNLESS those values have been input by the user, who is assumed to know better. If an interface (e.g. ccp4i) sets the value to a default, the program really has no way of knowing that it was the interface and not a user who knows their data which has input the value. Just my two ha'porth... Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] CCP4 GUI
Clemens Vonrhein wrote: One thing I found very confusing though, is that the com-files created by the CCP4i will often have (nearly) all possible keywords set, even if I haven't changed any of the defaults in the gui. Often, a CCP4 program has defaults itself and only requires keywords if one wants to change things - which is nice, since it leads e.g. to a very short SCALA comand-file. I'm not always convinced that the settings done by the CCP4i interface (when keeping all edfaults) correspond to the defaults as implemented in the program itself. This of course depends on whether the program author wrote their best set of defaults into the GUI or the program, which in turn depends on whether the program author wrote the GUI or not. I tend to assume that everyone is running through the GUI these days, and make sure that the GUI defaults are the sensible ones (although I try and keep the program source in step). If someone asks me how best to run one of my programs, the answer is therefore to use the GUI to generate a command script and start from there. Kevin
Re: [ccp4bb] rmsd calculation
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. Eleanor 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
Re: [ccp4bb] CCP4 GUI
I would agree with Clemens that the Scala GUI task generates far too many keyworded commands, for things which have sensible defaults in the program. One problem conundrum for the GUI (because it works by generating a script without actually running the program) is that the GUI has no way of knowing what defaults are set in the program (particularly if they are dynamic depending on the data). But this could be managed better than it is in all cases. Phil On 11 May 2007, at 08:31, Clemens Vonrhein wrote: On Thu, May 10, 2007 at 02:46:44PM +0100, Kolstoe S.E. wrote: The most useful aspect of the ccp4i GUI is its automatic generation of com files. However, I would prefer the GUI to output a .com file into my working directory (rather than the obscure location they are saved to now) every time I run a program so that I can then tinker with it and add any extra keywords I want to. I often use the GUI to get a 'second opinion' about good default values and options for a given CCP4 program - especially if the documentation is a bit confusing. Kind of double-checking if I understood the documentation correctly. One thing I found very confusing though, is that the com-files created by the CCP4i will often have (nearly) all possible keywords set, even if I haven't changed any of the defaults in the gui. Often, a CCP4 program has defaults itself and only requires keywords if one wants to change things - which is nice, since it leads e.g. to a very short SCALA comand-file. I'm not always convinced that the settings done by the CCP4i interface (when keeping all edfaults) correspond to the defaults as implemented in the program itself. Maybe any parameter setting unchanged from the values in the $CCP4/ccp4i/tasks/*.def file should be internally flagged as being at the 'default value' - resulting in them _not_ being written to the com-file? This way any potential change in defaults inside the actual program would have immediate effect, even if the CCP4i hasn't been updated yet. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] xsect.dat=cossec.lib?
Bernhard Rupp wrote: Dear Coders, Do I see this correctly that crossec.lib is the XSECT.DAT file from Don Cromer's FPRIME program? If so, has there ever been an update? Mine is from some reel tape I got from him long ago when I ported the code...seems to be the same. Thx, br Bernhard Rupp www.ruppweb.org I believe that is so - Eleanor
Re: [ccp4bb] rmsd calculation. .
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Excellent! Thank you Gerard, Miguel Gerard DVD Kleywegt escribió: But my understanding is that Iain's procedure gives the rmsds of the _aligned_ C-alphas, whereas Jenny actually seems to be more interested in those that she excludes from the alignment. I may be wrong, but in these cases, I use lsqman (from DVD) or lsqkab (from ccp4) to superpose the proteins (using one as reference) according to a particular scheme (Jenny's 1-40,60-100) and then write a script to calculate the rmsds for the interesting 41-59 residues. There may be an easier way, which I'll be interested to learn about. hola miguel, i would use the rmsd command in lsqman, like so: read m1 m1.pdb read m2 m2.pdb expl m1 a1-40 a60-100 m2 a1 a60 rmsd m1 a41-59 m2 a41 --gerard ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGRDtWF6oOrDvhbQIRAiYIAJ9Zsh5KNyqzfWhz2WaaRYlRUfKXTwCeLQOK YtSKkl+Q4N3TF8MganziUDs= =TWIp -END PGP SIGNATURE-
[ccp4bb] CNS problem: anneal.inp segmentation fault
Hi all
Apologies for the non-ccp4 question - hopefully some of you who use CNS can
help me - I have a problem with anneal.inp in CNS:
When I run the anneal script for my structure containing novel ligand, the
program fails before the start of the torsion dynamics with no error message
- except SEGMENTATION FAULT at the bash commandline.
With quiet output, the last lines in the output file are:
ASSFIL: file /usr/local/CNS/cns_solve_1.1/libraries/toppar/torsionmdmods
opened.
MESSage=NORM
EVALUATE: symbol $MESSAGE_OLD_TMOD set to NORM (string)
ECHO=FALSe {OFF}
EVALUATE: symbol $ECHO_OLD_TMOD set to FALSE (logical)
NEXTCD: condition evaluated as false
Program version= 1.1 File version= 1.1
SELRPN: 0 atoms have been selected out of 4883
so the torsionmods routine (and everything before it) ran fine but the
torsion dynamics never started.
My pdb, mtf, top and par files all work fine for minimization so I don't
think there's anything wrong with them.
I have been using CNSv1.1 on this Linux machine for some time so it's not a
compile problem.
I can run the same routine on the same PC, from the same script, with the
same protein but with a different ligand and there's no fault.
Can anyone suggest a solution? I've tried just about everything short of
running the whole script manually from the command line!
Sincerely
Jean Watermeyer
Re: [ccp4bb] . .
Hi Emmanuel, Perhaps a little more information ? What was the Z-score and LLG in PHASER ? I take it the translation function solution is fairly well separated from the rest ? Are you sure the spacegroup is correct ? How complete is the model before refinement ? Not to be paranoid, but Hexagonal/Trigonal settings support merohedral twinning... best, Iain -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Emmanuel Prata Sent: Friday, May 11, 2007 10:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb]. . Dear all, I have a structure (with 6 dissulphide bridges) at fairly low resolution (3A) that I am trying to refine with Refmac. I've used phaser with a template with 72% sequence identity. RFZ was 3.4 and TFZ 6.6, without clashes, with 80.7% of completeness. Space group was p3121 (pointless) and Rmerge 0.12. When i tried refmac, Rfac drop to 24%, but Rfree only drop to 41%. Can anybody explain this fact? Thanks in advance, Emmanuel Prata de Souza
[ccp4bb] Filament Lifetime
I think the filament from one of our x-ray generators must be a record breaker. Yesterday it clocked up its 6000th hour or 250th day on the job, not counting down / holiday time. The intensity had only dropped by around 25 % of the value it was when I put it in, eight-and-a-half months ago... Really, this filament is like the horror-movie bad guy who just won't die - it survived countless power drop-outs and surges, the rough treatment of everyone from undergraduates to postdocs, and still it kept on and on... So, I decided to give it a break, as it has already smashed the Guinness world record for filament lifetimes (I checked) - I removed and replaced this beauty today, even though it's still working. I thought about framing it and keeping it on display in the generator lab for future generations to marvel at, but I got greedy - It will be up on eBay soon. Discounts available for academic institutions, etc Have a nice weekend (it's my birthday!) Cheers Rigaku! Mark _ Dr Mark Agacan Scientific Officer, Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, College of Life Sciences, Dow St., University of Dundee, Dundee, DD1 5EH Tel: +44 1382 388751 Fax: +44 1382 345764 _
[ccp4bb]
Dear all, I have a structure (with 6 dissulphide bridges) at fairly low resolution (3A) that I am trying to refine with Refmac. I've used phaser with a template with 72% sequence identity. RFZ was 3.4 and TFZ 6.6, without clashes, with 80.7% of completeness. Space group was p3121 (pointless) and Rmerge 0.12. When i tried refmac, Rfac drop to 24%, but Rfree only drop to 41%. Can anybody explain this fact? Thanks in advance, Emmanuel Prata de Souza
Re: [ccp4bb] xsect.dat=cossec.lib?
On Friday 11 May 2007 00:57, Bernhard Rupp wrote: Dear Coders, Do I see this correctly that crossec.lib is the XSECT.DAT file from Don Cromer's FPRIME program? If so, has there ever been an update? I do not know the history of crossec.lib, but the X-ray scattering server http://skuld.bmsc.washington.edu/scatter/AS_form.html uses values from the Brennan Cowen (1992) library that are updated versions of the original Cromer work. -- Ethan A MerrittCourier Deliveries: 1959 NE Pacific Dept of Biochemistry Health Sciences Building University of Washington - Seattle WA 98195-7742
Re: [ccp4bb] rmsd calculation
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 signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] rmsd calculation
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
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] Laue for heavy atoms, etc.
does anyone know of any reports where heavy atom positions were identified by any method (or mol. rep.) in a Laue data set (or sets)? also - i thought there was some Laue work out there on watching virus nucleic acids move around in a crystal, so again, if anyone knows any references (or names, etc.)... thx -bryan
Re: [ccp4bb] Program to find the center of mass
WOW. There are so many ways to do it. Thank you all for replying. Nian Huang Department of Biochemistry Univ of Texas Southwestern Medical Center On 5/10/07, Charlie Bond [EMAIL PROTECTED] wrote: Just to complete the set, in pdb-mode for emacs, if you do pdb-increment-centroid 0 0 0 (e.g. to move a molecule to the origin), it reports the original centroid. Cheers, Charlie -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia [EMAIL PROTECTED] +61 8 6488 4406
