[ccp4bb] MIND in shelxd
Dear all How to decide for minimum distance between heavy atoms in shelxd esp w.r.t. S-SAD. Thanx in advance Monica
Re: [ccp4bb] coot problems to decrease R FREE
Hello Peter, 1、THE RESOLUTION OF THE DATA IS 2.5 angstrom. After first refinement of > refmac5 I got R factor which is 0.26 and R FREE which is 0.31. My question > is what the final R factor and R FREE should be after several rounds of > refinement by refmac5 and coot. > answer can be found here: Acta Cryst. D65, 297-300 (2009) Direct link: http://phenix-online.org/papers/lv5003_reprint.pdf 2、At which map level（e/A3 or rmsd）should I refine the data by coot? > I guess you meant "refine model parameters".. just a remark. We normally refine atomic (and non-atomic) model parameters against measured data using some agreement criteria and a minimization method.. etc etc, you know all this! As to your actual question: if you hope for a meaningful answer, at least you need to tell what map you use, otherwise you'll get some spam. Pavel
Re: [ccp4bb] Confusion about space group nomenclature
Upon further contemplation: Someone who builds a right-handed helix into a left-handed map is an enantiopath. Enantiopathy can be treated with Enantiomab ® although some people prefer a daily dose of enantiostatins. These generics are made by Irratiopharm. BR
Re: [ccp4bb] Confusion about space group nomenclature
On 21 April 2014 21:57, Bernhard Rupp wrote: > > > So the point is to use a meaningful qualifier that, applied as an > adjective to a space group, describes what happens if that space group acts > on a chiral object. Now the ‘enantio’ creeps in: enantio means other, > opposite, and morphos, gestalt, form or so. (Where is Tassos when you need > him…) so: The adjective of those 65 who are "not possessing improper > rotations" as "enantiomorphic", is completely illogical. They are exactly > the ones which do NOT change the ‘morph’ of any ‘enantio’. They, > logically I maintain, are ‘non-enantiogen’ because they generate no > opposite. The 11 pairs of non-enantiogenic SGs that that exist however > indeed form enantiomorphic pairs, even as groups in absence of the need to > act on a (chiral) object. One then can argue, as Ian did, that they form > chiral pairs. However, that is not necessarily a justification to call > these individual SGs themselves chiral. > > To me, the only satisfactory statement is that the 65 space groups “not > possessing improper rotations” are non-enantiogenic, and 22 of them form > enantiomorphic pairs. None of them change the handedness of a chiral object. > Bernhard, Sorry ignore previous empty message (must have accidentally hit a keyboard shortcut for 'Send': Gmail should make it much harder to hit Send accidentally!). I was going to say that I didn't quite follow your argument. The point I was making in my reply was that 'enantiomorphic' refers to the unit cell contents, _not_ to merely the unit cell including its space-group symmetry elements, which is what I meant by 'space-group diagram'. The latter of course possesses the symmetry of the Cheshire group which has additionally symmetry elements, e.g. additional inversion centre and translational elements in many cases. 'Enantiomorphic' means "that for which an enantiomorph (non-superposable mirror image) exists". So the 65 space groups, including their unit-cell contents, are enantiomorphic by that definition, because there exists for each one an enantiomorph of the unit cell contents. We are after all talking only about a mirror-inverted image of an object not the mirror-inverted object (one can argue about whether an image in a mirror 'exists' since it's merely a mathematical construct). In fact in this sense there's no difference between enantiomorphic and chiral (since that also means "having a non-superposable mirror image"). The fact that the enantiomorph (i.e. with D-amino acids and left-handed alpha helices) can't actually exist in Nature is irrelevant, the point is that it's only a mathematical construct. As I said there's really no distinction between 'enantiomorphic' and 'chiral'. However in the sense in which 'chiral' is being used to described the 11, it is clearly being applied to the space-group diagram only, so the space-group diagrams for P1, P21, P212121, P4, P622 etc. are achiral (and non-enantiomorphic in this limited sense), whereas those for P31, P41212 etc are chiral (and enantiomorphic). The unit-cell contents are in all these cases enantiomorphic in the wider sense defined above. This is why I said you need to take care about what objects the words are describing: enantiomorphic and chiral mean the same but they are being used to desscribe 2 different objects! Cheers -- Ian
Re: [ccp4bb] anomalous signal for Mg and Calcium
Further to what Nat wrote which I completely agree with, you should tell us the following: 1. Expecting signal of a Calcium atom and expected signal of a Magnesium atom. 2. Are there any intrinsic anomalous scatterers in the structure that you trust such as sulfurs from methionines and cysteines or even selenium at selenomethionines? What are their expected signals and do you see those signals? If not, why not? Basically, these should give one a positive control which they can check their experiment with. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Faisal Tarique [faisaltari...@gmail.com] Sent: Monday, April 21, 2014 5:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] anomalous signal for Mg and Calcium Dear all Just in the continuation ...
Re: [ccp4bb] anomalous signal for Mg and Calcium
On Mon, Apr 21, 2014 at 3:36 PM, Faisal Tarique wrote: > Just in the continuation of my previous mail i again want to ask few > question on the metalloprotiens..Apart from factors like occupancy, B > factor, coordination sphere and metal ion-ligand distances to distinguish > Mg or calcium, can anomalous signal tell the identity and the type of > metal ion bound to the protein, specifically in the case of Mg and Calcium. > Short answer: if you see a peak in the anomalous difference map, it's almost certainly calcium, but if you don't see a peak, you still can't rule out calcium. Longer answer: magnesium almost never has observable anomalous signal at the wavelengths we normally use for data collection. The exception is if you collect extremely redundant data; Wayne Hendrickson has a very convincing example of this (I saw it in a talk, but I'll see if I can find a reference). Calcium anomalous signal depends on the data quality, but with good data and full occupancy it can show up in the anomalous difference map even at the SeMet K edge (~0.9794Å). However, this is not guaranteed, especially if it's not very tightly bound. At 2.6Å resolution it may be more difficult to distinguish, especially if you have other stronger anomalous scatterers. Collecting very redundant data will help a lot. .An anomalous data analyzed through Xtriage (phenix) gives a signal of > 0.097 with Magnesium while the same gives a signal of 0.1062 with Caclium ( > both data sets showing Anomalous flag as true )..can anybody shed some > light on which is more true ?? > I don't understand this - what exactly is the difference between the datasets? Anyway, that number is really not intended to be interpreted this way. > the data has maximum resolution of 2.6A and i had kept Mg atom at the > active site ( protein was incubated with 5mM MgCl2)..just because it is > not matching a typical octahedral geometry and exact metal ion-oxygen > distance as represented by Cambridge structural database (CSD) my reviewer > has asked me to check anomalous signal for both Mg and Ca and ( he is > expecting that scattering metal ion it to be Ca ) give appropriate reason > for putting Mg there..please give suggestions. > In addition to the anomalous maps, check the difference map (Fo-Fc) and B-factors after refinement with either element at full occupancy. If it is correctly identified, the difference map should be relatively flat and the B-factor should be similar to the coordinating atoms. Negative difference map peaks and/or a high B-factor suggest that the element is too heavy; positive peaks and/or low B-factors indicate the opposite. -Nat
[ccp4bb] anomalous signal for Mg and Calcium
Dear all Just in the continuation of my previous mail i again want to ask few question on the metalloprotiens..Apart from factors like occupancy, B factor, coordination sphere and metal ion-ligand distances to distinguish Mg or calcium, can anomalous signal tell the identity and the type of metal ion bound to the protein, specifically in the case of Mg and Calcium..An anomalous data analyzed through Xtriage (phenix) gives a signal of 0.097 with Magnesium while the same gives a signal of 0.1062 with Caclium ( both data sets showing Anomalous flag as true )..can anybody shed some light on which is more true ?? the data has maximum resolution of 2.6A and i had kept Mg atom at the active site ( protein was incubated with 5mM MgCl2)..just because it is not matching a typical octahedral geometry and exact metal ion-oxygen distance as represented by Cambridge structural database (CSD) my reviewer has asked me to check anomalous signal for both Mg and Ca and ( he is expecting that scattering metal ion it to be Ca ) give appropriate reason for putting Mg there..please give suggestions.. your help would be greatly appreciated -- Regards Faisal School of Life Sciences JNU
[ccp4bb] Trouble Refining Ligand in Phenix
Hi Everyone, I am trying to refine a structure with a phosphorylated amino acid. After refining in Phenix, the Fo-Fc density (green) overlaps the 2Fo-Fc density for all atoms of the derivatized amino acid in Coot, almost as if I had not built in the residue. I am loading a .cif for the derivative when I run phenix.refine. I have also tried ReadySet, but when I click the "Run in phenix.refine" button, I see the message Error interpreting command line argument as parameter definition: "refine_65-coot-2.metal.edits" RuntimeError: Unexpected end of output. Am I just seeing noise, or is Phenix not actually refining this portion of the model? I would appreciate any suggestions. Best, Chris
Re: [ccp4bb] Confusion about space group nomenclature
On 21 April 2014 21:57, Bernhard Rupp wrote: > > > So the point is to use a meaningful qualifier that, applied as an > adjective to a space group, describes what happens if that space group acts > on a chiral object. Now the ‘enantio’ creeps in: enantio means other, > opposite, and morphos, gestalt, form or so. (Where is Tassos when you need > him…) so: The adjective of those 65 who are "not possessing improper > rotations" as "enantiomorphic", is completely illogical. They are exactly > the ones which do NOT change the ‘morph’ of any ‘enantio’. They, > logically I maintain, are ‘non-enantiogen’ because they generate no > opposite. The 11 pairs of non-enantiogenic SGs that that exist however > indeed form enantiomorphic pairs, even as groups in absence of the need to > act on a (chiral) object. One then can argue, as Ian did, that they form > chiral pairs. However, that is not necessarily a justification to call > these individual SGs themselves chiral. > > To me, the only satisfactory statement is that the 65 space groups “not > possessing improper rotations” are non-enantiogenic, and 22 of them form > enantiomorphic pairs. None of them change the handedness of a chiral object. > > > > Common use seems to be illogically “enantiomorphic” for the 65, and > semi-illogical, “chiral” for the 22 forming the 11 em pairs. Is that what > everybody including IUCr agrees upon? What does the ACA Standards > commission have to say? Who has an authoritative answer? Let there be light. > > > > Cheers, BR > > > > > > *From:* Ian Tickle [mailto:ianj...@gmail.com] > *Sent:* Sunday, April 20, 2014 4:52 PM > *To:* b...@hofkristallamt.org > *Cc:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Confusion about space group nomenclature > > > > > Hi Bernhard > > My understanding, gleaned from ITC-A and ITC-B is that the 65 space groups > listed here: http://www.ccp4.ac.uk/dist/html/alternate_origins.html that > I assume you are referring to, are "enantiomorphic", which is defined as > "not possessing improper rotations" (see > http://pd.chem.ucl.ac.uk/pdnn/symm2/enantio1.htm). The non-superposable > mirror image of a chiral object is called its enantiomorph, from Latin > meaning "opposite form". The chiral object by itself is one of a pair of > enantiomers, each being the enantiomorph of the other. > > You need to be clear when talking about chirality whether you are > referring to the space-group (or point-group) diagrams or to the contents > of the unit cell. Not all the 65 enantiomorphic space group diagrams are > chiral, even though the unit cells may be (you can have a > non-enantiomorphic molecule crystallising in an enantiomorphic space group, > but not vice versa). > > For example no triclinic, monoclinic or orthorhombic enantiomorphic SG > diagrams are chiral (they are superposable on their mirror images), so > enantiomorphic space group diagrams such as those of P1, P2, P21, P222, > P212121 etc. do not have enantiomorphs (they can be regarded as their own > enantiomorphs). However enantiomorphic space group diagrams containing 3, > 4 or 6-fold screw axes are all chiral so do have enantiomorphs, e.g. there > are enantiomorphic pairs P31 & P32, P41 & P43, P41212 & P43212 etc. > > HTH! > > Cheers > > -- Ian > > > > On 20 April 2014 00:35, Bernhard Rupp wrote: > > Hi Fellows, > > > > because confusion is becoming a popular search term on the bb, let me > admit to one more: > > What is the proper class name for the 65 space groups (you know, those): > > > > Are > > (a)these 65 SGs the chiral SGs and the 22 in the 11 enantiomorphic > pairs the enantiomorphic SGs? > > Or > > (b) the opposite? > > > > In other words, is (a) enantiomorphic a subclass of chiral or (b) chiral > a subclass of enantiomorphic? > > Small molecule crystallography literature seems to tend to (b) whereas in > macro I often find (in terms of number of class members) chiral > > enantiomorphic. Interestingly, did not find an authoritative definition in > ITC-A. > > > > Logical is neither. The 65 are perhaps enantiostatic because they do not > change handedness (as opposed to enantiogen), and the 22 are enantiodyadic > (or so). I am sure Tassos will enlighten us on that one…. > > > > So, (a) or (b) or ? > > > > Happy Easter, BR > > > > > > > > >
Re: [ccp4bb] Confusion about space group nomenclature
Hi Fellows, thanks for the comments. Some of them agree with what I found through more (small mol) literature search. Let me explain why I am pestilent about this: If people who are already in the know use a weird term but have common understanding what it means, be it. If I introduce it in a textbook or introductory article, not so. It needs to make sense to someone who hears this term the first time. As it stopped making sense to me, I guess they’d be confused too. An important point made, was to distinguish between objects that can be chiral (i.e. have a certain defined handedness, χείρ cheir, hand), and space groups, which inherently are just a mathematical concept and in essence a set of instructions of how to deal with an object, and not chiral themselves. Ian’s space group diagrams, in contrast, are objects and they can display chirality and not be superimposable (i.e. superimpossible?). Space groups just act upon objects, be they chiral or not. So the point is to use a meaningful qualifier that, applied as an adjective to a space group, describes what happens if that space group acts on a chiral object. Now the ‘enantio’ creeps in: enantio means other, opposite, and morphos, gestalt, form or so. (Where is Tassos when you need him…) so: The adjective of those 65 who are "not possessing improper rotations" as "enantiomorphic", is completely illogical. They are exactly the ones which do NOT change the ‘morph’ of any ‘enantio’. They, logically I maintain, are ‘non-enantiogen’ because they generate no opposite. The 11 pairs of non-enantiogenic SGs that that exist however indeed form enantiomorphic pairs, even as groups in absence of the need to act on a (chiral) object. One then can argue, as Ian did, that they form chiral pairs. However, that is not necessarily a justification to call these individual SGs themselves chiral. To me, the only satisfactory statement is that the 65 space groups “not possessing improper rotations” are non-enantiogenic, and 22 of them form enantiomorphic pairs. None of them change the handedness of a chiral object. Common use seems to be illogically “enantiomorphic” for the 65, and semi-illogical, “chiral” for the 22 forming the 11 em pairs. Is that what everybody including IUCr agrees upon? What does the ACA Standards commission have to say? Who has an authoritative answer? Let there be light. Cheers, BR From: Ian Tickle [mailto:ianj...@gmail.com] Sent: Sunday, April 20, 2014 4:52 PM To: b...@hofkristallamt.org Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Confusion about space group nomenclature Hi Bernhard My understanding, gleaned from ITC-A and ITC-B is that the 65 space groups listed here: http://www.ccp4.ac.uk/dist/html/alternate_origins.html that I assume you are referring to, are "enantiomorphic", which is defined as "not possessing improper rotations" (see http://pd.chem.ucl.ac.uk/pdnn/symm2/enantio1.htm). The non-superposable mirror image of a chiral object is called its enantiomorph, from Latin meaning "opposite form". The chiral object by itself is one of a pair of enantiomers, each being the enantiomorph of the other. You need to be clear when talking about chirality whether you are referring to the space-group (or point-group) diagrams or to the contents of the unit cell. Not all the 65 enantiomorphic space group diagrams are chiral, even though the unit cells may be (you can have a non-enantiomorphic molecule crystallising in an enantiomorphic space group, but not vice versa). For example no triclinic, monoclinic or orthorhombic enantiomorphic SG diagrams are chiral (they are superposable on their mirror images), so enantiomorphic space group diagrams such as those of P1, P2, P21, P222, P212121 etc. do not have enantiomorphs (they can be regarded as their own enantiomorphs). However enantiomorphic space group diagrams containing 3, 4 or 6-fold screw axes are all chiral so do have enantiomorphs, e.g. there are enantiomorphic pairs P31 & P32, P41 & P43, P41212 & P43212 etc. HTH! Cheers -- Ian On 20 April 2014 00:35, Bernhard Rupp wrote: Hi Fellows, because confusion is becoming a popular search term on the bb, let me admit to one more: What is the proper class name for the 65 space groups (you know, those): Are (a)these 65 SGs the chiral SGs and the 22 in the 11 enantiomorphic pairs the enantiomorphic SGs? Or (b) the opposite? In other words, is (a) enantiomorphic a subclass of chiral or (b) chiral a subclass of enantiomorphic? Small molecule crystallography literature seems to tend to (b) whereas in macro I often find (in terms of number of class members) chiral > enantiomorphic. Interestingly, did not find an authoritative definition in ITC-A. Logical is neither. The 65 are perhaps enantiostatic because they do not change handedness (as opposed to enantiogen), and the 22 are enantiodyadic (or so). I am sure Tassos will enli
Re: [ccp4bb] Phenix composite omit map
Hi Chen, I will answer you on the phenix mailing list! All the best, Tom T On Apr 21, 2014, at 10:53 AM, Chen Zhao wrote: Dear all, Hello! I am now running into a simple technical problem but I just cannot figure it out. I am trying to create a composite omit map by phenix, but when I typed in the command phenix.composite_omit_map XXX.eff based on the instructions on http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm, I got the error message "command not found". Could anybody help me out? Thank you so much in advance! Sincerely, Chen
[ccp4bb] Phenix composite omit map
Dear all, Hello! I am now running into a simple technical problem but I just cannot figure it out. I am trying to create a composite omit map by phenix, but when I typed in the command phenix.composite_omit_map XXX.eff based on the instructions on http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm, I got the error message "command not found". Could anybody help me out? Thank you so much in advance! Sincerely, Chen
Re: [ccp4bb] scaling HKL2000
1. You should always use the absorption correction (your previous e-mail). 2. The statistics are bad because the crystal was not cryoprotected properly -- data are contaminated with ice. You need to decrease the box size during data integration to 24 x 24 mm. This will result in rejecting ice-affected reflections. Dominika Monica Mittal wrote: > Dear all > I need an advice at the part of scale.log file that i am attaching herewith > this mail that do i have to compromise the resolution as I/sig and Rsymm seem to be bad in resolution shell 2.3 to 2.18. > Kindly suggest > Thanx > Monica Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-6378 (phone) *** 214-645-6353 (fax)
Re: [ccp4bb] coot problems to decrease R FREE
Dear Peter, > I'm a novice of coot and ccp4. Now I'm doing refinement using both refmac5 > and coot.Here are some problems I'm facing. Really hope you can give me > some suggestions. > > 1、THE RESOLUTION OF THE DATA IS 2.5 angstrom. After first refinement of > refmac5 I got R factor which is 0.26 and R FREE which is 0.31. My question is > what the final R factor and R FREE should be after several rounds of > refinement by refmac5 and coot. As low as it can reasonably be. Which is of course a lousy target but the purpose of model refinement is to make it as good as possible, not to achieve a certain R-free. That said, at this resolution, the PDB average is about 25% for R-free. > 2、At which map level（e/A3 or rmsd）should I refine the data by coot? You refine against the whole map, but for viewing purposes you should change the map contour level during building. For the majority of the map you should be able to see stuff well above an rmsd of 1.0 for the 2mFo-DFc map. At the difficult bits you may need to go below 1.0, but no so low that you can fool yourself. The proper height for the difference map depends as a bit on the situation. I usually just turn it down until obvious noise peaks (small negative peaks in the solvent) appear. That typically ends up somewhere between 3 and 4 rmsd. > 3、Can you give me some tips and strategies about how to use coot to > decrease R free? now I just use some basic tricks such as fit density and > Ramachandran plot to refine the data. This is what I do for your kind of resolution: set the weight for refinement in COOT to 50 or 40 (the default is 60) and switch on torsion restraints and possibly Ramachandran restraints. Then I go through the entire structure residue by residue (space bar) refining windows of three residues (with the 't' key) and fixing everything that I can (that includes obvious solvent molecules). Symmetry should always be switched on and NCS ghosts (if available too). When that is done you can focus on the remaining difficult bits by looking at the difference map peaks in COOT and at validation reports from WHAT_CHECK, and MolProbity. So now for the bit where I plug my own stuff: you can try PDB_REDO (http://xtal.nki.nl/PDB_REDO for the server, there is also a stand-alone version) to take a lot of work out of your hands. It optimises your refinement in Refmac and, rebuilds side-chain and tries to find peptide flips that improve you Ramachandran plot and fit with the maps. You also get a lot of validation information that may help you with further rebuilding of your model. Cheers, Robbie > > > Best regards, > > > Peter Chen >
[ccp4bb] scaling HKL2000
Dear all I need an advice at the part of scale.log file that i am attaching herewith this mail that do i have to compromise the resolution as I/sig and Rsymm seem to be bad in resolution shell 2.3 to 2.18. Kindly suggest Thanx Monica Shell Lower Upper Average Average Norm. Linear Square limitAngstrom I error stat. Chi**2 R-fac R-fac 50.00 5.70 9015.9 157.865.3 9.801 0.052 0.060 5.70 4.52 7052.3 122.654.8 8.818 0.057 0.068 4.52 3.95 5642.499.745.9 8.667 0.060 0.068 3.95 3.59 3592.280.450.3 13.981 0.088 0.090 3.59 3.33 2111.747.931.7 9.035 0.095 0.101 3.33 3.14 1499.236.525.5 6.179 0.090 0.095 3.14 2.98 904.428.722.8 4.657 0.100 0.099 2.98 2.85 641.625.622.0 3.632 0.112 0.105 2.85 2.74 460.824.021.5 2.986 0.126 0.110 2.74 2.65 340.823.021.4 2.710 0.151 0.131 2.65 2.56 254.522.521.4 2.060 0.168 0.126 2.56 2.49 201.622.621.9 2.371 0.213 0.644 2.49 2.42 181.223.422.7 1.851 0.235 0.173 2.42 2.37 126.723.723.3 1.517 0.305 0.224 2.37 2.31 126.725.224.8 1.488 0.323 0.203 2.31 2.26-7.233.132.9 1.725 0.000 0.218 2.26 2.22 1648.671.362.6 43.073 0.234 0.350 2.22 2.18 -59.734.934.9 1.599 0.000 0.376 2.18 2.1465.929.429.2 0.986 0.607 0.324 2.14 2.1058.730.029.9 0.904 0.660 0.413 All reflections 1700.447.432.3 5.069 0.080 0.074
