Re: [ccp4bb] SORTMTZ error status = 256
I don't know what this error is, but you might like to know that the program Pointless can be used as an alternative to sortmtz, with the bonus that it might help you determine the spacegroup You can get it either from our ftp site here eg ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.2.9.linux or from the CCP4 prerelease page http://www.ccp4.ac.uk/prerelease/ Phil On 13 Nov 2007, at 01:15, hari jayaram wrote: Hi , I have a low resolution dataset at 3.2 to 3.5 Å resolution , upon running scala I get the following rather cryptic error SORTMTZ detected error on obtaining record from sort procedure in return phase, status = 256 I am slightly unsure of the spacegroup and have been trying to process and scale the mtz file from mosflm in the various possibilities. I get the error when I try to process this dataset with the other possibilities from mosflm ( P3 and weirdly enough C222). Is this telling me something about my data or is it a bug. Googling revealed only one unanswered post right here on ccp4bb The same set of images when processed as P1 give an rmerge of around 0.13 to 3.2 A Thanks hari Jayaram postdoc, Brandeis University The detailed error is given below a name=outSORTMTZh3Header Information For Output MTZ File / h3/a pre SORTMTZ detected error on obtaining record from sort procedure in return phase, status = 256 SORTMTZ: Sorting failed Times: User: 5.5s System:0.3s Elapsed: 0:11 /pre /html
Re: [ccp4bb] Clipper: Agarwal density gradients and AtomShapeFn::rho_grad
OK, that's a good question. Unfortunately the answer is hard, otherwise
I would have done it already.
The a[] and b[] coeffs are the Gaussian coefficients used for
calculating an atomic shape function in reciprocal space, i.e. for use
in a structure factor calculation.
The aw[] and bw[] coeffs are the corresponding Gaussian coefficients
used for calculating the electron density in real space.
For anisotropic atoms, you can't use bw, so the class constructs
uaninv[], which is a vector of aniso Gaussian coefficients which combine
both the ADP and shape function coefficients.
So this function:
ftype AtomShapeFn::rho( const Coord_orth xyz ) const
{
// iso
const Coord_orth dxyz( xyz - coord_ );
if ( is_iso ) return rho( dxyz.lengthsq() );
// aniso
return occ_ * ( aw[0]*exp( uaninv[0].quad_form( dxyz ) ) +
aw[1]*exp( uaninv[1].quad_form( dxyz ) ) +
aw[2]*exp( uaninv[2].quad_form( dxyz ) ) +
aw[3]*exp( uaninv[3].quad_form( dxyz ) ) +
aw[4]*exp( uaninv[4].quad_form( dxyz ) ) +
aw[5]*exp( uaninv[5].quad_form( dxyz ) ) );
}
returns the electron density at position xyz in the cell due to the atom
located at coord_. The corresponding isotropic form is simple, but when
you want aniso density, you need to construct the quadratic form of the
difference coodinate with the U_aniso tensor.
To implement the corresponding gradient function, there are two possible
approaches:
1. Calculate it by finite difference methods, using 4 calls to the above
function. This is computationally wasteful and less precise, but simple
to do, and you should always do this anyway as a cross-check of the
analytical approach.
2. Calculate is analytically by differentiating the above expression
with respect to dxyz.x(), dxyz.y(), dxyz.z(). This will probably be
about twice as fast as the above method, and more precise.
If you can do this, I'll be very glad to incorporate the code. If you
get stuck, get back to me and I'll see if I can do it, although I am
pressed for time at the moment.
Kevin
Athanasios Dousis wrote:
Hello all,
I have the latest Clipper libraries (v2.0), and I'd like to calculate
the Agarwal density gradients for anisotropic atomic displacement
parameters. Unfortunately, the method
clipper::AtomShapeFn::rho_grad(...) only works for the isotropic ADP's.
Is there code available for the anisotropic parameters? If no, do you
have any advice on how to implement the density gradients? I understand
how to do this in principle, but I'm somewhat confused by the aw[.] and
bw[.] coefficients in the code. Are these related to the Jacobian
determinant of the reciprocal-real space transformation?
Also, please let me know if there is a more appropriate forum to ask
this question.
Thank you,
Nasos Dousis
[ccp4bb] Poinless and space group P 4 3 2
Dear all, When running Pointless 1.2.0 (see summary below), I get the cubic space group P 4 3 2 (mosflm gave P 2 3 or P 4 3 2) !--SUMMARY_BEGIN-- Best Solution space group P 4 3 2 Reindex operator: [h,k,l] Laue group probability: 1.000 Systematic absence probability: 0.975 Total probability: 0.975 Space group confidence: 0.964 Laue group confidence 1.000 !--SUMMARY_END-- However, although I have multiple models (ensemble) with approximately 30% sequence identity (44% homology), I'm not able to get any reasonable solution with Phaser. As we know the protein can form dimers and even trimers, is it possible that Poinless is giving a higher space group because of pseudo-symmetry in this case..? Does anyone has got experience with Pointless and this kind of space group please..? Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] Pointless and space group P 4 3 2
Dear all, When running Pointless 1.2.0 (see summary below), I get the cubic space group P 4 3 2 (mosflm gave P 2 3 or P 4 3 2) !--SUMMARY_BEGIN-- Best Solution space group P 4 3 2 Reindex operator: [h,k,l] Laue group probability: 1.000 Systematic absence probability: 0.975 Total probability: 0.975 Space group confidence: 0.964 Laue group confidence 1.000 !--SUMMARY_END-- However, although I have multiple models (ensemble) with approximately 30% sequence identity (44% homology), I'm not able to get any reasonable solution with Phaser. As we know the protein can form dimers and even trimers, is it possible that Poinless is giving a higher space group because of pseudo-symmetry in this case..? Does anyone has got experience with Pointless and this kind of space group please..? Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
Re: [ccp4bb] Poinless and space group P 4 3 2
Dear Kristof, I recently had lots of trouble with molrep in space group F432. Both Phaser and Molrep failed, only Amore produced a solution. Hope that helps. Manfred. * * *Dr. Manfred S. Weiss * * * * Team Leader * * * * EMBL Hamburg OutstationFon: +49-40-89902-170 * * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 * * D-22603 Hamburg Email: [EMAIL PROTECTED] * * GERMANY Web: www.embl-hamburg.de/~msweiss/ * * * On Tue, 13 Nov 2007, Kristof Van Hecke wrote: Dear all, When running Pointless 1.2.0 (see summary below), I get the cubic space group P 4 3 2 (mosflm gave P 2 3 or P 4 3 2) !--SUMMARY_BEGIN-- Best Solution space group P 4 3 2 Reindex operator: [h,k,l] Laue group probability: 1.000 Systematic absence probability: 0.975 Total probability: 0.975 Space group confidence: 0.964 Laue group confidence 1.000 !--SUMMARY_END-- However, although I have multiple models (ensemble) with approximately 30% sequence identity (44% homology), I'm not able to get any reasonable solution with Phaser. As we know the protein can form dimers and even trimers, is it possible that Poinless is giving a higher space group because of pseudo-symmetry in this case..? Does anyone has got experience with Pointless and this kind of space group please..? Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
Re: [ccp4bb] Poinless and space group P 4 3 2
You should certainly try the other P 4x 3 2 space groups (x=1,2,3) in case the assignment of screw axes is wrong Phil On 13 Nov 2007, at 13:17, Kristof Van Hecke wrote: Dear all, When running Pointless 1.2.0 (see summary below), I get the cubic space group P 4 3 2 (mosflm gave P 2 3 or P 4 3 2) !--SUMMARY_BEGIN-- Best Solution space group P 4 3 2 Reindex operator: [h,k,l] Laue group probability: 1.000 Systematic absence probability: 0.975 Total probability: 0.975 Space group confidence: 0.964 Laue group confidence 1.000 !--SUMMARY_END-- However, although I have multiple models (ensemble) with approximately 30% sequence identity (44% homology), I'm not able to get any reasonable solution with Phaser. As we know the protein can form dimers and even trimers, is it possible that Poinless is giving a higher space group because of pseudo-symmetry in this case..? Does anyone has got experience with Pointless and this kind of space group please..? Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more information.
Re: [ccp4bb] Pointless and space group P 4 3 2
Dont forget pointless gives a point group so you could have spacegroup P4123 too - check that in MR Could might well have a trimer sitting on the cubic 3-fold, but then the oligimer will be generated by the crystal symmetry, and you need only search with a monomer. Eleanor Kristof Van Hecke wrote: Dear all, When running Pointless 1.2.0 (see summary below), I get the cubic space group P 4 3 2 (mosflm gave P 2 3 or P 4 3 2) !--SUMMARY_BEGIN-- Best Solution space group P 4 3 2 Reindex operator: [h,k,l] Laue group probability: 1.000 Systematic absence probability: 0.975 Total probability: 0.975 Space group confidence: 0.964 Laue group confidence 1.000 !--SUMMARY_END-- However, although I have multiple models (ensemble) with approximately 30% sequence identity (44% homology), I'm not able to get any reasonable solution with Phaser. As we know the protein can form dimers and even trimers, is it possible that Poinless is giving a higher space group because of pseudo-symmetry in this case..? Does anyone has got experience with Pointless and this kind of space group please..? Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
Re: [ccp4bb] B-factors, H/D exchange and protein flexibility
On Tuesday 13 November 2007 06:41, Brad Bennett wrote: I would be interested then to know how the community feels about the correlation of B-factors to protein flexibility. It is generally accepted that these are linked but are there any new papers that address this? This is the basis of TLSMD analysis, and TLS refinement in general. TLSM is described in Painter Merritt (2006) Acta Cryst. D62, 439-450 http://skuld.bmsc.washington.edu/~tlsmd -- Ethan A MerrittCourier Deliveries: 1959 NE Pacific Dept of Biochemistry Health Sciences Building University of Washington - Seattle WA 98195-7742
Re: [ccp4bb] B-factors, H/D exchange and protein flexibility
Dear Brad, the flexibility, that is how far a protein is stabilized with cold and heat denaturation of a protein, this inturn depends on 1.solvation enthalpy of nonpolar moieties(need more energy,so there needs to be some randomness) 2.shift in temparature due to the enthalpy associated with transfer of peptide group into water 3.its all depend truly on enthalpy convergence temperature and entropy convergence temperature. infact both quantities are characterised with large enthapy and entropy compensation and; the temperature. thanks On Nov 13, 2007 6:07 PM, Ethan Merritt [EMAIL PROTECTED] wrote: On Tuesday 13 November 2007 06:41, Brad Bennett wrote: I would be interested then to know how the community feels about the correlation of B-factors to protein flexibility. It is generally accepted that these are linked but are there any new papers that address this? This is the basis of TLSMD analysis, and TLS refinement in general. TLSM is described in Painter Merritt (2006) Acta Cryst. D62, 439-450 http://skuld.bmsc.washington.edu/~tlsmdhttp://skuld.bmsc.washington.edu/%7Etlsmd -- Ethan A MerrittCourier Deliveries: 1959 NE Pacific Dept of Biochemistry Health Sciences Building University of Washington - Seattle WA 98195-7742 -- S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany
[ccp4bb] Postdoc and PhD position
*A post-doc position and a PhD position in structural biology is available in the group of * *Prof. Dietmar A. Plattner* *at* *Institute of Organic Chemistry and Biochemistry, Albert-Ludwigs-University Freiburg/Germany* The project involves investigations of structure-function relationships of fungal ligninolytic redox enzymes (e. g. peroxidases, laccases, ref. Blodig et al., JMB, 851, 2001; Piontek et al., JBC, 37663, 2002) by means of X-ray crystallography. The studies will be part of the integrated project BIORENEW (6th EU-Framework Programme), which involves 26 partners from academic institutions and from industry. Further information under www.chemie.uni-freiburg.de/orgbio/w3platt *Requirements:* I) Post-doc position: PhD in protein crystallography. Experience with purification and crystallization of proteins, data collection and processing, structure determination, refinement, modeling and analysis of model structures. Knowledge of enzyme kinetic and UNIX is a plus. II) PhD position: Graduation in chemistry or a related field, preferably with a biochemical topic. Experience with purification, crystallization or X-ray structure determination of proteins would be an asset. Both positions: The ability to work independently and team spirit. The positions are open immediately. Employment will be according to the regulations of the German public service (50 % for the PhD position, no tuitions fees). *Application:* Send your CV and a letter of recommendation by email to: Dr. Klaus Piontek Email: [EMAIL PROTECTED] Albert-Ludwigs-University Freiburg Institute of Organic Chemistry and Biochemistry, Room 401 H Albertstrasse 21 D-79104 Freiburg Germany Phone: ++49-761-203-6036 Fax: ++49-761-203-8714 -- Dr. Klaus Piontek Albert-Ludwigs-University Freiburg Institute of Organic Chemistry and Biochemistry, Room 401 H Albertstrasse 21 D-79104 Freiburg Germany Phone: ++49-761-203-6036 Fax: ++49-761-203-8714 Email: [EMAIL PROTECTED] Web: http://www.chemie.uni-freiburg.de/orgbio/w3platt/
[ccp4bb]
Somebody out there who could direct me to a nice review of protein powder diffractometry including the application of Rietveld refinement to such data. Any hint appreciated many thanks in advance Marius Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: [EMAIL PROTECTED] http://users.physik.tu-muenchen.de/marius/
[ccp4bb]
Hi I don't know about reviews, but there were a couple of papers a few years ago that might have clues in their references - Margiolaki et al, Acta Cryst D61, 423-432 (2005) Basso et al Acta Cryst D61, 1612-1625 (2005) On 13 Nov 2007, at 19:59, Marius Schmidt wrote: Somebody out there who could direct me to a nice review of protein powder diffractometry including the application of Rietveld refinement to such data. Any hint appreciated many thanks in advance Marius Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: [EMAIL PROTECTED] http://users.physik.tu-muenchen.de/marius/ Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] [ccp4bb
Diffraction from protein powder is a relatively new development which requires the beam properties of synchrotrons. As you know, of course, the number of Debye-Scherrer rings are increasing dramatically with diffraction angle. Since proteins have such a large unit cell, the reflections are very closely spaced in angle and make the ring pattern extremely crowded. Only with advanced data reduction methods the overlap of the ring intensities can be deconvoluted up to a certain resolution. This is typically in the 3 A range for moderately sized proteins. So, I dont expect any review to be older than 10 years. From the literature I know that the structures that come out of these investigations are identical or at least extremely similar to those from single crystals. Greetings Marius It would be interesting to know about such reviews if they exist. I would worry that in powder form the structure of the protein is not the same as in solution, that is, proteins would denature upon dehydration. So are there any powders for which the structure is still intact? Conversely, in crystalline form, we know that the structure is (can be) relevant. The best example I can think of that borders on your question is the case of insulin. Insulin is stored and preserved in crystalline form and the crystals are very small and the protein is active (so the structure must be relevant). (The size of the crystals matters for medical purposes, that's another story.) So when we think of a powder as a collection of very small crystals - as is typically the case in organic and inorganic chemistry, then your question is very good indeed. But other than insulin, I cannot think of many examples. Lysozyme is sold as a crystalline powder. So are some other egg proteins, such as albumin, lactalbumin, etc. In a lot of other cases a crystalline suspension is sold (for example xylose isomerase), but I think it does not survive when dried. If experiments have been done and reviews have been written, I would expect them to be old (30-40 years). Mark -Original Message- From: Marius Schmidt [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Tue, 13 Nov 2007 12:59 pm Subject: [ccp4bb] Somebody out there who could direct me to a nice review of protein powder diffractometry including the application of Rietveld refinement to such data. Any hint appreciated many thanks in advance Marius Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: [EMAIL PROTECTED] http://users.physik.tu-muenchen.de/marius/ _ ___ Check Out the new free AIM(R) Mail -- Unlimited storage and industry-leading spam and email virus protection. Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: [EMAIL PROTECTED] http://users.physik.tu-muenchen.de/marius/
Re: [ccp4bb] DTT sensitive?
This may not apply in your case but it is not uncommon for a protein to precipitate in a microcrystalline shower when put in cold. Once it worms up, the crystals dissolve and the precipitate clears up. It is easy to check under a high magnification microscope. Cheers, N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT, Bld. 436, D007 Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Joe Sent: Tuesday, November 13, 2007 2:30 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] DTT sensitive? Hi there, I see enormous precipitate of my receptor protein when I take it out of freezer. But all the precipitate dissolved quickly after I added 1mM DTT to the solution. Does this mean that some surface Cys are causing problem? Or why is the protein so sensitive to DTT? Anybody experienced this kind? Any advice is appreciated. -Joe
Re: [ccp4bb] DTT sensitive?
Did you check the pH of your DTT and the protein solution before and after? I have had some experience with DTT changing pH (as might well be expected...). Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.467.4049 cel: 773.608.9185 email: [EMAIL PROTECTED] *** - Original Message - From: Joe [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, November 13, 2007 2:30 PM Subject: [ccp4bb] DTT sensitive? Hi there, I see enormous precipitate of my receptor protein when I take it out of freezer. But all the precipitate dissolved quickly after I added 1mM DTT to the solution. Does this mean that some surface Cys are causing problem? Or why is the protein so sensitive to DTT? Anybody experienced this kind? Any advice is appreciated. -Joe
Re: [ccp4bb] DTT sensitive?
The other possibility is 400 mM imidazole in the buffer. The precipitate looks like silk. On 11/13/07, Bryan W. Lepore [EMAIL PROTECTED] wrote: you didn't say how you know its protein - is it? interesting though.
Re: [ccp4bb] DTT sensitive?
It did not contain DTT when frozen. On 11/13/07, deena [EMAIL PROTECTED] wrote: Are you sure its 1mM DTT, because DTT itself precipitates in the freezer. Deena On Nov 13, 2007, at 3:30 PM, Joe wrote: Hi there, I see enormous precipitate of my receptor protein when I take it out of freezer. But all the precipitate dissolved quickly after I added 1mM DTT to the solution. Does this mean that some surface Cys are causing problem? Or why is the protein so sensitive to DTT? Anybody experienced this kind? Any advice is appreciated. -Joe Deena Abells Oren, PhD Manager, Structural Biology Resource Center Rockefeller University 1230 York Ave New York, NY 10065-6399 phone: 212-327-7429
Re: [ccp4bb] DTT sensitive?
The precipitate does not disappear automaticly if I don't add DTT. If it's the precipitate of imidazole, then why DTT can dissolve it? thanks On 11/13/07, Sanishvili, Ruslan [EMAIL PROTECTED] wrote: This may not apply in your case but it is not uncommon for a protein to precipitate in a microcrystalline shower when put in cold. Once it worms up, the crystals dissolve and the precipitate clears up. It is easy to check under a high magnification microscope. Cheers, N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT, Bld. 436, D007 Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Joe Sent: Tuesday, November 13, 2007 2:30 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] DTT sensitive? Hi there, I see enormous precipitate of my receptor protein when I take it out of freezer. But all the precipitate dissolved quickly after I added 1mM DTT to the solution. Does this mean that some surface Cys are causing problem? Or why is the protein so sensitive to DTT? Anybody experienced this kind? Any advice is appreciated. -Joe
[ccp4bb] non crystallographic symmetry and space group /symmetry determination : reviews?
i can't seem to find any reviews that specifically consider how NCS influences space group / symmetry determination - though there are plenty individual accounts. can anyone cite a review or even a book chapter on such a topic? or maybe even some cases of non-obvious indexing errors? of course if there are some individual cases that would be welcome also. -bryan
