Re: [ccp4bb] B-factor standardization
> If I am not wrong, I remember that someone proposed to standardize > B-factors of protein atoms as “BS = B - Bave”, where Bave is the average > B-factor of the protein. This will make some of BS negative (if B
Re: [ccp4bb] B-factor standardization
Dear Oliviero, On one aspect of your query, this analysis dissected the different sources of disorder contributions to B factors:- Diamond, R Acta Cryst (1990). *A46*, 425-435 All best wishes, John On Thu, Apr 5, 2018 at 2:49 PM, Oliviero Carugo < oliviero.car...@univie.ac.at> wrote: > Dears, > > everybody knows that B-factors may change amongst different crystal > structures and that they need to be standardized when different protein > crystal structures are compared. > > If I am not wrong, I remember that someone proposed to standardize > B-factors of protein atoms as “BS = B - Bave”, where Bave is the average > B-factor of the protein. Such standardization is based on the hypothesis > that independent sources of disorder add in determining the final B-factor. > BS should represent atomic B-factors depurated by all factors different > from atom oscillation, since Bave differences are neutralized. > > Does anyone can help me in finding a publication (80s or 90s) where these > BS values are used? > > Thanks! > > Oliviero > -- Professor John R Helliwell DSc
Re: [ccp4bb] B-factor standardization
On Thursday, 05 April 2018 15:49:44 Oliviero Carugo wrote: > Dears, > > everybody knows that B-factors may change amongst different crystal > structures and that they need to be standardized when different protein > crystal structures are compared. > > If I am not wrong, I remember that someone proposed to standardize > B-factors of protein atoms as “BS = B - Bave”, where Bave is the average > B-factor of the protein. Such standardization is based on the hypothesis > that independent sources of disorder add in determining the final > B-factor. BS should represent atomic B-factors depurated by all factors > different from atom oscillation, since Bave differences are neutralized. That sounds like flawed logic to me. If you were going to do this at all, I think you would have to start by comparing the residual B factors after removing TLS contributions. > Does anyone can help me in finding a publication (80s or 90s) where > these BS values are used? I think there are better tools available now than there were 25 years ago. I wouldn't go back that far to choose one without first considering the work and thought that has been put into structure analysis in the meantime. If nothing else, you might consider that "Bave" as calculated from the "Biso" (really Beq) column in typical PDB files is a less than perfect approximation [Acta Cryst. 2012 A67:512-516] Ethan > Thanks! > > Oliviero -- Ethan A Merritt, Dept of Biochemistry Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] B-factor standardization
Oliviero, We published a paper in 2003 in which we normalized B-factors to do a comparison of relative mobility or flexibility. The reference is: Gourinath et al. Structure 11:1621-1627 (2003). The jargon we used for Bave of the protein is . In our case, to be conservative in our interpretation of B-factor comparisons, we excluded random turns from the calculation and only included alpha helices and beta sheets, because we were trying to get a handle on the degree of excess flexibility of the less ordered regions of a large structure. -Daniel On Thu, Apr 5, 2018 at 9:49 AM, Oliviero Carugo < oliviero.car...@univie.ac.at> wrote: > Dears, > > everybody knows that B-factors may change amongst different crystal > structures and that they need to be standardized when different protein > crystal structures are compared. > > If I am not wrong, I remember that someone proposed to standardize > B-factors of protein atoms as “BS = B - Bave”, where Bave is the average > B-factor of the protein. Such standardization is based on the hypothesis > that independent sources of disorder add in determining the final B-factor. > BS should represent atomic B-factors depurated by all factors different > from atom oscillation, since Bave differences are neutralized. > > Does anyone can help me in finding a publication (80s or 90s) where these > BS values are used? > > Thanks! > > Oliviero >
Re: [ccp4bb] B-factor blurring
Hi Mike, my favourite summary on B factor sharpening/blurring is here: Acta Crystallogr D Biol Crystallogr. 2006 Aug;62(Pt 8):923-32. Epub 2006 Jul 18. Considerations for the refinement of low-resolution crystal structures. DeLaBarre B, Brunger AT. Hope that helps, Tomas On Mon, Nov 17, 2014 at 8:01 PM, Mike Lawrence lawre...@wehi.edu.au wrote: Dear all can anyone help me with literatures references to B-factor blurring as a technique to reveal low resolution features in an electron density map? I have seen the poster from Andrea Thorn at http://shelx.uni-ac.gwdg.de/~athorn/pdf/thorn_iucr2014_poster.pdf but was wondering if there were any alternative references? with many thanks! Mike Mike Lawrence, PhD Associate Professor and WEHI Fellow Structural Biology Division Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville Victoria 3052, AUSTRALIA Tel. 61-3-9345-2693 Fax 61-3-9345-2686 Email: lawre...@wehi.edu.au __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __
Re: [ccp4bb] B-factor blurring
Mike, you can have a look here (from page 52 and on): http://phenix-online.org/presentations/fem_06MAY2014.pdf There it is shown that map kurtosis can be used as an optimization criterion for choosing the best sharpening B. Pavel On Mon, Nov 17, 2014 at 5:01 PM, Mike Lawrence lawre...@wehi.edu.au wrote: Dear all can anyone help me with literatures references to B-factor blurring as a technique to reveal low resolution features in an electron density map? I have seen the poster from Andrea Thorn at http://shelx.uni-ac.gwdg.de/~athorn/pdf/thorn_iucr2014_poster.pdf but was wondering if there were any alternative references? with many thanks! Mike Mike Lawrence, PhD Associate Professor and WEHI Fellow Structural Biology Division Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville Victoria 3052, AUSTRALIA Tel. 61-3-9345-2693 Fax 61-3-9345-2686 Email: lawre...@wehi.edu.au __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __
Re: [ccp4bb] B-factor statistics around an ion
Hi Tim, a non-ccp4 solution (since you haven't gotten any suggestion yet).. 1) Get atom selection of atoms involved into ion coordination: phenix.metal_coordination model.pdb 2) Using atom selection from above extract portion of PDB that contains atoms in question: phenix.pdb_atom_selection model.pdb atom_selection_string_here --write-pdb-file=partial.pdb 3) Get average B: phenix.pdbtools partial.pdb model_statistics=true Remark: steps 2)-3) can be done in one go: phenix.b_factor_statistics model.pdb selection=atom_selection_string_here If this is of general interest I can wrap 1)-3) into one command. Good luck, Pavel On Thu, Jan 23, 2014 at 4:36 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, could anyone suggest a way to get the average B-factor from a PDB-file of those atoms a specific ion binds to (e.g. as judged by header LINK records or a distance interval)? I would like to get this number for all K-ions from a set of PDB-files, and I hope there is a quicker way than using coot to click on the surrounding atoms and transfer the numbers into a chart. Best, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFS4QziUxlJ7aRr7hoRAtlAAKCei/Ehfg71Xir3pkvWvTQg93YwEQCePFM6 2kPFPJw8aZySVYnLaQCjKR4= =q9pT -END PGP SIGNATURE-
Re: [ccp4bb] B factor of the loop
yes - but keep in mind your protein is in the context of the crystal lattice, so flexible regions in solution are likely to be stabilized in the crystal lattice. So if you color by B also look at the symmetry mates. And you should also submit both structures to the TLSMD server and look at those results. http://skuld.bmsc.washington.edu/~tlsmd/ Jürgen On Mar 3, 2013, at 4:35 PM, Faisal Tarique wrote: Dear all Can B factor in the crystal structure be the criteria to look into the flexibility of a region or domain.? Also if two structures are at different resolutions. Faisal -- .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] B factor of the loop
Indeed! If the B factors are rather large compared to the globular protein core (assuming there is a globular core being that the protein crystallized), one can make the assumption, especially within a loop region, that this is an indirect measurement of flexibility. However, as Jürgen pointed out, it IS imperative to take a close look at the crystal packing in the unit cell. For instance, if the loop region were to make hydrogen bond or electrostatic interactions with a symmetry mate, you must be careful in your conclusion. Might I recommend a paper that uses B factors as a direct correlation with heteronuclear NOEs to compare two almost identical structures (both of which contain disordered regions? Wang, Y., Fisher, J.C., Assem, M., Matthew, R., Sublet, J, Xiao, L., Roussel, M.F., and Kriwacki, R.W. (2011). Structural basis for the diverse cell cycle regulatory functions of the intrinsically disordered protein, p21 Cip1. Nature Chemical Biology, 7, 214-221. You can always confirm disordered or flexible loop segments using limited proteolysis. Best, John John Fisher, M.D./PhD St. Jude Children's Research Hospital Department of Structural Biology Department of Oncology On Sun, Mar 3, 2013 at 3:52 PM, Bosch, Juergen jubo...@jhsph.edu wrote: yes - but keep in mind your protein is in the context of the crystal lattice, so flexible regions in solution are likely to be stabilized in the crystal lattice. So if you color by B also look at the symmetry mates. And you should also submit both structures to the TLSMD server and look at those results. http://skuld.bmsc.washington.edu/~tlsmd/ Jürgen On Mar 3, 2013, at 4:35 PM, Faisal Tarique wrote: Dear all Can B factor in the crystal structure be the criteria to look into the flexibility of a region or domain.? Also if two structures are at different resolutions. Faisal -- .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] B factor
Hi Amit, you can manually define the range of a spectrum in PyMol: spectrum [parameter], [spectrum type], minimum=[min], maximum=[max] -- if you want to color according to B-factor this will translate to e.g. : spectrum b, blue_white_red, minimum=0, maximum=50 hth, Arjen On May 12, 2011, at 8:31 PM, Luthra,Amit wrote: Hey all, I would like to make one ribbon diagram of the structure showing the B factor in different colors (contour levels). I am using pymol but it is not representing the perfect contour level of B factor. Is any other program where I can change the color according to B factor? Thanks Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [w] http://spirocheteresearch.uchc.edu
Re: [ccp4bb] B factor
Hi Amit, you can manually define the range of a spectrum in PyMol: spectrum [parameter], [spectrum type], minimum=[min], maximum=[max] -- if you want to color according to B-factor this will translate to e.g. : spectrum b, blue_white_red, minimum=0, maximum=50 hth, Arjen On May 12, 2011, at 8:31 PM, Luthra,Amit wrote: Hey all, I would like to make one ribbon diagram of the structure showing the B factor in different colors (contour levels). I am using pymol but it is not representing the perfect contour level of B factor. Is any other program where I can change the color according to B factor? Thanks Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [w] http://spirocheteresearch.uchc.edu
Re: [ccp4bb] B factor
hello sir , in chimera its available in module Render by Attribute. go through this link http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html . regards On Fri, May 13, 2011 at 12:01 AM, Luthra,Amit alut...@uchc.edu wrote: Hey all, I would like to make one ribbon diagram of the structure showing the B factor in different colors (contour levels). I am using pymol but it is not representing the perfect contour level of B factor. Is any other program where I can change the color according to B factor? Thanks Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [w] http://spirocheteresearch.uchc.edu -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy India
Re: [ccp4bb] B factor Coloring in Pymol
Hi Ron Mmmm... not really but thanks for the info:) I have my Bfactor column assigned in percent conservation so the B value ranges from say 30% to 100%. I want to colour my molecule accordingly. Pymol allows B factor colouring but seems only to allow 3 colour choices. It used to allow 4 colour choices say WYOR I was wondering if any one had an idea how I could trick Pymol into accepting say 4 colours. Sorry if I was not clearer in the previous. Thanks again advance. Gina -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Rob Nicholls Sent: Wednesday, March 31, 2010 3:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] B factor Coloring in Pymol Hi, I'm aware of two ways to do this: by writing the colour as a word, e.g: color white, (mypdbfile//A/*/*) which will colour a whole chain. Or by using rgb colours, e.g: set_color newcolor0 = [1,1,1]; color newcolor0, (mypdbfile//A/2/*) which will colour individual residues (residue 2 in this case) Pymol should accept a script containing such lines. Hope that helps, Rob On 31 Mar 2010, at 15:00, Clayton, Gina Martyn wrote: Dear Everyone Slightly off topic... I am trying to colour a structure by B factor in Pymol. More specifically I am colouring conserved residues (value in b factor). I want to use 4 colours - say white, yellow, orange, red. However it seems that Pymol now only allows 3 colours to be used - I tried the script from the Wiki site, but Pymol will not accept the 4 rgb colours. Does anyone have an idea how I can colour with 4 colours (but not rainbow too confusing). Thanks in advance for any help Best Gina Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] B factor Coloring in Pymol
Hi Robert That seems like a great suggestion! I will give it a shot and let CCP4BB know if it works Thanks Gina -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Robert Campbell Sent: Wednesday, March 31, 2010 4:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] B factor Coloring in Pymol Hi Gina, On Wed, 31 Mar 2010 15:00:34 -0400 Clayton, Gina Martyn gina_clay...@merck.com wrote: I am trying to colour a structure by B factor in Pymol. More specifically I am colouring conserved residues (value in b factor). I want to use 4 colours - say white, yellow, orange, red. However it seems that Pymol now only allows 3 colours to be used - I tried the script from the Wiki site, but Pymol will not accept the 4 rgb colours. Does anyone have an idea how I can colour with 4 colours (but not rainbow too confusing). Say, your b-factor values range from 0-10, and your object is called protein, then you could do: color white, protein color yellow, protein b 2.5 color orange, protein b 5.0 color red, protein b 7.5 If you want to automate that process, then you need to write a script that determines, the b-factor limits for the 4 colours based on the b-factors present in your structure. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.ca http://pldserver1.biochem.queensu.ca/~rlc Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] B-factor problem
Sampath Natarajan wrote: Dear All, I am refining a structure with 2.5A resolution by refmac5. I could find the solution by MR using molrep. After fitting the model, I refined the structure again with 0.3 weighting term, but the output PDB file shows many splits in the residues. So I used 'auto' as a weighting term, then I didn't find any splits. At the same time I noticed that figure of merits is not increasing after model fitting. But the correlation coefficient is more than 80%. Also while refining with auto weighting term, the figure of merit goes down about 25% than previous. Finally I find that some of the residues show high B factor. Could anyone give suggestions to reduce the B-factor? Thanks in advance! Yours sincerely, Sampath There are several Qs here but you must remember that initial refinement protocols straight from an MR solution are somewhat different to those you would use later. High B factors may be useful - they often indicate where something is wrong, and ditto poor geometry. These are the regions you will probably need to rebuild. Eleanor , to the
Re: [ccp4bb] B-factor problem
Hi, What is the lower limit of the weighting term one can use. If the data is around 2A can one use 0.04 or less and which type of refinement is more useful when one is doing the initial refinement (isotropic, aisotropic, overall or mixed). sincerely Debajyoti On Tue, 17 Jun 2008 Roger Rowlett wrote : Sampath Natarajan wrote: Dear All, I am refining a structure with 2.5A resolution by refmac5. I could find the solution by MR using molrep. After fitting the model, I refined the structure again with 0.3 weighting term, but the output PDB file shows many splits in the residues. So I used 'auto' as a weighting term, then I didn't find any splits. At the same time I noticed that figure of merits is not increasing after model fitting. But the correlation coefficient is more than 80%. Also while refining with auto weighting term, the figure of merit goes down about 25% than previous. Finally I find that some of the residues show high B factor. Could anyone give suggestions to reduce the B-factor? Thanks in advance! Yours sincerely, Sampath For 2.5A data, the refmac default X-ray weighting factor of 0.3 is typically much too high, and does not appropriately apply geometric constraints. (That is why your proteins chains are breaking up.) An alternative to the auto weighting function is to set your own weighting factor and monitor rmsBOND and rmsANGLE deviations in the final model. If the final rmsBOND is on the order of 0.015 A and rmsBOND is on the order of 1.5 degrees then your choice of weighting factor is reasonable. For medium resolution data in the 2.2-2.8A range, I would start with an X-ray weighting factor of about 0.05 or so. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
Re: [ccp4bb] B-factor problem
Sampath Natarajan wrote: Dear All, I am refining a structure with 2.5A resolution by refmac5. I could find the solution by MR using molrep. After fitting the model, I refined the structure again with 0.3 weighting term, but the output PDB file shows many splits in the residues. So I used 'auto' as a weighting term, then I didn't find any splits. At the same time I noticed that figure of merits is not increasing after model fitting. But the correlation coefficient is more than 80%. Also while refining with auto weighting term, the figure of merit goes down about 25% than previous. Finally I find that some of the residues show high B factor. Could anyone give suggestions to reduce the B-factor? Thanks in advance! Yours sincerely, Sampath For 2.5A data, the refmac default X-ray weighting factor of 0.3 is typically much too high, and does not appropriately apply geometric constraints. (That is why your proteins chains are breaking up.) An alternative to the auto weighting function is to set your own weighting factor and monitor rmsBOND and rmsANGLE deviations in the final model. If the final rmsBOND is on the order of 0.015 A and rmsBOND is on the order of 1.5 degrees then your choice of weighting factor is reasonable. For medium resolution data in the 2.2-2.8A range, I would start with an X-ray weighting factor of about 0.05 or so. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
Re: [ccp4bb] B-factor problem
On 17 Jun 2008, at 19:56, Roger Rowlett wrote: Sampath Natarajan wrote: Dear All, I am refining a structure with 2.5A resolution by refmac5. I could find the solution by MR using molrep. After fitting the model, I refined the structure again with 0.3 weighting term, but the output PDB file shows many splits in the residues. So I used 'auto' as a weighting term, then I didn't find any splits. At the same time I noticed that figure of merits is not increasing after model fitting. But the correlation coefficient is more than 80%. Also while refining with auto weighting term, the figure of merit goes down about 25% than previous. Finally I find that some of the residues show high B factor. Could anyone give suggestions to reduce the B-factor? Thanks in advance! Yours sincerely, Sampath For 2.5A data, the refmac default X-ray weighting factor of 0.3 is typically much too high, and does not appropriately apply geometric constraints. (That is why your proteins chains are breaking up.) ***Restraints*** really. Constraints are something really different (for one things they imply that they cannot be violated but must be exactly reproduced, so a weighting term for a constraint does not exists). I think we must avoid confusion, since implementation with bond/angle constraints (torsional refinement) are available. An alternative to the auto weighting function is to set your own weighting factor and monitor rmsBOND and rmsANGLE deviations in the final model. If the final rmsBOND is on the order of 0.015 A and rmsBOND is on the order of 1.5 degrees then your choice of weighting factor is reasonable. For medium resolution data in the 2.2-2.8A range, I would start with an X-ray weighting factor of about 0.05 or so. Although that the general advice above is of course valid and it reflects common practice, it would be fare to iterate once more that this remained for a while a somewhat controversial issue. In my opinion it is getting settled lately, given the RMSZ in more recent versions of refmac which might be a better quantity to follow - as suggested in the papers by Ian Tickle, eg: Acta Crystallogr D Biol Crystallogr. 2007 Dec;63(Pt 12):1274-81; author reply 1282-3. Epub 2007 Nov 16. Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values. Tickle IJ. I claim no expertise and the math is above my head mostly, but I got pretty much convinced by that work for what I want to be doing and its good reading even for the mathematically challenged, like myself. Tassos Cheers, -- -- -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
Re: [ccp4bb] B-factor problem
On Tuesday 17 June 2008 09:08:24 am Sampath Natarajan wrote: Dear All, I am refining a structure with 2.5A resolution by refmac5. I could find the solution by MR using molrep. After fitting the model, I refined the structure again with 0.3 weighting term, but the output PDB file shows many splits in the residues. So I used 'auto' as a weighting term, then I didn't find any splits. At the same time I noticed that figure of merits is not increasing after model fitting. But the correlation coefficient is more than 80%. Also while refining with auto weighting term, the figure of merit goes down about 25% than previous. Finally I find that some of the residues show high B factor. Could anyone give suggestions to reduce the B-factor? It is worth remembering that B is a measure of the uncertainty in the atomic position. So one generic answer is that to reduce B you need to be more certain about where your atoms are :-) If/when your model correctly describes the mean position for each atom, then B can be interpreting as representing 'motion' or more properly speaking displacement about that mean position. But if your atoms are not in the right place, then their high B factors are simply telling you that the calculated X-ray density doesn't support your current model. So following automated MR, high B factors are best viewed as a hint as to where your model needs to be rebuilt.
Re: [ccp4bb] B factor calculation
in ccp4, baverage does the job. Mark Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ On 4 Jun 2008, at 21:40, xu zhen wrote: Hi, everyone, I am preparing the table of data collection and refinement statics. In this table, I need to list the average B factor of protein, ligand and water seperately, can you tell me how to calculate thoes numbers? Zhen _ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx
Re: [ccp4bb] B factor calculation
For example, this will show you complete statistics about B-factors: phenix.pbdtools your_model.pdb --show-adp-statistics this will show you complete statistics about stereochemistry: phenix.pbdtools your_model.pdb --show-geometry-statistics For more information: http://www.phenix-online.org/ or ask me directly. Cheers, Pavel. On 6/4/2008 12:40 PM, xu zhen wrote: Hi, everyone, I am preparing the table of data collection and refinement statics. In this table, I need to list the average B factor of protein, ligand and water seperately, can you tell me how to calculate thoes numbers? Zhen _ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx
Re: [ccp4bb] B-factor sharpening in CCP4 or Coot
There is a CAD option to apply a scale and B factor to any set of data, and an FFT option to apply a scale and B factor to any column in the map. Check the documentation for whether you need SCALE 1 -10.0 or SCALE 1 +10.0 ! Eleanor Jeff Lee wrote: Hi, I have a question for everyone. I wanted to up-weight my high resolution terms in my electron density map by applying a B-factor sharpening term. I have mtz files produced from DM and I usually use Coot to generate my electron density maps. I was wondering is there an easy way to apply a B-factor sharpening term in Coot? If not, is there a program in ccp4 where by I can set the B-sharp factor? Thanks Jeff
Re: [ccp4bb] B-factor sharpening in CCP4 or Coot
Eleanor was kind enough to modify truncate years ago for me to do this - I would guess the feature is still there. Thanks again Eleanor! Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jeff Lee Sent: Wednesday, June 13, 2007 1:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] B-factor sharpening in CCP4 or Coot Hi, I have a question for everyone. I wanted to up-weight my high resolution terms in my electron density map by applying a B-factor sharpening term. I have mtz files produced from DM and I usually use Coot to generate my electron density maps. I was wondering is there an easy way to apply a B-factor sharpening term in Coot? If not, is there a program in ccp4 where by I can set the B-sharp factor? Thanks Jeff -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] B-factor sharpening in CCP4 or Coot
Senility is, in fact, setting in. It was a modified version of CAD! Sorry for the confusion. To further compound the confusion, I am not sure if my solution is what you are really looking for, although I suspect you should try it. What we did was use an overall negative B-factor to achieve a sharpening effect (Cell 119(3):393-405). Others had done this before (David Borhani comes to mind)anyway, it can be very, very useful. Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Soisson, Stephen Michael Sent: Wednesday, June 13, 2007 1:23 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] B-factor sharpening in CCP4 or Coot Eleanor was kind enough to modify truncate years ago for me to do this - I would guess the feature is still there. Thanks again Eleanor! Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jeff Lee Sent: Wednesday, June 13, 2007 1:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] B-factor sharpening in CCP4 or Coot Hi, I have a question for everyone. I wanted to up-weight my high resolution terms in my electron density map by applying a B-factor sharpening term. I have mtz files produced from DM and I usually use Coot to generate my electron density maps. I was wondering is there an easy way to apply a B-factor sharpening term in Coot? If not, is there a program in ccp4 where by I can set the B-sharp factor? Thanks Jeff -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] B-factor Space gr questions!
Hi Ibrahim, On 04/06/07, Ibrahim M. Moustafa [EMAIL PROTECTED] wrote: Hi all, While reading a crystallographic paper describing the structure of an apo-protein and its complex I noticed that the authors described the space goup as P6122 for the unit cell: a=141.9, b=143.9, c=380.4 Could this be considered as a typo or I'm missing something here! the requirement for the hexagonal is a = b # Cright? You are correct, for Hexagonal, a=b - so It's got to be a typo - data most processing software wouldn't let you do this. Another observation in that paper too: the B-factors for the 2.4 A and 3.2 A structures are 39 and 40?? Does this make sense to anyone? They're quoting Wilson B-factors, I imagine. A small but rather important difference - where was this published? The last question: In the same paper, for the complex structure R and Rfree are equal (30%) is that an indication for improper refinement in these published structure? I'd love to hear your comments on that too. Well, it certainly is a little suspicious looking - I've had similar experiences to Ed, regarding similar R Rfrees from rigid rigid body refinement prior to positional refinement. Have the authors deposited the Structure factors? I would use EDS to check the maps out: eds.bmc.uu.se/eds/ thanks, Ibrahim HTH, Dave -- --- David Briggs, PhD. Father Crystallographer www.dbriggs.talktalk.net iChat AIM ID: DBassophile --- Anyone who is capable of getting themselves made President should on no account be allowed to do the job. - Douglas Adams
Re: [ccp4bb] B-factor Space gr questions!
Yes; a==b for P6i - prob. a typo.. B factors at 3.2A are hard to fix - it will depend on scaling convention to some extent.. Can you download the data and re-run refinement for your own satisfaction. If R ==Rfree for the complex then I suspect they did not transfer the FreeR flags from the apo-protein data to the complex. Again if the data is available you may be able to check this. Eleanor Ibrahim M. Moustafa wrote: Hi all, While reading a crystallographic paper describing the structure of an apo-protein and its complex I noticed that the authors described the space goup as P6122 for the unit cell: a=141.9, b=143.9, c=380.4 ! Could this be considered as a typo or I'm missing something here! the requirement for the hexagonal is a = b # Cright? Another observation in that paper too: the B-factors for the 2.4 A and 3.2 A structures are 39 and 40?? Does this make sense to anyone?? The last question: In the same paper, for the complex structure R and Rfree are equal (30%) is that an indication for improper refinement in these published structure? I'd love to hear your comments on that too. thanks, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., Uinversity Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 --
Re: [ccp4bb] B-factor Space gr questions!
Hi All, Thanks a lot for all reply with valuable inputs. In my original post: I meant a = b does not equal c. I used # for does not equal. Many asked where is that paper published! Actually the paper is under revision. When reading, I assumed the unit cell dimensions (or the space group) is a typo as others thought. The low B value for the low resolution structure makes me suspicious that something is wrong. In my little experience, and as others mentioned, B-factor is expected to be around 70-80 for 2.8 A structure and very likely higher for 3.0 A structure. David Briggs suggested that they reported the Wilson B-factor; however, clearly, it is reported as the B-factor of the refined structure. Also, the Rwork = Rfree indicated that something is not right with the refinement protocol but I was not sure what that could be! The suspect that they did not transfer the FreeR sounds reasonable explanation. thanks a lot, Ibrahim At 03:50 AM 6/5/2007, Eleanor Dodson wrote: Yes; a==b for P6i - prob. a typo.. B factors at 3.2A are hard to fix - it will depend on scaling convention to some extent.. Can you download the data and re-run refinement for your own satisfaction. If R ==Rfree for the complex then I suspect they did not transfer the FreeR flags from the apo-protein data to the complex. Again if the data is available you may be able to check this. Eleanor Ibrahim M. Moustafa wrote: Hi all, While reading a crystallographic paper describing the structure of an apo-protein and its complex I noticed that the authors described the space goup as P6122 for the unit cell: a=141.9, b=143.9, c=380.4 ! Could this be considered as a typo or I'm missing something here! the requirement for the hexagonal is a = b # Cright? Another observation in that paper too: the B-factors for the 2.4 A and 3.2 A structures are 39 and 40?? Does this make sense to anyone?? The last question: In the same paper, for the complex structure R and Rfree are equal (30%) is that an indication for improper refinement in these published structure? I'd love to hear your comments on that too. thanks, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., Uinversity Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 -- -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 --
Re: [ccp4bb] B-factor Space gr questions!
You have a good point there and I would be interested in hearing some other opinions, so I take the liberty of reposting- My instinctive preference is that each structure should be supported solely by the data that is deposited with it - (one dataset one structure) but in terms of good science we want to produce the best model we can, and that might be the rigid-body-located structure from another dataset. In particular the density for the ligand might be clearer before overfitting with the low resolution data. Even if the free-R set is not preserved for the new crystal, R and R-free tend to diverge rapidly once any kind of fitting with a low data/param is performed, so I think the new structure must not have been refined much beyond rigid body (and over-all B which is included in any kind of refinement). And that choice may be well justified. Ed cdekker wrote: Hi, Your reply to the ccp4bb has confused me a bit. I am currently refining a low res structure and realise that I don't know what to expect for final R and Rfree - it is definitely not what most people would publish. So the absolute values of R and Rfree are not telling me much, the only gauge I have is that as long as both R and Rfree are decreasing I am improving the model (and yes, at the moment that is only rigid body refinement). In your email reply you suggest that even though a refinement to convergence that will lead to an increased Rfree (and lower R? - a classic case of overfitting!) would be a better model than the rigid-body-refined only model. This is what confuses me. I can see your reasoning that starting with an atomic model to solve low-res data can lead to this behaviour, but then should the solution not be a modification of the starting model (maybe high B-factors?) to compensate for the difference in resolution of model and data? Carien On 4 Jun 2007, at 19:38, Edward A Berry wrote: Ibrahim M. Moustafa wrote: The last question: In the same paper, for the complex structure R and Rfree are equal (30%) is that an indication for improper refinement in these published structure? I'd love to hear your comments on that too. Several times I solved low resolution structures using high resolution models, and noticed that R-free increased during atomic positional refinement. This could be expected from the assertion that after refinement to convergence, the final values should not depend on the starting point: If I had started with a crude model and refined against low resolution data, Rfree would not have gone as low as the high-resolution model, so if I start with the high resolution model and refine, Rfree should worsen to the same value as the structure converges to the same point. Thinking about the main purpose of the Rfree statistic, in a very real way this tells me that the model was better before this step of refinement, and it would be better to omit the minimization step. Perhaps this is what the authors did. On the other hand it does not seem quite right submit a model that has simply been rigid-body-refined against the data- I would prefer to refine to convergence and submit the best model that can be supported by the data alone, rather than a better model which is really the model from a better dataset repositioned in the new crystal. Ed The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] B-factor Space gr questions!
Wouldn't the desirability of this depend on the extent to which the molecule has moved between the high-resolution and low-resolution datasets ? I would have thought that there was an effective information transfer between R-work and R-free once the rigid body movements became too large, which might provide one with an over-optimistic idea of what the R-free would be with the high-resolution model with the low-resolution data. Phil Princeton NJ Edward A Berry wrote: Even if the free-R set is not preserved for the new crystal, R and R-free tend to diverge rapidly once any kind of fitting with a low data/param is performed, so I think the new structure must not have been refined much beyond rigid body (and over-all B which is included in any kind of refinement). And that choice may be well justified. Ed cdekker wrote: Hi, Your reply to the ccp4bb has confused me a bit. I am currently refining a low res structure and realise that I don't know what to expect for final R and Rfree - it is definitely not what most people would publish. So the absolute values of R and Rfree are not telling me much, the only gauge I have is that as long as both R and Rfree are decreasing I am improving the model (and yes, at the moment that is only rigid body refinement). In your email reply you suggest that even though a refinement to convergence that will lead to an increased Rfree (and lower R? - a classic case of overfitting!) would be a better model than the rigid-body-refined only model. This is what confuses me. I can see your reasoning that starting with an atomic model to solve low-res data can lead to this behaviour, but then should the solution not be a modification of the starting model (maybe high B-factors?) to compensate for the difference in resolution of model and data? Carien On 4 Jun 2007, at 19:38, Edward A Berry wrote: Ibrahim M. Moustafa wrote: The last question: In the same paper, for the complex structure R and Rfree are equal (30%) is that an indication for improper refinement in these published structure? I'd love to hear your comments on that too. Several times I solved low resolution structures using high resolution models, and noticed that R-free increased during atomic positional refinement. This could be expected from the assertion that after refinement to convergence, the final values should not depend on the starting point: If I had started with a crude model and refined against low resolution data, Rfree would not have gone as low as the high-resolution model, so if I start with the high resolution model and refine, Rfree should worsen to the same value as the structure converges to the same point. Thinking about the main purpose of the Rfree statistic, in a very real way this tells me that the model was better before this step of refinement, and it would be better to omit the minimization step. Perhaps this is what the authors did. On the other hand it does not seem quite right submit a model that has simply been rigid-body-refined against the data- I would prefer to refine to convergence and submit the best model that can be supported by the data alone, rather than a better model which is really the model from a better dataset repositioned in the new crystal. Ed
Re: [ccp4bb] B-factor Space gr questions!
On Tuesday 05 June 2007 12:19, Edward A Berry wrote: You have a good point there and I would be interested in hearing some other opinions, so I take the liberty of reposting- My instinctive preference is that each structure should be supported solely by the data that is deposited with it - (one dataset one structure) but in terms of good science we want to produce the best model we can, and that might be the rigid-body-located structure from another dataset. I don't think that is quite the right way to look at it. In general we refine our model so that it both - agrees with the data - agrees with a priori knowledge In maximum likelihood terms: we want to find the model that is the most likely explanation for our observed data. An inherently unlikely model is also an inherently unlikely explanation. Therefore we focus on likely models. We impose geometric restraints because we believe that we have a better a priori expectation for bond lengths and angles than can be determined de novo from the data in this one experiment. Similarly we impose the known sequence of our protein on the model, even if the maps are not sufficiently good to identify each amino acid directly from the electron density. If we have an a priori expectation for the conformation of the whole protein, or large pieces of it, then we should account for this in the model, even if the data is not sufficiently good to reproduce this expectation de novo. Therefore if you have a high-resolution structure available, the best treatment of low-resolution data may well be to place the known structure as a rigid body. If you suspect hinge motions or other large scale inter-domain shifts, you might want to refine the hinge angle explicitly, but unfortunately our usual refinement programs are not really set up for this. These are important issues, and are close to the heart of the Maximum Likelihood approach to model refinement. Ethan cdekker wrote: Hi, Your reply to the ccp4bb has confused me a bit. I am currently refining a low res structure and realise that I don't know what to expect for final R and Rfree - it is definitely not what most people would publish. So the absolute values of R and Rfree are not telling me much, the only gauge I have is that as long as both R and Rfree are decreasing I am improving the model (and yes, at the moment that is only rigid body refinement). In your email reply you suggest that even though a refinement to convergence that will lead to an increased Rfree (and lower R? - a classic case of overfitting!) would be a better model than the rigid-body-refined only model. This is what confuses me. I can see your reasoning that starting with an atomic model to solve low-res data can lead to this behaviour, but then should the solution not be a modification of the starting model (maybe high B-factors?) to compensate for the difference in resolution of model and data? Carien On 4 Jun 2007, at 19:38, Edward A Berry wrote: Ibrahim M. Moustafa wrote: The last question: In the same paper, for the complex structure R and Rfree are equal (30%) is that an indication for improper refinement in these published structure? I'd love to hear your comments on that too. Several times I solved low resolution structures using high resolution models, and noticed that R-free increased during atomic positional refinement. This could be expected from the assertion that after refinement to convergence, the final values should not depend on the starting point: If I had started with a crude model and refined against low resolution data, Rfree would not have gone as low as the high-resolution model, so if I start with the high resolution model and refine, Rfree should worsen to the same value as the structure converges to the same point. Thinking about the main purpose of the Rfree statistic, in a very real way this tells me that the model was better before this step of refinement, and it would be better to omit the minimization step. Perhaps this is what the authors did. On the other hand it does not seem quite right submit a model that has simply been rigid-body-refined against the data- I would prefer to refine to convergence and submit the best model that can be supported by the data alone, rather than a better model which is really the model from a better dataset repositioned in the new crystal. Ed The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] B-factor Space gr questions!
Ibrahim M. Moustafa wrote: The last question: In the same paper, for the complex structure R and Rfree are equal (30%) is that an indication for improper refinement in these published structure? I'd love to hear your comments on that too. Several times I solved low resolution structures using high resolution models, and noticed that R-free increased during atomic positional refinement. This could be expected from the assertion that after refinement to convergence, the final values should not depend on the starting point: If I had started with a crude model and refined against low resolution data, Rfree would not have gone as low as the high-resolution model, so if I start with the high resolution model and refine, Rfree should worsen to the same value as the structure converges to the same point. Thinking about the main purpose of the Rfree statistic, in a very real way this tells me that the model was better before this step of refinement, and it would be better to omit the minimization step. Perhaps this is what the authors did. On the other hand it does not seem quite right submit a model that has simply been rigid-body-refined against the data- I would prefer to refine to convergence and submit the best model that can be supported by the data alone, rather than a better model which is really the model from a better dataset repositioned in the new crystal. Ed
