[ccp4bb] fwd:
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Re: [ccp4bb] Refmac and sigma value
Hi Uma, Altering sigma affects the strength of geometry restraints throughout the model - bonds, angles, etc. Choosing a very low sigma will cause geometry to be more tightly restrained towards ideal values, which is why you observe improvements in Coot validation. Note that strengthening the geometry weight causes the observations (data) to be less influential in refinement. The risk of this is that your model may no longer appropriately/optimally describe your data. You can assess this locally by manual inspection of the electron density, and globally by considering overall refinement statistics (as reported at the bottom of the Refmac5 log file). Ideally, you want your model to both describe the data and have reasonable geometry. Regards Rob On 26 Apr 2012, at 21:26, Uma Ratu wrote: Hi, Alex: Which sigma do you mean? The one for automatic weight, not for Jelly-body refinement. I did not turn the Jelly-body refinement on. Thanks Ros On Thu, Apr 26, 2012 at 4:08 PM, aaleshin aales...@burnham.org wrote: Hi Uma, Which sigma do you mean? The one for Jelly-body refinement? J-B sigma=0.01 means very small fraction of the gradient will be used in each step. It is used usually with very low resolution (less then 3A) Alex On Apr 26, 2012, at 11:38 AM, Uma Ratu wrote: Dear All: I use Refmac5 to refine my structure model. When I set the sigma value to 0.3 (as recommended from tutorial), the resulted model has many red-bars by coot validation (geometry, rotamer, especially, Temp Facotr). I then lower the sigma value to 0.1, the resulted model is much improved by coot validation. I then lower the sigma value to 0.01, the resulted model is almost perfect, by coot validation and Molprobity. My question is: what is the risk for very low value sigma value? Thank you for your advice Ros
[ccp4bb] Summary Re: anyone scrapping an Raxis-IV?
Thank you for all your suggestions. Rigaku have discovered that shorting a couple of the output leads together means the new type can be used as a replacement for the old type. I'm very happy to say that it works! This is a similar solution to that suggested by Herman Schreuder. Kevin Roberts pointed to generally available replacements that required a change in voltage Others were kind enough to tip me of about machines due to be replaced. I'm not sure I should identify them in public, but thank you anyway. Peter On 17 April 2012 09:58, Peter Moody pcem1bigfi...@gmail.com wrote: Is anyone about to re-cycle a Rigaku RAXIS-IV? One of the inverters that power the erase lamps in ours is smoking, and Rigaku have not been able to source a replacement for us, hence the message to the BB. Our machine was made in November 1996 and uses the type of inverter connected with four pairs of wires (Rigaku can source the more recent 3-pair types). I can give more detail, pictures etc. but would not want to clutter up your inboxes. This is not the first of these inverters to fail, so it would also be nice to find a source so we can keep going with it a while longer. By we of course I mean I, as is the machine I play with whilst more serious people collect data on our more modern system, I clarify this just in case anyone should think my colleagues here are also stuck in the 20th century Thanks, Peter Peter Moody Henry Wellcome Laboratories University of Leicester Lancaster Road Leicester LE1 9HN UK tel. +44 (0)116 229 7097 http://www2.le.ac.uk/departments/biochemistry/staff/moodyhttp://redir.aspx?C=1a0a7175d81e495690bfd3f4b0e0afafURL=http%3a%2f%2fwww2.le.ac.uk%2fdepartments%2fbiochemistry%2fstaff%2fmoody
Re: [ccp4bb] Publication ethics Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
have a look at this case, no danger of your coordinates going to anyone but yourself if you do it this way: http://publicationethics.org/case/author-creates-bogus-email-accounts-proposed-reviewers On 26 Apr 2012, at 12:02, Jrh wrote: Dear Colleagues, I have followed this thread with great interest. It reminds me of the Open Commission Meeting of the Biological Macromolecules Commission in Geneva in 2002 at the IUCr Congress. Ie at which it was concluded that protein coordinates and diffraction data would not be provided to referees. The ethics and rights of readers, authors and referees is a balancing act, as Jeremy and others have emphasised these different constituency's views. The aim of this email though is to draw your attention to the Committee on Publication Ethics (COPE) work and case studies, which are extensive. Ie see:- http://publicationethics.org/ The COPE Forum will also provide advice on case submissions that are made of alleged publication malpractice, various of which are quite subtle. The processes as well though following on from obvious malpractice eg how a university research malpractice committee can be convened are also detailed. Greetings, John Prof John R Helliwell DSc On 26 Apr 2012, at 06:10, Jeremy Tame jt...@tsurumi.yokohama-cu.ac.jp wrote: The problem is it is not the PI who is jumping, it may be a postdoc he/she is throwing. Priority makes careers (look back at the Lavoisier/Priestly, Adams/LeVerrier or Cope/Marsh controversies), and the history of scientific reviewing is not all edifying. Too many checks, not enough balances. Science is probably better served if the author can publish without passing on the pdb model to a potentially unscrupulous reviewer, and if there are minor errors in the published paper then a competing group also has reason to publish its own view. The errors already have to evade the excellent validation tools we now have thanks to so many talented programmers, and proper figures and tables (plus validation report) should be enough for a review. The picture we have of haemoglobin is now much more accurate than the ones which came out decades ago, but those structures were very useful in the mean time. A requirement of resolution better than 2 Angstroms would probably stop poor models entering PDB, but I don't think it would serve science as a whole. Science is generally a self-correcting process, rather than a demand for perfection in every paper. Computer software follows a similar pattern - bug reports don't always invalidate the program. I have happily released data and coordinates via PDB before publication, even back in the 1990s when this was unfashionable, but would not do so if I felt it risked a postdoc failing to publish a key paper before competitors. It might be helpful if journals were more amenable to new structures of solved proteins as the biology often emerges from several models of different conformations or ligation states. But in a publish or perish world, authors need rights too. Reviewers do a necessary job, but there is a need for balance. The attached figure shows a French view of Le Verrier discovering Uranus, while Adams uses his telescope for a quite different purpose. Adams_Leverrier.jpg On Apr 26, 2012, at 2:01 AM, Ethan Merritt wrote: On Wednesday, April 25, 2012 09:40:01 am James Holton wrote: If you want to make a big splash, then don't complain about being asked to leap from a great height. This gets my vote as the best science-related quote of the year. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Refmac and sigma value
Hi Uma, The optimal weight is indeed resolution dependent, but hard to predict. In Refmac you can follow LLfree when you optimize the restraint weight and also keep an eye on the gap between R and R-free (it should not be too wide). Like Rob said, your geometry should be 'reasonable'. This may be a bit vague, but there is no clear target for bond/angle rmsd at a given resolution (some referees will disagree). If you look at the rmsZ values Refmac gives, the target is a bit clearer: rmsZ 1.000. The average rmsZ does go down with resolution (i.e. lower resolution gives lower rmsZ), but an ideal value cannot be given easily (or at all). Tightening the restraints improves the effective data/parameter ratio of your model. You can also improve it by adding additional restrains (e.g. NCS restraints) or by removing parameters (e.g. changing the complexity of your B-factor model). Note that the absence of geometric outliers does not prove that your model is optimal. If you use too tight restraints you can end up hiding genuine fitting errors. Cheers, Robbie Date: Fri, 27 Apr 2012 10:04:11 +0200 From: herman.schreu...@sanofi.com Subject: Re: [ccp4bb] Refmac and sigma value To: CCP4BB@JISCMAIL.AC.UK It all will depend on the resolution. At low resolution, relaxing the geometric restraints will allow the refinement program to tweak the model such that the difference between Fobs and Fcalc is minimized, but not that the model gets closer to the truth. I once struggled for a long time with a 3.5Åish data set with a protein where the most important feature was a rather flexible loop. It was before maximum likelyhood methods and Rfrees and the only way I could get rid of the model bias was to use extremely tight geometric restraints. The Rfactor would go up, but suddenly the electron density maps would no longer accept incorrectly placed side chains and new features, not present in the model, would appear. So my advice: at low resolution use as tight restraints as possible and monitor with Rfree if you are going in the right direction. At high or very high resolution, you can follow what your diffraction data tells you. In fact many very high resolution structures ( 1.5 Å) have higher rmsd's for bond lenghts and angles as medium resolution structures. However, at medium or low resolution there is not enough data to justify to relax the geometric restraints too much. Best regards, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robert Nicholls Sent: Friday, April 27, 2012 9:25 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac and sigma value Hi Uma, Altering sigma affects the strength of geometry restraints throughout the model - bonds, angles, etc. Choosing a very low sigma will cause geometry to be more tightly restrained towards ideal values, which is why you observe improvements in Coot validation. Note that strengthening the geometry weight causes the observations (data) to be less influential in refinement. The risk of this is that your model may no longer appropriately/optimally describe your data. You can assess this locally by manual inspection of the electron density, and globally by considering overall refinement statistics (as reported at the bottom of the Refmac5 log file). Ideally, you want your model to both describe the data and have reasonable geometry. Regards Rob On 26 Apr 2012, at 21:26, Uma Ratu wrote: Hi, Alex: Which sigma do you mean? The one for automatic weight, not for Jelly-body refinement. I did not turn the Jelly-body refinement on. Thanks Ros On Thu, Apr 26, 2012 at 4:08 PM, aaleshin aales...@burnham.org wrote: Hi Uma, Which sigma do you mean? The one for Jelly-body refinement? J-B sigma=0.01 means very small fraction of the gradient will be used in each step. It is used usually with very low resolution (less then 3A) Alex On Apr 26, 2012, at 11:38 AM, Uma Ratu wrote: Dear All: I use Refmac5 to refine my structure model. When I set the sigma value to 0.3 (as recommended from tutorial), the resulted model has many red-bars by coot validation (geometry, rotamer, especially, Temp Facotr). I then lower the sigma value to 0.1, the resulted model is much improved by coot validation. I then lower the sigma value to 0.01, the resulted model is almost perfect, by coot validation and Molprobity. My question is: what is the risk for very low value sigma value? Thank you for your advice Ros
Re: [ccp4bb] commercially available proteins
Just in case you are blocking with BSA, how about, e. coli beta-galactosidase (114 KDa) ?. It's commercially available but you probably have cells already making it in the lab On 26 April 2012 19:29, Peter Hsu hsuu...@u.washington.edu wrote: Hi all, Sorry for the very off topic problem. I'm looking for a loading control for my westerns (doing in vitro assays). Due to separation/antibody specificity issues, I need super good separation between 70 and 100 kDa, oftentimes running those markers all the way to the bottom of the gel. If I'm careful, I can usually keep the 55kDa marker still on the gel, but my loading control is smaller and runs off. Does anyone know of a commercially available protein that's relatively cheap, has an antibody against it, and is either between 55-70kDa, or 100kDa to add into my experiments so I can have a loading control? Thanks and sorry again for the off topic question. All the best, Peter
Re: [ccp4bb] Refmac and sigma value
Two points. 1) the fit to ideal geometry as flagged in coot validation does not guarantee a correct model - the best model should be the one that fits the experimental data best, without having unlikely geometry. You could easily get a model with perfect geometry which was incorrectly placed in the unit cell.. 2) the AUTO weighting in REFMAC tries to take into account resolution of the data,and Rfree Have you used that? It isn't infallible of course.. Eleanor On 27 April 2012 10:57, Robbie Joosten robbie_joos...@hotmail.com wrote: Hi Uma, The optimal weight is indeed resolution dependent, but hard to predict. In Refmac you can follow LLfree when you optimize the restraint weight and also keep an eye on the gap between R and R-free (it should not be too wide). Like Rob said, your geometry should be 'reasonable'. This may be a bit vague, but there is no clear target for bond/angle rmsd at a given resolution (some referees will disagree). If you look at the rmsZ values Refmac gives, the target is a bit clearer: rmsZ 1.000. The average rmsZ does go down with resolution (i.e. lower resolution gives lower rmsZ), but an ideal value cannot be given easily (or at all). Tightening the restraints improves the effective data/parameter ratio of your model. You can also improve it by adding additional restrains (e.g. NCS restraints) or by removing parameters (e.g. changing the complexity of your B-factor model). Note that the absence of geometric outliers does not prove that your model is optimal. If you use too tight restraints you can end up hiding genuine fitting errors. Cheers, Robbie -- Date: Fri, 27 Apr 2012 10:04:11 +0200 From: herman.schreu...@sanofi.com Subject: Re: [ccp4bb] Refmac and sigma value To: CCP4BB@JISCMAIL.AC.UK It all will depend on the resolution. At low resolution, relaxing the geometric restraints will allow the refinement program to tweak the model such that the difference between Fobs and Fcalc is minimized, but not that the model gets closer to the truth. I once struggled for a long time with a 3.5Åish data set with a protein where the most important feature was a rather flexible loop. It was before maximum likelyhood methods and Rfrees and the only way I could get rid of the model bias was to use extremely tight geometric restraints. The Rfactor would go up, but suddenly the electron density maps would no longer accept incorrectly placed side chains and new features, not present in the model, would appear. So my advice: at low resolution use as tight restraints as possible and monitor with Rfree if you are going in the right direction. At high or very high resolution, you can follow what your diffraction data tells you. In fact many very high resolution structures ( 1.5 Å) have higher rmsd's for bond lenghts and angles as medium resolution structures. However, at medium or low resolution there is not enough data to justify to relax the geometric restraints too much. Best regards, Herman -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Robert Nicholls *Sent:* Friday, April 27, 2012 9:25 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Refmac and sigma value Hi Uma, Altering sigma affects the strength of geometry restraints throughout the model - bonds, angles, etc. Choosing a very low sigma will cause geometry to be more tightly restrained towards ideal values, which is why you observe improvements in Coot validation. Note that strengthening the geometry weight causes the observations (data) to be less influential in refinement. The risk of this is that your model may no longer appropriately/optimally describe your data. You can assess this locally by manual inspection of the electron density, and globally by considering overall refinement statistics (as reported at the bottom of the Refmac5 log file). Ideally, you want your model to both describe the data and have reasonable geometry. Regards Rob On 26 Apr 2012, at 21:26, Uma Ratu wrote: Hi, Alex: Which sigma do you mean? The one for automatic weight, not for Jelly-body refinement. I did not turn the Jelly-body refinement on. Thanks Ros On Thu, Apr 26, 2012 at 4:08 PM, aaleshin aales...@burnham.org wrote: Hi Uma, Which sigma do you mean? The one for Jelly-body refinement? J-B sigma=0.01 means very small fraction of the gradient will be used in each step. It is used usually with very low resolution (less then 3A) Alex On Apr 26, 2012, at 11:38 AM, Uma Ratu wrote: Dear All: I use Refmac5 to refine my structure model. When I set the sigma value to 0.3 (as recommended from tutorial), the resulted model has many red-bars by coot validation (geometry, rotamer, especially, Temp Facotr). I then lower the sigma value to 0.1, the resulted model is much improved by coot validation. I then lower the sigma value to 0.01, the
Re: [ccp4bb] negative density at some places in the side chain of residues
What I would do - not net ideal! 1) the ASP looks in the wrong place - shift it into green density and one OE is probably a water.. 2) MET notoriously hard to model - I suspect there often are multiple conformations.. And of course at some wave lengths the S contribution should be down weighted by f' - the default is to use the S scattering for CuKa wavelength.. 3) I think you need to flip the GLY O and then refit the adjacent residues 4) SER is often in 2 conformations - I suspect that is the case here.. Eleanor On 26 April 2012 22:03, Antony Oliver antony.oli...@sussex.ac.uk wrote: Alaksa, 1) What rmsd / sigma are you contouring your density at ? i.e. are you down in the noise or are you at a reasonable value for your Fo-Fc map? 2) It looks like some of your side-chains appear to have more than one conformation - it's fairly easy in Coot to position and model both. Tony. --- Mobile Account --- On 26 Apr 2012, at 21:55, Alaksa xtal.cc...@gmail.com wrote: Dear all I am refining the crystal structure of a protein (Rfree and Rvalue are 25 and 20 A respectively). However, I am getting the negative density at some places in the side chain of residues. All side chains are properly fitting into the blue density, however red density blobs are also present at the same place along with blue density . At some other place this red density is also present in the main chain along with blue density (see the attached snaps). If I have mutate the residues to alanine then density becomes blue, but when change into the original residue, after refmac5 again it is showing red blob. Also if I rotate the chain to place it in green density, but after running refmac it attain original position having red blob. I am not using TLS. I am seeking some strategy so that the problem can be solved. Please suggest me the possible reasons and remedy. Also i am naive in crystallography. Thanks Alaksa coot2.png coot1.png coot3.png coot4.png
[ccp4bb] X-PLOR
Hi, Could someone explain to me the scientific details of the protocols used in X-PLOR to (1) build explicit hydrogen atoms onto X-ray structures and (2) optimize their positions? Many thanks in advance. Greetings, Nadir -- Pr. Nadir T. Mrabet Structural Molecular Biochemistry INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabetat medecine.uhp-nancy.fr
Re: [ccp4bb] detergent crystal?
Hongjun, I am in agreement with Bert as DDM is exceedingly difficult to crystallize, even in organic solvents. This is one of the reasons it is so expensive. However, you can produce a lot of quasi-crystals that do show low resolution diffraction. As Bert said, you may have protein/detergent crystals that are just poorly ordered. I would disagree with Bert only slightly concerning these crystals in that while you might suppose that most or all of the lattice contacts are mediated by detergent and not by protein. Instead, you might also be observing protein-protein contacts being disturbed by less than optimal detergent contacts (either detergent-detergent or detergent-protein). Try changing the detergent to decyl-maltoside (DM) to see if you get similar results. It was the change from DDM to DM that really gave great crystals for the 13-subunit bovine cytochrome c oxidase. Another thing to watch out for is the dreaded contamination factor, either by protein or detergent. I have seen cases where crystals were from a contaminating protein (such as those which may bind to Ni-affinity resin and are not separated by gel filtration) at as low as 1% (by weight) contamination. More insidious is detergent contamination. DDM is is the beta anomer, but all batches are contaminated with varying amounts of the alpha anomer. The alpha anomers of alkyl glycoside detergents tend to crystallize much more readily than the beta anomers. Despite their best efforts, manufacturers occasionally produce batches with a high level of alpha anomer contamination. I have personally tested a batch of beta-octyl glucoside (from a very reputable company) that did not dissolve; other batches from a different company were cloudy when making a 10% stock solution. Alpha-octyl glucoside is not soluble below ~32C and make some very nice crystals in aqueous solution at room temperature. So try a batch of DDM from another source. Best of luck, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On Apr 26, 2012, at 5:32 PM, Van Den Berg, Bert wrote: Generally speaking it is quite hard to crystallize DDM since it is so soluble (20% in water). You most likely have protein crystals (of course containing a lot of detergent as well) that are just not ordered, presumably because most or all of the lattice contacts are mediated by detergent and not by protein. Unfortunately this is the norm for membrane protein crystallization. Good luck, Bert From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 于洪军 [hongju...@moon.ibp.ac.cn] Sent: Friday, April 27, 2012 6:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] detergent crystal? Hi, I am trying to screen crystals of membrane protein in DDM solutions. I got crystals and its diffraction pattern as I enclosed. Membrane protein crystallization seems quite different from soluble protein. The condition contains PEG400. I learn from other topic here that PEG400 can easily produce DDM detergent crystals. Is it detergent crystal ? Can I tell this from the diffraction pattern? Advices would be greatly appreciated. Thank you. Hongjun
[ccp4bb] protease inhibitor
Hi All, Does any one add protease inhibitor to purified protein just before setting trays? If yes what is the typical % that should be added ? regards rashmi
Re: [ccp4bb] Refmac and sigma value
Dear All: Thank you very much for you comments and advices. Now I have a better understanding on this issue. regards Ros On Fri, Apr 27, 2012 at 9:25 AM, Eleanor Dodson eleanor.dod...@york.ac.ukwrote: Two points. 1) the fit to ideal geometry as flagged in coot validation does not guarantee a correct model - the best model should be the one that fits the experimental data best, without having unlikely geometry. You could easily get a model with perfect geometry which was incorrectly placed in the unit cell.. 2) the AUTO weighting in REFMAC tries to take into account resolution of the data,and Rfree Have you used that? It isn't infallible of course.. Eleanor On 27 April 2012 10:57, Robbie Joosten robbie_joos...@hotmail.com wrote: Hi Uma, The optimal weight is indeed resolution dependent, but hard to predict. In Refmac you can follow LLfree when you optimize the restraint weight and also keep an eye on the gap between R and R-free (it should not be too wide). Like Rob said, your geometry should be 'reasonable'. This may be a bit vague, but there is no clear target for bond/angle rmsd at a given resolution (some referees will disagree). If you look at the rmsZ values Refmac gives, the target is a bit clearer: rmsZ 1.000. The average rmsZ does go down with resolution (i.e. lower resolution gives lower rmsZ), but an ideal value cannot be given easily (or at all). Tightening the restraints improves the effective data/parameter ratio of your model. You can also improve it by adding additional restrains (e.g. NCS restraints) or by removing parameters (e.g. changing the complexity of your B-factor model). Note that the absence of geometric outliers does not prove that your model is optimal. If you use too tight restraints you can end up hiding genuine fitting errors. Cheers, Robbie -- Date: Fri, 27 Apr 2012 10:04:11 +0200 From: herman.schreu...@sanofi.com Subject: Re: [ccp4bb] Refmac and sigma value To: CCP4BB@JISCMAIL.AC.UK It all will depend on the resolution. At low resolution, relaxing the geometric restraints will allow the refinement program to tweak the model such that the difference between Fobs and Fcalc is minimized, but not that the model gets closer to the truth. I once struggled for a long time with a 3.5Åish data set with a protein where the most important feature was a rather flexible loop. It was before maximum likelyhood methods and Rfrees and the only way I could get rid of the model bias was to use extremely tight geometric restraints. The Rfactor would go up, but suddenly the electron density maps would no longer accept incorrectly placed side chains and new features, not present in the model, would appear. So my advice: at low resolution use as tight restraints as possible and monitor with Rfree if you are going in the right direction. At high or very high resolution, you can follow what your diffraction data tells you. In fact many very high resolution structures ( 1.5 Å) have higher rmsd's for bond lenghts and angles as medium resolution structures. However, at medium or low resolution there is not enough data to justify to relax the geometric restraints too much. Best regards, Herman -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Robert Nicholls *Sent:* Friday, April 27, 2012 9:25 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Refmac and sigma value Hi Uma, Altering sigma affects the strength of geometry restraints throughout the model - bonds, angles, etc. Choosing a very low sigma will cause geometry to be more tightly restrained towards ideal values, which is why you observe improvements in Coot validation. Note that strengthening the geometry weight causes the observations (data) to be less influential in refinement. The risk of this is that your model may no longer appropriately/optimally describe your data. You can assess this locally by manual inspection of the electron density, and globally by considering overall refinement statistics (as reported at the bottom of the Refmac5 log file). Ideally, you want your model to both describe the data and have reasonable geometry. Regards Rob On 26 Apr 2012, at 21:26, Uma Ratu wrote: Hi, Alex: Which sigma do you mean? The one for automatic weight, not for Jelly-body refinement. I did not turn the Jelly-body refinement on. Thanks Ros On Thu, Apr 26, 2012 at 4:08 PM, aaleshin aales...@burnham.org wrote: Hi Uma, Which sigma do you mean? The one for Jelly-body refinement? J-B sigma=0.01 means very small fraction of the gradient will be used in each step. It is used usually with very low resolution (less then 3A) Alex On Apr 26, 2012, at 11:38 AM, Uma Ratu wrote: Dear All: I use Refmac5 to refine my structure model. When I set the sigma value to 0.3 (as recommended from tutorial), the resulted model has many
Re: [ccp4bb] detergent crystal?
Wouldn't the lack of solubility of the alpha form of DDM suggest an easy purification protocol for the beta form? JPK On Fri, Apr 27, 2012 at 8:40 AM, R. M. Garavito rmgarav...@gmail.comwrote: Hongjun, I am in agreement with Bert as DDM is exceedingly difficult to crystallize, even in organic solvents. This is one of the reasons it is so expensive. However, you can produce a lot of quasi-crystals that do show low resolution diffraction. As Bert said, you may have protein/detergent crystals that are just poorly ordered. I would disagree with Bert only slightly concerning these crystals in that while you might suppose that most or all of the lattice contacts are mediated by detergent and not by protein. Instead, you might also be observing protein-protein contacts being disturbed by less than optimal detergent contacts (either detergent-detergent or detergent-protein). Try changing the detergent to decyl-maltoside (DM) to see if you get similar results. It was the change from DDM to DM that really gave great crystals for the 13-subunit bovine cytochrome c oxidase. Another thing to watch out for is the dreaded contamination factor, either by protein or detergent. I have seen cases where crystals were from a contaminating protein (such as those which may bind to Ni-affinity resin and are not separated by gel filtration) at as low as 1% (by weight) contamination. More insidious is detergent contamination. DDM is is the beta anomer, but all batches are contaminated with varying amounts of the alpha anomer. The alpha anomers of alkyl glycoside detergents tend to crystallize much more readily than the beta anomers. Despite their best efforts, manufacturers occasionally produce batches with a high level of alpha anomer contamination. I have personally tested a batch of beta-octyl glucoside (from a very reputable company) that did not dissolve; other batches from a different company were cloudy when making a 10% stock solution. Alpha-octyl glucoside is not soluble below ~32C and make some very nice crystals in aqueous solution at room temperature. So try a batch of DDM from another source. Best of luck, Michael ** *R. Michael Garavito, Ph.D.* *Professor of Biochemistry Molecular Biology* *603 Wilson Rd., Rm. 513** * *Michigan State University * *East Lansing, MI 48824-1319* *Office:** **(517) 355-9724 Lab: (517) 353-9125*** *FAX: (517) 353-9334Email: rmgarav...@gmail.com* ** On Apr 26, 2012, at 5:32 PM, Van Den Berg, Bert wrote: Generally speaking it is quite hard to crystallize DDM since it is so soluble (20% in water). You most likely have protein crystals (of course containing a lot of detergent as well) that are just not ordered, presumably because most or all of the lattice contacts are mediated by detergent and not by protein. Unfortunately this is the norm for membrane protein crystallization. Good luck, Bert -- *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 于洪军 [ hongju...@moon.ibp.ac.cn] *Sent:* Friday, April 27, 2012 6:07 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] detergent crystal? Hi, I am trying to screen crystals of membrane protein in DDM solutions. I got crystals and its diffraction pattern as I enclosed. Membrane protein crystallization seems quite different from soluble protein. The condition contains PEG400. I learn from other topic here that PEG400 can easily produce DDM detergent crystals. Is it detergent crystal ? Can I tell this from the diffraction pattern? Advices would be greatly appreciated. Thank you. Hongjun -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] X-PLOR
Nadir, There is an explicit bulletin board for questions regarding CNS and XPLOR. I would suggest posting your question there. http://tech.dir.groups.yahoo.com/group/cnsbb/ Cheers, Francisco -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nadir T. Mrabet Sent: Friday, April 27, 2012 6:34 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] X-PLOR Hi, Could someone explain to me the scientific details of the protocols used in X-PLOR to (1) build explicit hydrogen atoms onto X-ray structures and (2) optimize their positions? Many thanks in advance. Greetings, Nadir -- Pr. Nadir T. Mrabet Structural Molecular Biochemistry INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabetat medecine.uhp-nancy.fr
Re: [ccp4bb] detergent crystal?
Jacob, The solubility of the alpha anomer of DDM is actually not bad (it's only really bad for the alkyl glucosides), just the phase behavior is different. Still getting pure beta anomer is the tough problem, which is part of the reason it is so expensive. Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On Apr 27, 2012, at 10:54 AM, Jacob Keller wrote: Wouldn't the lack of solubility of the alpha form of DDM suggest an easy purification protocol for the beta form? JPK On Fri, Apr 27, 2012 at 8:40 AM, R. M. Garavito rmgarav...@gmail.com wrote: Hongjun, I am in agreement with Bert as DDM is exceedingly difficult to crystallize, even in organic solvents. This is one of the reasons it is so expensive. However, you can produce a lot of quasi-crystals that do show low resolution diffraction. As Bert said, you may have protein/detergent crystals that are just poorly ordered. I would disagree with Bert only slightly concerning these crystals in that while you might suppose that most or all of the lattice contacts are mediated by detergent and not by protein. Instead, you might also be observing protein-protein contacts being disturbed by less than optimal detergent contacts (either detergent-detergent or detergent-protein). Try changing the detergent to decyl-maltoside (DM) to see if you get similar results. It was the change from DDM to DM that really gave great crystals for the 13-subunit bovine cytochrome c oxidase. Another thing to watch out for is the dreaded contamination factor, either by protein or detergent. I have seen cases where crystals were from a contaminating protein (such as those which may bind to Ni-affinity resin and are not separated by gel filtration) at as low as 1% (by weight) contamination. More insidious is detergent contamination. DDM is is the beta anomer, but all batches are contaminated with varying amounts of the alpha anomer. The alpha anomers of alkyl glycoside detergents tend to crystallize much more readily than the beta anomers. Despite their best efforts, manufacturers occasionally produce batches with a high level of alpha anomer contamination. I have personally tested a batch of beta-octyl glucoside (from a very reputable company) that did not dissolve; other batches from a different company were cloudy when making a 10% stock solution. Alpha-octyl glucoside is not soluble below ~32C and make some very nice crystals in aqueous solution at room temperature. So try a batch of DDM from another source. Best of luck, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On Apr 26, 2012, at 5:32 PM, Van Den Berg, Bert wrote: Generally speaking it is quite hard to crystallize DDM since it is so soluble (20% in water). You most likely have protein crystals (of course containing a lot of detergent as well) that are just not ordered, presumably because most or all of the lattice contacts are mediated by detergent and not by protein. Unfortunately this is the norm for membrane protein crystallization. Good luck, Bert From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 于洪军 [hongju...@moon.ibp.ac.cn] Sent: Friday, April 27, 2012 6:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] detergent crystal? Hi, I am trying to screen crystals of membrane protein in DDM solutions. I got crystals and its diffraction pattern as I enclosed. Membrane protein crystallization seems quite different from soluble protein. The condition contains PEG400. I learn from other topic here that PEG400 can easily produce DDM detergent crystals. Is it detergent crystal ? Can I tell this from the diffraction pattern? Advices would be greatly appreciated. Thank you. Hongjun -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
[ccp4bb] Off-topic: PDB deposition of multiple structure factor files
Dear All, With my most recent PDBe deposition, in addition to the native data, I had intended to deposit the anomalous data, used for structure determination, and make it available for download. This turned out to be less straightforward than I had anticipated, because the current PDB convention is to only allow a single structure factor file for experimental data (usually the native dataset), available for download from the PDB. In my case, the anomalous data were concatenated with the native data into a single cif file (this worked and made sense, because both for both datasets the unit cell dimensions are virtually identical). I imagine it would be beneficial to be able to make available more than a single structure factor file, including the ones derived from experimental phasing, in the PDB, along with the final coordinates, without concatenating the data into a single file (which may lead to confusion to users when downloaded). Is this anything the PDB is already working to implement in the near future (perhaps via the coming PDBx format)? Best regards, Florian
Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files
again, it looks like this is particular to the US portal. We submit via the European www.pdbe.org and can submit multiple datasets. See 2XGF for an example. Note: I think from www.rcsb.org only one file can be downloaded, but www.pdbe.org clearly shows both. Although you are in the US, you can use the pdbe deposition tool AUTODEP - or the Japanese one, if you like. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 27 Apr 2012, at 20:23, Florian Schmitzberger wrote: Dear All, With my most recent PDBe deposition, in addition to the native data, I had intended to deposit the anomalous data, used for structure determination, and make it available for download. This turned out to be less straightforward than I had anticipated, because the current PDB convention is to only allow a single structure factor file for experimental data (usually the native dataset), available for download from the PDB. In my case, the anomalous data were concatenated with the native data into a single cif file (this worked and made sense, because both for both datasets the unit cell dimensions are virtually identical). I imagine it would be beneficial to be able to make available more than a single structure factor file, including the ones derived from experimental phasing, in the PDB, along with the final coordinates, without concatenating the data into a single file (which may lead to confusion to users when downloaded). Is this anything the PDB is already working to implement in the near future (perhaps via the coming PDBx format)? Best regards, Florian
Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files
Dear Mark, This is interesting. I also had submitted my data via the PDBe (European portal). While they allow deposition of multiple datasets, only a single file can apparently be made available for download from the site. In contrast to your case, for my deposition the second deposited dataset is not explicitly listed though. Cheers, Florian On Apr 27, 2012, at 2:35 PM, Mark J van Raaij wrote: again, it looks like this is particular to the US portal. We submit via the European www.pdbe.org and can submit multiple datasets. See 2XGF for an example. Note: I think from www.rcsb.org only one file can be downloaded, but www.pdbe.org clearly shows both. Although you are in the US, you can use the pdbe deposition tool AUTODEP - or the Japanese one, if you like. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 27 Apr 2012, at 20:23, Florian Schmitzberger wrote: Dear All, With my most recent PDBe deposition, in addition to the native data, I had intended to deposit the anomalous data, used for structure determination, and make it available for download. This turned out to be less straightforward than I had anticipated, because the current PDB convention is to only allow a single structure factor file for experimental data (usually the native dataset), available for download from the PDB. In my case, the anomalous data were concatenated with the native data into a single cif file (this worked and made sense, because both for both datasets the unit cell dimensions are virtually identical). I imagine it would be beneficial to be able to make available more than a single structure factor file, including the ones derived from experimental phasing, in the PDB, along with the final coordinates, without concatenating the data into a single file (which may lead to confusion to users when downloaded). Is this anything the PDB is already working to implement in the near future (perhaps via the coming PDBx format)? Best regards, Florian --- Florian Schmitzberger, PhD Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, Seeley G. Mudd 123 Boston, MA 02115, US Tel: 001 617 432 5603
Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files
On Friday, April 27, 2012 11:23:13 am Florian Schmitzberger wrote: Dear All, With my most recent PDBe deposition, in addition to the native data, I had intended to deposit the anomalous data, used for structure determination, and make it available for download. This turned out to be less straightforward than I had anticipated, because the current PDB convention is to only allow a single structure factor file for experimental data (usually the native dataset), available for download from the PDB. In my case, the anomalous data were concatenated with the native data into a single cif file (this worked and made sense, because both for both datasets the unit cell dimensions are virtually identical). I imagine it would be beneficial to be able to make available more than a single structure factor file, including the ones derived from experimental phasing, in the PDB, along with the final coordinates, without concatenating the data into a single file (which may lead to confusion to users when downloaded). Is this anything the PDB is already working to implement in the near future (perhaps via the coming PDBx format)? The PDB has always been perfectly happy to accept whatever SF files I send them. On rare occasions they have gotten mangled in the process, but that's a separate issue :-) But re-reading your Email, I see that your concern is that there is only a single link on the structure's web page for download. I.e., an issue of retrieval rather than a problem with deposition. Still, I don't see anything inherently confusing about a file that contains multiple data sets. That will be true for any MAD experiment. Have you asked the PDB whether there is a mechanism for making supplemental files visible on the auto-generated web page? Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files
It might be a portal issue. But the pdb staff is very helpful in getting this deposited. We deposited data of I think 4 crystals and 3 wavelengths with different phase sets in 2008. (The data was anisotropic, 3.5/4.2 A resolution, model building was not straight forward, so we wanted to preserve as much information as possible. If memory serves right, we have experimental fobs, anisotropy corrected fobs, a derivative and a semet dataset; if you're interested, pdb code is 3dhw, have a look at the sf-file) hth, Jens On Fri, 2012-04-27 at 20:35 +0200, Mark J van Raaij wrote: again, it looks like this is particular to the US portal. We submit via the European www.pdbe.org and can submit multiple datasets. See 2XGF for an example. Note: I think from www.rcsb.org only one file can be downloaded, but www.pdbe.org clearly shows both. Although you are in the US, you can use the pdbe deposition tool AUTODEP - or the Japanese one, if you like. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 27 Apr 2012, at 20:23, Florian Schmitzberger wrote: Dear All, With my most recent PDBe deposition, in addition to the native data, I had intended to deposit the anomalous data, used for structure determination, and make it available for download. This turned out to be less straightforward than I had anticipated, because the current PDB convention is to only allow a single structure factor file for experimental data (usually the native dataset), available for download from the PDB. In my case, the anomalous data were concatenated with the native data into a single cif file (this worked and made sense, because both for both datasets the unit cell dimensions are virtually identical). I imagine it would be beneficial to be able to make available more than a single structure factor file, including the ones derived from experimental phasing, in the PDB, along with the final coordinates, without concatenating the data into a single file (which may lead to confusion to users when downloaded). Is this anything the PDB is already working to implement in the near future (perhaps via the coming PDBx format)? Best regards, Florian
[ccp4bb] water picking
All, For those who still don't use Coot is there an automatic water picking procedure in CCP4? Many years ago there was a peakmax which is now for Patterson peaks only. Then there was routine through Arp/wArp. Now is Coot only. Is this right? Thanks. Vaheh Oganesyan, PhD Antibody Discovery and Protein Engineering MedImmune, LLC. 1 MedImmune Way, Gaithersburg, MD 20878 oganesy...@medimmune.commailto:oganesy...@medimmune.com To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. inline: image001.gif
[ccp4bb] Anisotropic diffraction
Dear crystallographers A very basic question, for anisotropic diffraction, does data truncation with ellipsoidal method change the symmetry? For example, if untruncated data is space group P6, will truncated data index as P622 or P2? Thank you. Theresa
Re: [ccp4bb] Anisotropic diffraction
Anisotropic truncation should have no effect on the space group symmetry. On 04/27/12 15:18, Theresa Hsu wrote: Dear crystallographers A very basic question, for anisotropic diffraction, does data truncation with ellipsoidal method change the symmetry? For example, if untruncated data is space group P6, will truncated data index as P622 or P2? Thank you. Theresa -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files
We (JCSG) too have been depositing multiple data sets (including unmerged original index intensities for each wavelength and even for multiple crystals when one was used for phasing and another for refinement, and MAD phases and DM modified map coefficients) since 2004 without problems. These are all in separate data loops of a single structure factor file. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jens Kaiser Sent: Friday, April 27, 2012 11:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files It might be a portal issue. But the pdb staff is very helpful in getting this deposited. We deposited data of I think 4 crystals and 3 wavelengths with different phase sets in 2008. (The data was anisotropic, 3.5/4.2 A resolution, model building was not straight forward, so we wanted to preserve as much information as possible. If memory serves right, we have experimental fobs, anisotropy corrected fobs, a derivative and a semet dataset; if you're interested, pdb code is 3dhw, have a look at the sf-file) hth, Jens On Fri, 2012-04-27 at 20:35 +0200, Mark J van Raaij wrote: again, it looks like this is particular to the US portal. We submit via the European www.pdbe.org and can submit multiple datasets. See 2XGF for an example. Note: I think from www.rcsb.org only one file can be downloaded, but www.pdbe.org clearly shows both. Although you are in the US, you can use the pdbe deposition tool AUTODEP - or the Japanese one, if you like. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 27 Apr 2012, at 20:23, Florian Schmitzberger wrote: Dear All, With my most recent PDBe deposition, in addition to the native data, I had intended to deposit the anomalous data, used for structure determination, and make it available for download. This turned out to be less straightforward than I had anticipated, because the current PDB convention is to only allow a single structure factor file for experimental data (usually the native dataset), available for download from the PDB. In my case, the anomalous data were concatenated with the native data into a single cif file (this worked and made sense, because both for both datasets the unit cell dimensions are virtually identical). I imagine it would be beneficial to be able to make available more than a single structure factor file, including the ones derived from experimental phasing, in the PDB, along with the final coordinates, without concatenating the data into a single file (which may lead to confusion to users when downloaded). Is this anything the PDB is already working to implement in the near future (perhaps via the coming PDBx format)? Best regards, Florian
Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files
so perhaps the problem indeed is sending different wavelengths as one file...in our case there is only one crystal, one wavelength, i.e. one loop, while I clearly submitted all three wavelengths. Quoting Miller, Mitchell D.: We (JCSG) too have been depositing multiple data sets (including unmerged original index intensities for each wavelength and even for multiple crystals when one was used for phasing and another for refinement, and MAD phases and DM modified map coefficients) since 2004 without problems. These are all in separate data loops of a single structure factor file. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jens Kaiser Sent: Friday, April 27, 2012 11:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files It might be a portal issue. But the pdb staff is very helpful in getting this deposited. We deposited data of I think 4 crystals and 3 wavelengths with different phase sets in 2008. (The data was anisotropic, 3.5/4.2 A resolution, model building was not straight forward, so we wanted to preserve as much information as possible. If memory serves right, we have experimental fobs, anisotropy corrected fobs, a derivative and a semet dataset; if you're interested, pdb code is 3dhw, have a look at the sf-file) hth, Jens On Fri, 2012-04-27 at 20:35 +0200, Mark J van Raaij wrote: again, it looks like this is particular to the US portal. We submit via the European www.pdbe.org and can submit multiple datasets. See 2XGF for an example. Note: I think from www.rcsb.org only one file can be downloaded, but www.pdbe.org clearly shows both. Although you are in the US, you can use the pdbe deposition tool AUTODEP - or the Japanese one, if you like. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 27 Apr 2012, at 20:23, Florian Schmitzberger wrote: Dear All, With my most recent PDBe deposition, in addition to the native data, I had intended to deposit the anomalous data, used for structure determination, and make it available for download. This turned out to be less straightforward than I had anticipated, because the current PDB convention is to only allow a single structure factor file for experimental data (usually the native dataset), available for download from the PDB. In my case, the anomalous data were concatenated with the native data into a single cif file (this worked and made sense, because both for both datasets the unit cell dimensions are virtually identical). I imagine it would be beneficial to be able to make available more than a single structure factor file, including the ones derived from experimental phasing, in the PDB, along with the final coordinates, without concatenating the data into a single file (which may lead to confusion to users when downloaded). Is this anything the PDB is already working to implement in the near future (perhaps via the coming PDBx format)? Best regards, Florian Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es
[ccp4bb] MAMCM reminder
The 42nd Mid-Atlantic Macromolecular Crystallography meeting will be held at the University of Virginia from May 31 June 2, 2012. There are several reasons why you should make your plans now! Most of the blocks of hotel rooms will be released to the public and conference rates will expire on Monday, April 30th, 2012. Also, after Monday University Housing will charge a $50 late registration fee. Additionally, space is limited for the Saturday workshops, and slots are filling up. Details of the meeting can be found at http://www.mid-atlantic.org/ . We are also excited to announce TWO $250 poster prizes, one for students and one for postdocs! Respectfully, Drs. David Cooper, Peter Horanyi and Michael Purdy Co-Directors of the 42nd MAMCM http://www.mid-atlantic.org We would like to thank our sponsors: Agilent Technologies Inc., Art Robbins Instruments, Bruker, Emerald BioSystems, Formulatrix, HKL Research Inc., Labcyte, MiTeGen, Rigaku Americas Corporation, Rockland Immunochemicals, and TTP LabTech.
Re: [ccp4bb] water picking
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear , according to my 'man watpeak' and 'man peakmax' in ccp4-6.2.993 there is no restrictionof these programs to Patterson peaks (which would anyhow require a total rewrite, considering that peakmax acts on maps rather than Pattersion maps). Maybe the answer can be more conclusive to you if you would explain why you want to know. Regards, Tim On 04/27/12 21:11, Oganesyan, Vaheh wrote: All, For those who still don't use Coot is there an automatic water picking procedure in CCP4? Many years ago there was a peakmax which is now for Patterson peaks only. Then there was routine through Arp/wArp. Now is Coot only. Is this right? Thanks. Vaheh Oganesyan, PhD Antibody Discovery and Protein Engineering MedImmune, LLC. 1 MedImmune Way, Gaithersburg, MD 20878 oganesy...@medimmune.commailto:oganesy...@medimmune.com To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. - -- - -- 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 Mozilla - http://enigmail.mozdev.org/ iD8DBQFPmxx7UxlJ7aRr7hoRAp1jAKC+5Pj8Y0/Zj3gXe0gv87zcHUdh8wCfYiT2 kEwhW0Rm2EvPnCRTXXy1JWM= =cXEX -END PGP SIGNATURE-
Re: [ccp4bb] Anisotropic diffraction
Birtley and Curry used a novel optimization method, in their paper Crystallization of foot-and-mouth disease virus 3C protease: surface mutagenesis and a novel crystal-optimization strategy, which might be inspiring for you. 在 2012年4月28日 上午3:21，David Schuller dj...@cornell.edu 写道： Anisotropic truncation should have no effect on the space group symmetry. On 04/27/12 15:18, Theresa Hsu wrote: Dear crystallographers A very basic question, for anisotropic diffraction, does data truncation with ellipsoidal method change the symmetry? For example, if untruncated data is space group P6, will truncated data index as P622 or P2? Thank you. Theresa -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China Tel:+86-10-62772291 Fax:+86-10-62773145 E-mail:che...@xtal.tsinghua.edu.cn 北京市海淀区清华大学生命科学馆201-212室 邮编：100084
