Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
Although Zby's remarks re precision are beyond my original bewilderment about listed zepto-meter range digits (sans precision measure), I wonder whether the argument that we have so many data and thus a quite high precision (n.b. not accuracy) can be attained, is perhaps somewhat optimistic. What we measure or assign as a 'spot' is largely predetermined by various integration, profile, box selection, etc, parameters and whatever does not fit that spot model cannot be properly accounted for. I therefore argue that any precision estimate is probably biased towards optimism by the limitations of the particular reflection spot model. Most reflection 'spots' are dirty little creatures with tentacles, fuzz, bumps, etc In the listed mmCIF case the senseless printing of double precision format was actually the simple point to be made. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zbyszek Otwinowski Sent: Dienstag, 22. Juli 2014 23:49 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Protein Crystallography challenges Standard Model precision The least-square procedure for unit cell parameter refinement provides very precise estimates of uncertainty. Why they are so precise? Because we use many thousands of unmerged reflections to determine the precision 1 to 6 parameters (unit cell parameters). However, although error propagation through the least squares provides precision of about 0.001 A, or better in some cases, this is only precision not accuracy, and the precision is calculated typically with respect to the unit cell parameters averaged across the exposed volume of a crystal. In practice, the range of unit cell parameters within a crystal can be quite broad, and when we consider accuracy it is not clear, which unit cell parameters should be a reference point. Typically, the distribution of unit cell parameters in a crystal will not follow Gaussian distribution. Therefore, the accuracy of unit cell parameters determination is not well defined, even when we know the experimental conditions very well and propagate experimental uncertainties correctly. Variability of unit cell parameters can be quite high for data sets from different samples. However, description of this variability is typically not related to the very high precision of determination of unit cell parameters for an individual sample. Zbyszek On 07/22/2014 12:33 PM, Tim Gruene wrote: Dear Zbyszek, when you optimise a set of parameters against a set of data, I guess you can also provide their errors. If I understand correctly, this comes with least-squares-routines. I only pointed out that cell errors are listed in the XDS output (provided you refine them, of course). I am sure those errors are well defined. Best wishes, Tim On 07/22/2014 06:53 PM, Zbyszek Otwinowski wrote: Error estimates for the unit cell dimensions in macromolecular crystallography belong to atypical category of uncertainty estimates. Random error contribution in most cases is below 0.001A, so it can be neglected. Wavelength calibration error can be also made very small; however, I do not know how big it is in practice. Goniostat wobble error is taken into account in Scalepack refinement. Crystal-to-detector distance is not used in postrefinement/global refinement. Due to the measurement error being very small, even small variations in unit cell parameters can be detected within cryocooled crystals. These variations almost always are _orders_of_magnitude_larger_ than measurement uncertainty. Current practise is not to investigate the magnitude of the changes in the unit cell parameters, but when beam smaller than crystal is used, observing variations as large as 1A is not unusual. The main question is: what the unit cell uncertainty means? For most samples I could defend to use values: 0.001A, 0.01A, 0.1A and 1A as reasonable, depending on particular point of view. Without defining what the unit cell uncertainty means, publishing its values is pointless. Zbyszek Otwinowski Hi Bernhard, A look at the methods section might give you a clue. Neither XDS nor XSCALE create mmCIF - files (you are talking about mmCIF, not CIF - subtle, but annoying difference), so that the choice is limited. I guess some programmer (rather than a scientist ;-) )used a simple printf commmand for a double precision number so the junk is left over from the memory region or other noise common to conversions. XDS actually prints error estimates for the cell dimensions in CORRECT.LP which could be added to the mmCIF file - a cif (sic!) file, I believe, requires those, by the way and checkCIF would complain about their absence. Cheers, Tim On 07/22/2014 01:01 PM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0
[ccp4bb] correlated alternate confs - validation?
Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups' geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar. occupancy refine AfaIct this does what I want. True? Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 mailto:b...@ruppweb.org b...@ruppweb.org mailto:b...@hofkristallamt.org b...@hofkristallamt.org http://www.ruppweb.org/ http://www.ruppweb.org/ ---
Re: [ccp4bb] correlated alternate confs - validation?
Hi Bernhard, The validation of alternates is indeed quite poor and any improvements would probably depend on proper annotation by the depositor, particularly in complex correlated cases. For your model I would probably make the two waters alternates of each other. That way, it is easier to select out one of the two alternate conformations. Cheers, Robbie Sent from my Windows Phone Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups' geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar. occupancy refine AfaIct this does what I want. True? Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 mailto:b...@ruppweb.org b...@ruppweb.org mailto:b...@hofkristallamt.org b...@hofkristallamt.org http://www.ruppweb.org/ http://www.ruppweb.org/ ---
Re: [ccp4bb] Off-Topic Q / X Ray FLuoresence Scan Vs XANES
Dear Tarek There are several things to consider: 1-At an MX beamline the X-ray fluorescence (XRF) scans are usually used to define good energies for measurement of anomalous data. While XANES and XRF in general are similar techniques, they are used for very different applications. This said, it would in principal be possible to do these experiments at an MX beamline. However, in real-life the resolution of both the monochromator and the detector(s) will most likely not be sufficient to obtain high-resolution XANES data. Also, XANES usually employs evacuated endstations, a feature rarely seen at MX beamlines. Another factor is the uncalibrated detectors. In MX we usually take raw counts as an arbitrary signal for the scans. In Xanes you are interested in absolute values calibrated towards the incident photon flux (I0). 2-f'' is in fact directly proportional to the measured signal, but it is not exactly a fit. It's relation to f' is defined by the Kramers-Kronig relation: http://skuld.bmsc.washington.edu/scatter/AS_kk.html 3-as mentioned before, the data most likely will not be of high enough quality for these estimations. Also you would have to measure reference data of defined oxidation states at the exact same setup. If you are interested in these kinds of experiments you should preferably apply for beamtime at an dedicated instrument, preferably at a synchrotron where you can also use an MX beamline. Best, Florian __ Paul Scherrer Institut Florian Dworkowski Beamline Scientist X10SA WSLA/219 CH-5232 Villigen PSI Telefon: +41 56 310 35 84 E-Mail: florian.dworkow...@psi.ch From: Tarek DawoD [mailto:tkda...@yahoo.com] Sent: Dienstag, 22. Juli 2014 22:40 Subject: Off-Topic Q / X Ray FLuoresence Scan Vs XANES Doing Fluroscence scan for protein crystal at Cu wavelength prior MAD or SAD experiment shows usually fig like this https://www.dropbox.com/s/800463dlcmws6d4/fig.png 1- Fig A should represent X ray fluorescence scan. is it the same as X ray absorption scan. what does count represent in fig A (is it equal to the intensity of the emission). 2- i am wondering whether F double prime in Fig B is just a fit for counts in Fig A, it looks the same. could F or counts be converted to I/I0 or F/I0 to replot the data against these value as in XANES. in other word, Is X ray fluorescence scan in fig A the same as X-ray absorption near-edge structure (XANES)? could XANES be collected at the same beamline where diffraction data are collected for crystal ? 3- could data from Fluorescence scan in Fig A or B used to determine the oxidation or coordination number for the metal say copper for example in protein? thank YOU regards T. DawoD
Re: [ccp4bb] protein crystals?
Dear Atul, I suggest to run SDS-PAGE with your crystals. You can even use micro-crystalline precipitate that you probably have from optimization stage. May be protein dissociated into subunits in the crystallization conditions. But I am not sure because I know nothing about your protein. Also, how do you cryoprotect crystals? 22.07.2014 16:18, Atul Kumar пишет: Hi all, I am trying to crystallize 92 Kda protein. I have got crystals in Znso4, crystals are sensitive to radiation and died after few frames. Unit cell parameters are a=94.53, b=11.49, c=39.69 (90, 102.3, 90) in C2 space group (as suggested by mosflm). I tried to calculate mathews coeff and it seems like only 10 kda protein can fit in the given unit cell dimension with 44% solvent. Crystal appear in o/n and they have sharp edges but after that I notice perturbation to crystal shape in the drop. I was wondering whether I have crystals of degraded protein or it is because of the poor latices? I have also attached the image of diffraction pattern. I would be happy to get useful suggestions. thanks regards Atul -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osi...@gmail.com
Re: [ccp4bb] ICCBM15 workshop completely full / overbooked
As far as the *ICCBM15 pre-conference workshop* is concerned (consisting of short presentations, practical demonstrations and hands-on exercises taught by an international team of experts), the workshop is already completely overbooked. Students, postdocs and scientists interested in the latest crystal-growth methodologies and advances in serial crystallography, neutron diffraction and other exciting techniques can still *join ICCBM15* (Sep. 17 - 20, Hamburg, www.iccbm15.org) but also here the number of free places is steadily decreasing, so better sign up sooner than later. Chairpersons: Christian Betzel and Jeroen Mesters
[ccp4bb] CCP4-6.4.0 Update 020
Dear CCP4 Users An update for the CCP4-6.4.0 series has just been released, consisting of the following changes • crank: – bug fix in bp3 – update to overcome OMP problem • ctruncate: – update to 1.15.9 • aimless: – update to 0.3.7 • pointless: – update to 1.9.11 – fix for inconsistency in number of reflections read from XDS_ASCII.hkl wrt XSCALE • blend: – update to 0.5.3 • ample: – update to accommodate new MrBUMP – fix for results table – new interface options • mrbump: – minor fix to the fasta search option Note that auto-updates work only with CCP4 6.4.0 series, therefore please upgrade if necessary. The Update Manager is now included in the package so you do not need to install it separately. In addition, all available updates will be installed automatically if you are using Setup Manager for CCP4 installation. Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk. Many thanks for using CCP4. The CCP4 Core Team -- Scanned by iCritical.
Re: [ccp4bb] correlated alternate confs - validation?
I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups’ geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar… occupancy refine AfaIct this does what I want. True? Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ ---
Re: [ccp4bb] correlated alternate confs - validation?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups’ geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar… occupancy refine AfaIct this does what I want. True? Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ --- - -- - -- 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/ iD8DBQFTz7qjUxlJ7aRr7hoRAs9cAKD4LFul9cmKYgsV5n6o3LZqTgHI6wCfZ4fS 2CdyyS0zWMjryhZrwgA2mZk= =iogi -END PGP SIGNATURE-
Re: [ccp4bb] correlated alternate confs - validation?
?? Refmac knows because of the group definition, otherwise I cannot force grouped occupancy refinement. There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of (whatever) residue/water. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] correlated alternate confs - validation? -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar occupancy refine AfaIct this does what I want. True? -- -- Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ -- - - -- - -- 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/ iD8DBQFTz7qjUxlJ7aRr7hoRAs9cAKD4LFul9cmKYgsV5n6o3LZqTgHI6wCfZ4fS 2CdyyS0zWMjryhZrwgA2mZk= =iogi -END PGP SIGNATURE-
Re: [ccp4bb] correlated alternate confs - validation?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, That's right, the definition is not in the PDB, but REFMAC sensibly handles it this way. It is certainly a short-coming if not bug in the PDB (definition). Best, Tim On 07/23/2014 04:49 PM, Bernhard Rupp wrote: ?? Refmac knows because of the group definition, otherwise I cannot force grouped occupancy refinement. There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of (whatever) residue/water. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] correlated alternate confs - validation? Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar occupancy refine AfaIct this does what I want. True? -- - -- Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ -- - - - -- - -- 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/ iD8DBQFTz85KUxlJ7aRr7hoRAoeqAKCGBTg8nowXCCFfbp9kfZsCYr2fHgCgoJhp CPPMzM1r6DEZv2DJi4vwXmI= =bMXr -END PGP SIGNATURE-
Re: [ccp4bb] correlated alternate confs - validation?
I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 23 Jul 2014, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, That's right, the definition is not in the PDB, but REFMAC sensibly handles it this way. It is certainly a short-coming if not bug in the PDB (definition). Best, Tim On 07/23/2014 04:49 PM, Bernhard Rupp wrote: ?? Refmac knows because of the group definition, otherwise I cannot force grouped occupancy refinement. There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of (whatever) residue/water. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] correlated alternate confs - validation? Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar occupancy refine AfaIct this does what I want. True? -- - -- Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ -- - - - -- - -- 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/ iD8DBQFTz85KUxlJ7aRr7hoRAoeqAKCGBTg8nowXCCFfbp9kfZsCYr2fHgCgoJhp CPPMzM1r6DEZv2DJi4vwXmI= =bMXr
Re: [ccp4bb] correlated alternate confs - validation?
On Wed, Jul 23, 2014 at 3:25 AM, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: The practice at the PDB after deposition used to be to remove water alternate position indicators - although obviously to keep their partial occupancies. This has not been my experience - see for example: http://www.rcsb.org/pdb/files/2GKG.pdb which was deposited as a PDB file, not mmCIF. -Nat
[ccp4bb] AW: [ccp4bb] correlated alternate confs - validation?
One could check if the alternate conformations are part of a continuous alternate zone or if they make contact (no contact, no association). However, I think it is time to abandon the PDB format and move to cif or some other format. My 2 cents, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances C. Bernstein Gesendet: Mittwoch, 23. Juli 2014 17:20 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 23 Jul 2014, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, That's right, the definition is not in the PDB, but REFMAC sensibly handles it this way. It is certainly a short-coming if not bug in the PDB (definition). Best, Tim On 07/23/2014 04:49 PM, Bernhard Rupp wrote: ?? Refmac knows because of the group definition, otherwise I cannot force grouped occupancy refinement. There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of (whatever) residue/water. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] correlated alternate confs - validation? Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar occupancy refine AfaIct this does what I want. True? -- - -- Bernhard Rupp
Re: [ccp4bb] correlated alternate confs - validation?
An additional problem is existence of alternative conformations close to rotational axis that violate crystal symmetry. If we want to describe such correlated alternative configurations, we need to describe also how they transform by such rotational axis. This problems may also exists also for other packing contacts; however, for conformations close to rotational axis, symmetry operator cannot preserve conformer ID, and this issue cannot be avoided. Zbyszek Otwinowski I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groupsâ geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar⦠occupancy refine AfaIct this does what I want. True? Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ --- Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
[ccp4bb] Accuracy and precision of unit cell parameters
Dear Colleagues, Stimulated by Bernhard's posting, and whilst certainly beyond his sense of bewilderment, I recalled that there were studies on this issue. These are neatly summarised in the Topical review :- http://dx.doi.org/10.1107/S01087681269X By Frank Herbstein in Acta Cryst B I imagine colleagues will find this of interest. Best wishes, John Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol. Chair School of Chemistry, University of Manchester, Athena Swan Team. http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
Re: [ccp4bb] correlated alternate confs - validation?
I think there has been historically some glitch in the deposition of some refmac altloc waters So for example 4a9x from Buster is annotated correctly REMARK 3 PROGRAM : BUSTER 2.11.2 HETATM 9407 O HOH A2517 -22.429 1.144 -35.218 1.00 29.73 O HETATM 9408 O AHOH A2518 -18.933 -9.507 -28.753 0.50 3.00 O HETATM 9409 O BHOH A2518 -20.467 -9.093 -29.900 0.50 16.03 O so the A and B altloc retained. But for example in 4ac7 REMARK 3 PROGRAM : REFMAC 5.6.0117 where these two waters look like they originally were deposited as altloc waters HETATM 6205 O HOH A2043 -3.612 86.934 100.843 0.50 25.12 O ANISOU 6205 O HOH A2043 2630 2166 4747 -153 68 1496 O HETATM 6206 O HOH A2044 -3.506 85.122 100.190 0.50 22.20 O ANISOU 6206 O HOH A2044 3710 2476 2248862188 16 O and these two HETATM 6328 O HOH B2073 -1.182 117.989 73.544 0.50 15.63 O ANISOU 6328 O HOH B2073 2509 1684 1745408173289 O HETATM 6329 O HOH B2074 -0.561 117.641 72.161 0.50 14.37 O ANISOU 6329 O HOH B2074 2023 1187 2247107123 -211 O These waters also end up being annotated as close contacts in Remark 500 - which would not have happened if they had retained their altlocs. REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. ... REMARK 500 OHOH A 2043 OHOH A 2044 1.93 REMARK 500 OHOH B 2073 OHOH B 2074 1.56 Probably other examples can be retrieved but this latter file dates from my time at the PDBe and so may have been mangled at my hands. In my defence I think it is owing to the annotation step when the waters are renumbered to fit with the associated macromolecule N to C (for proteins). I think the script that was originally developed for this was not able to deal with waters with the same number but differing altlocs. Also alternate positions in this step can be associated with different residues by reason of being closer to one or other bit of chain. In this case they can have very different numbers - or chains. I think this can be handled better in the new mmCif-based annotation system with the cooperation of refinement program authors. all the best Martyn Martyn Symmons Cambridge Original message From : f...@bernstein-plus-sons.com Date : 23/07/2014 - 16:20 (GMTDT) To : CCP4BB@JISCMAIL.AC.UK Subject : Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 23 Jul 2014, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, That's right, the definition is not in the PDB, but REFMAC sensibly handles it this way. It is certainly a short-coming if not bug in the PDB (definition). Best, Tim On 07/23/2014 04:49 PM, Bernhard Rupp wrote: ?? Refmac knows because of the group definition, otherwise I cannot force grouped occupancy refinement. There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of (whatever) residue/water. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] correlated alternate confs - validation? Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
Where is it written that compactness of representation and accuracy/precision are the same thing? Is 1/3 more or less precise than 0.333 ? If mmCIF were a binary floating-point format file, there would be more decimal places in the precision of the stored value for the unit cell, despite fitting into only 4 bytes instead of the 13 bytes of text some seem offended to see below. Would that be better? Or worse? -James Holton MAD Scientist On 7/22/2014 4:01 AM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.org mailto:b...@ruppweb.org b...@hofkristallamt.org mailto:b...@hofkristallamt.org http://www.ruppweb.org/ ---
Re: [ccp4bb] correlated alternate confs - validation?
Dear Frances, I don't think that you can put the blame entirely on the 80 column limitation. The program SHELX76 was limited to 80 columns because the input came as punched cards. It introduced a simple concept, the /free variables/, that are frequently used to represent occupancies and can be used to to build complicated networks of disordered residues with interdependent occupancies. Restraints may be applied to linear sums of these free variables. Ever since, small molecule crystallographers have used this concept to refine the disorders that they frequently encounter. Best wishes, George On 07/23/2014 05:20 PM, Frances C. Bernstein wrote: I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 23 Jul 2014, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, That's right, the definition is not in the PDB, but REFMAC sensibly handles it this way. It is certainly a short-coming if not bug in the PDB (definition). Best, Tim On 07/23/2014 04:49 PM, Bernhard Rupp wrote: ?? Refmac knows because of the group definition, otherwise I cannot force grouped occupancy refinement. There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of (whatever) residue/water. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] correlated alternate confs - validation? Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar occupancy refine AfaIct this does what I want. True?
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
The representation is simply non-parsimonious. There is no meaning to the zepto-meter digits. Numquam ponenda est pluralitas sine necessitate. BR From: James Holton [mailto:jmhol...@lbl.gov] Sent: Wednesday, July 23, 2014 9:58 PM To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Protein Crystallography challenges Standard Model precision Where is it written that compactness of representation and accuracy/precision are the same thing? Is 1/3 more or less precise than 0.333 ? If mmCIF were a binary floating-point format file, there would be more decimal places in the precision of the stored value for the unit cell, despite fitting into only 4 bytes instead of the 13 bytes of text some seem offended to see below. Would that be better? Or worse? -James Holton MAD Scientist On 7/22/2014 4:01 AM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta 99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits . Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ ---
Re: [ccp4bb] AW: [ccp4bb] correlated alternate confs - validation?
An ad hoc kludge that is admittedly undesirable but at least does not break anything with the PDB format could be as was done e.g. with the TLS and NCS records - put the alternate group definitions into a REMARK record... Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Wednesday, July 23, 2014 5:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: [ccp4bb] correlated alternate confs - validation? One could check if the alternate conformations are part of a continuous alternate zone or if they make contact (no contact, no association). However, I think it is time to abandon the PDB format and move to cif or some other format. My 2 cents, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances C. Bernstein Gesendet: Mittwoch, 23. Juli 2014 17:20 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 23 Jul 2014, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, That's right, the definition is not in the PDB, but REFMAC sensibly handles it this way. It is certainly a short-coming if not bug in the PDB (definition). Best, Tim On 07/23/2014 04:49 PM, Bernhard Rupp wrote: ?? Refmac knows because of the group definition, otherwise I cannot force grouped occupancy refinement. There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of (whatever) residue/water. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] correlated alternate confs - validation? Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
Greetings all - My interest in the rest of the discussion of experimental precision and error notwithstanding, and at the risk of stating explicitly what some might consider obvious, it seems to me that no one has actually (intentionally) asserted that they have determined the unit cell to 10^-20 meter precision. Rather, I find it far more likely that some program just output the floating point representation of a 3-decimal-place number without a proper 3-decimal-place format string (something like `printf(“%f”, _cell.length_a)` instead of `printf(“%5.3f”, _cell.length_a)`, perhaps). The extra digits are the “noise” of floating point rounding error. Notice the repeating 9’s and 0’s after 3 decimal places in each of the values in question: _cell.entry_id 4c69 _cell.length_a 100.152000427 == 100.152 _cell.length_b 58.3689994812 == 58.369 _cell.length_c 66.5449981689 == 66.545 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 == 99.252 _cell.angle_gamma 90.0 Each of these “extra precise” numbers should simply have been output with only 3 decimal places. But I suppose this still doesn’t answer the original question of *which* program actually needs to be fixed. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jul 23, 2014, at 5:44 PM, Bernhard Rupp hofkristall...@gmail.commailto:hofkristall...@gmail.com wrote: The representation is simply non-parsimonious. There is no meaning to the zepto-meter digits. Numquam ponenda est pluralitas sine necessitate. BR From: James Holton [mailto:jmhol...@lbl.gov] Sent: Wednesday, July 23, 2014 9:58 PM To: b...@hofkristallamt.orgmailto:b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Protein Crystallography challenges Standard Model precision Where is it written that compactness of representation and accuracy/precision are the same thing? Is 1/3 more or less precise than 0.333 ? If mmCIF were a binary floating-point format file, there would be more decimal places in the precision of the stored value for the unit cell, despite fitting into only 4 bytes instead of the 13 bytes of text some seem offended to see below. Would that be better? Or worse? -James Holton MAD Scientist On 7/22/2014 4:01 AM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits.. Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.orgmailto:b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ --- This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
[ccp4bb] Post-doctoral position in Singapore at the Duke-NUS is available
Post-doctoral position in Singapore at the Duke-NUS is available A post-doctoral position is available at the laboratory of Shee-Mei Lok (http://www.loksheemeilab.com) in the emerging infectious disease program of the Duke-NUS. Duke-NUS graduate medical school situated in Singapore, is a global partnership between Duke University and the National University of Singapore. Projects undertaken by the post-doc will investigate the structure and function of important proteins contributing to the longevity and low rates of cancer in bats. Individuals with experience in crystallography, protein expression and purification are highly desirable. Interested individuals should send their CV, experience, research interest, and a list of three referees to Shee-mei Lok (sheemei@duke-nus.edu.sg)
[ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation?
Hello, A solution exists also for PDB records: As a consequence of a discussion with George which took place years ago, I have taken the liberty to extend the PDB record length of 80 characters and use additional characters to specify the group ID and their members list number and provided an interface to manipulate them. Thereby the PDB limitations were extended to adopt the SHELX philosophy of treating combined groups of any composition. ATOM 1 N GLY A 1 -31.334 -24.247 23.250 0.54 34.05 1A N 1 0 ATOM 2477 N GLY A 1 -29.650 -24.643 23.839 0.46 41.88 1B N 1 1 The records with our the group extension are not members of groups with partial occupancy. These two records shown are members of group ID 1, the atom in the first record belongs to group ID 1 members list number 0 and the second to group ID 1 and members list no 1. (The members lists begin with 0.) On Jul 24, 2014, at 1:02 AM, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances C. Bernstein Gesendet: Mittwoch, 23. Juli 2014 17:20 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS Jozef Stefan e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem. Mol. Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com
[ccp4bb] moleman2 install problem
Hi all, I’m trying to install a copy of moleman2 for my new Mac. (the version is 10.9.3). while I copy the osx_moleman2 from xutil directory I got the following message: The Finder can’t complete the operation because some data in “osx_moleman2” can’t be read or written. (Error code -36) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn
