Re: [ccp4bb] PyMOL v. Coot map 'level'
One cannot understand what is going on without knowing how this map was calculated. Maps calculated by the Electron Density Server have density in units of electron/A^3 if I recall, or at least its best effort to do so. This is what I was looking for! (i.e. what the units are) Thanks. :-) Yes, I'd downloaded the 2mFo-DFc map from the EDS, and got the same Coot v. PyMOL discrepancy whether or not I turned off the PyMOL map normalization feature. If you load the same map into Pymol and ask it to normalize the density values you should set your contour level to Coot's rmsd level. If you don't normalize you should use Coot's e/A^3 level. It is quite possible that they could differ by a factor of two. This was exactly the case. The map e/A^3 level (not the rmsd level) in Coot matched very well, visually, the map 'level' in PyMOL; they were roughly off by a factor of 2. I did end up also generating a 2mFo-DFc map using phenix, which fetched the structure factors of the model in which I was interested. The result was the same (i.e. PyMOL 'level' = Coot e/A^3 level ~ = 1/2 Coot's rmsd level) whether I used the CCP4 map downloaded from the EDS, or generated from the structure factors with phenix. Thanks All. Emily. Dale Tronrud On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote: Hello. I am struggling with an old question--old because I've found several discussions and wiki bits on this topic, e.g. on the PyMOL mailing list (http://sourceforge.net/p/pymol/mailman/message/26496806/ and http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the suggestions about how to fix the problem are not working for me, and I cannot figure out why. Perhaps someone here can help: I'd like to display (for beauty's sake) a selection of a model with the map about this selection. I've fetched the model from the PDB, downloaded its 2mFo-DFc CCP4 map, loaded both the map and model into both PyMOL (student version) and Coot (0.8.2-pre EL (revision 5592)), and decided that I would use PyMOL to make the figure. I notice, though, that the map 'level' in PyMOL is not equivalent to the rmsd level in Coot, even when I set normalization off in PyMOL. I expected that a 1.0 rmsd level in Coot would look identical to a 1.0 level in PyMOL, but it does not; rather, a 1.0 rmsd level in Coot looks more like a 0.5 level in PyMOL. Does anyone have insight they could share about the difference between how Coot and PyMOL loads maps? Maybe the PyMOL 'level' is not a rmsd? is there some other normalization factor in PyMOL that I should set? Or, perhaps there is a mailing list post out there that I've missed, to which you could point me. :-) Alternatively, does anyone have instructions on how to use Coot to do what I'm trying to do in PyMOL? In PyMOL I displayed the mesh of the 2Fo-Fc map, contoured at 1.0 about a 3-residue-long 'selection' like so: isomesh map, My_2Fo-Fc.map, 1.0, selection, carve=2.0, and after hiding everything but the selection, I have a nice picture ... but with a map at a level I cannot interpret in PyMOL relative to Coot :-/ Regards, Emily. -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlVo1L4ACgkQU5C0gGfAG10YkwCfROYPVXBK/pDS4z/zi5MNY1D+ nHIAnjOFiAkb6JbuIGWRWkBFDG5Xgc2K =hrPT -END PGP SIGNATURE-
Re: [ccp4bb] PyMOL v. Coot map 'level'
Hi Emilia et al., I tried to figure out the PyMOL vs. Coot normalization discrepancy a while ago. As far as I remember, PyMOL normalizes on the raw data array, while Coot normalizes across the unit cell. So if the data doesn't exactly cover the cell, the results might be different. Cheers, Thomas On 01 Jun 2015, at 11:37, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: One cannot understand what is going on without knowing how this map was calculated. Maps calculated by the Electron Density Server have density in units of electron/A^3 if I recall, or at least its best effort to do so. This is what I was looking for! (i.e. what the units are) Thanks. :-) Yes, I'd downloaded the 2mFo-DFc map from the EDS, and got the same Coot v. PyMOL discrepancy whether or not I turned off the PyMOL map normalization feature. If you load the same map into Pymol and ask it to normalize the density values you should set your contour level to Coot's rmsd level. If you don't normalize you should use Coot's e/A^3 level. It is quite possible that they could differ by a factor of two. This was exactly the case. The map e/A^3 level (not the rmsd level) in Coot matched very well, visually, the map 'level' in PyMOL; they were roughly off by a factor of 2. I did end up also generating a 2mFo-DFc map using phenix, which fetched the structure factors of the model in which I was interested. The result was the same (i.e. PyMOL 'level' = Coot e/A^3 level ~ = 1/2 Coot's rmsd level) whether I used the CCP4 map downloaded from the EDS, or generated from the structure factors with phenix. Thanks All. Emily. Dale Tronrud On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote: Hello. I am struggling with an old question--old because I've found several discussions and wiki bits on this topic, e.g. on the PyMOL mailing list (http://sourceforge.net/p/pymol/mailman/message/26496806/ and http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the suggestions about how to fix the problem are not working for me, and I cannot figure out why. Perhaps someone here can help: I'd like to display (for beauty's sake) a selection of a model with the map about this selection. I've fetched the model from the PDB, downloaded its 2mFo-DFc CCP4 map, loaded both the map and model into both PyMOL (student version) and Coot (0.8.2-pre EL (revision 5592)), and decided that I would use PyMOL to make the figure. I notice, though, that the map 'level' in PyMOL is not equivalent to the rmsd level in Coot, even when I set normalization off in PyMOL. I expected that a 1.0 rmsd level in Coot would look identical to a 1.0 level in PyMOL, but it does not; rather, a 1.0 rmsd level in Coot looks more like a 0.5 level in PyMOL. Does anyone have insight they could share about the difference between how Coot and PyMOL loads maps? Maybe the PyMOL 'level' is not a rmsd? is there some other normalization factor in PyMOL that I should set? Or, perhaps there is a mailing list post out there that I've missed, to which you could point me. :-) Alternatively, does anyone have instructions on how to use Coot to do what I'm trying to do in PyMOL? In PyMOL I displayed the mesh of the 2Fo-Fc map, contoured at 1.0 about a 3-residue-long 'selection' like so: isomesh map, My_2Fo-Fc.map, 1.0, selection, carve=2.0, and after hiding everything but the selection, I have a nice picture ... but with a map at a level I cannot interpret in PyMOL relative to Coot :-/ Regards, Emily. -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlVo1L4ACgkQU5C0gGfAG10YkwCfROYPVXBK/pDS4z/zi5MNY1D+ nHIAnjOFiAkb6JbuIGWRWkBFDG5Xgc2K =hrPT -END PGP SIGNATURE- -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
[ccp4bb] crystal habit/morphology and the relationship to unit cell contents
I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine which direction the screw axis is going with respect to top and the base of the pyramidal crystals (right image) so I can gauge how/why the crystals grow this way based on the cell contents. Thanks in advance. --paul
Re: [ccp4bb] PyMOL v. Coot map 'level'
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 You are correct about this. The magnitude of this effect depends on the amount of solvent in your crystal (which tends to be flatter) but it rarely reaches a factor of two. This does point out a serious flaw with contouring a map relative to its rms (one of many). If you calculate a map that just covers the interesting part, it probably contains a lot of features. The rms calculated from that region of the map alone will be larger and your features will look smaller. If you set a contour level relative to e/A^3 the appearance of the image will not depend on the region of space covered by your map nor the percentage of solvent in the crystal. Dale Tronrud On 6/1/2015 9:16 AM, Thomas Holder wrote: Hi Emilia et al., I tried to figure out the PyMOL vs. Coot normalization discrepancy a while ago. As far as I remember, PyMOL normalizes on the raw data array, while Coot normalizes across the unit cell. So if the data doesn't exactly cover the cell, the results might be different. Cheers, Thomas On 01 Jun 2015, at 11:37, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: One cannot understand what is going on without knowing how this map was calculated. Maps calculated by the Electron Density Server have density in units of electron/A^3 if I recall, or at least its best effort to do so. This is what I was looking for! (i.e. what the units are) Thanks. :-) Yes, I'd downloaded the 2mFo-DFc map from the EDS, and got the same Coot v. PyMOL discrepancy whether or not I turned off the PyMOL map normalization feature. If you load the same map into Pymol and ask it to normalize the density values you should set your contour level to Coot's rmsd level. If you don't normalize you should use Coot's e/A^3 level. It is quite possible that they could differ by a factor of two. This was exactly the case. The map e/A^3 level (not the rmsd level) in Coot matched very well, visually, the map 'level' in PyMOL; they were roughly off by a factor of 2. I did end up also generating a 2mFo-DFc map using phenix, which fetched the structure factors of the model in which I was interested. The result was the same (i.e. PyMOL 'level' = Coot e/A^3 level ~ = 1/2 Coot's rmsd level) whether I used the CCP4 map downloaded from the EDS, or generated from the structure factors with phenix. Thanks All. Emily. Dale Tronrud On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote: Hello. I am struggling with an old question--old because I've found several discussions and wiki bits on this topic, e.g. on the PyMOL mailing list (http://sourceforge.net/p/pymol/mailman/message/26496806/ and http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the suggestions about how to fix the problem are not working for me, and I cannot figure out why. Perhaps someone here can help: I'd like to display (for beauty's sake) a selection of a model with the map about this selection. I've fetched the model from the PDB, downloaded its 2mFo-DFc CCP4 map, loaded both the map and model into both PyMOL (student version) and Coot (0.8.2-pre EL (revision 5592)), and decided that I would use PyMOL to make the figure. I notice, though, that the map 'level' in PyMOL is not equivalent to the rmsd level in Coot, even when I set normalization off in PyMOL. I expected that a 1.0 rmsd level in Coot would look identical to a 1.0 level in PyMOL, but it does not; rather, a 1.0 rmsd level in Coot looks more like a 0.5 level in PyMOL. Does anyone have insight they could share about the difference between how Coot and PyMOL loads maps? Maybe the PyMOL 'level' is not a rmsd? is there some other normalization factor in PyMOL that I should set? Or, perhaps there is a mailing list post out there that I've missed, to which you could point me. :-) Alternatively, does anyone have instructions on how to use Coot to do what I'm trying to do in PyMOL? In PyMOL I displayed the mesh of the 2Fo-Fc map, contoured at 1.0 about a 3-residue-long 'selection' like so: isomesh map, My_2Fo-Fc.map, 1.0, selection, carve=2.0, and after hiding everything but the selection, I have a nice picture ... but with a map at a level I cannot interpret in PyMOL relative to Coot :-/ Regards, Emily. -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlVo1L4ACgkQU5C0gGfAG10YkwCfROYPVXBK/pDS4z/zi5MNY1D+ nHIAnjOFiAkb6JbuIGWRWkBFDG5Xgc2K =hrPT -END PGP SIGNATURE- -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlVskp8ACgkQU5C0gGfAG12urQCfQs1pkluJuYXVtULqNrBcBLE8 vykAoJ8fOqU2BnmGmNj+qspFX4/7Jo4T =LMS8 -END PGP SIGNATURE-
Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents
Maybe I confused the question by asking about the direction of the screw axis. I'm referring to the top and base of the actual crystal. If all the molecules in the unit cell are oriented in the same direction (with respect to the c cell), I want to know if there is a way to find out which direction those molecules are going in the physical crystal. --paul On 06/01/2015 12:59 PM, David Schuller wrote: The screw axis is either left-handed or right-handed (And the enantiomer, P62, will twist the opposite way). Therefore it doesn't even matter which you call the top and which you call the base. So, what exactly do you find confusing? On 06/01/15 12:20, Paul Paukstelis wrote: I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine which direction the screw axis is going with respect to top and the base of the pyramidal crystals (right image) so I can gauge how/why the crystals grow this way based on the cell contents. Thanks in advance. --paul
Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents
Hi Sorry about this, it's been a hard day and it's the first thing I thought of when I saw the pics of crystals... Brits of a certain age may be reminded of Gerry Anderson's UFOs... On 1 Jun 2015, at 17:20, Paul Paukstelis wrote: I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine which direction the screw axis is going with respect to top and the base of the pyramidal crystals (right image) so I can gauge how/why the crystals grow this way based on the cell contents. Thanks in advance. --paul Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] Allignment of multiple structures
I apologize if this question this question has been asked before but I still need help finding an answer to the following. I am looking for a program/web-server that will calculate the superposition of multiple structures (non-protein!) Thanks -- +++ Jens J. Birktoft Structural DNA Nanotechnology Department of Chemistry New York University e-mail: jens.kn...@gmail.com; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++
Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents
Can't you break the ambiguity if there is significant anomalous signal? So, you'd need to have collected data from a protein crystal with SeMet, or a heavy atom, or near the S edge, and know the orientation of the crystal w.r.t. the direction of the unique crystal axis (for instance from face indexing.) Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1306 E. University Blvd, Tucson, AZ 85721 Phone: 520 621 4168 s...@email.arizona.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Jeffrey Sent: Monday, June 01, 2015 12:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents I would have thought that what the indexing routine defined as [001] vs [00-1] would be essentially random as one would obtain the equivalent indexing in 622 in both up and down alignment of the crystallographic a/b/c axes with respect to crystal morphology. Phil Jeffrey Princeton On 6/1/15 1:44 PM, Scott Lovell wrote: Hi Paul, If you have access to diffractometer equipped with a 4-circle goniometer, you should be able to index the faces of the crystals. All you need to do is collect some images to index the lattice and determine the orientation matrix. Most instruments have software that allows one to then orient specific faces or crystallographic directions relative to various directions of the instrument (eg. camera, phi axis, direct beam, etc). So after indexing, you could then orient the [001] direction of the crystal towards the camera to determine if this is the top or the base. You can also determine the direction of the a/b axes [100] and [010] relative to the crystal and index the other faces. If you can also measure the interfacial angles, this may help you to confirm the indices. If you do this for a number of samples, is the top face always the [001] direction or is it the [00-1] direction for other crystals? Assuming that you are growing these crystals by hanging drop, my guess is that the base is in contact with the coverslip during growth and you observe this half pyramid habit. If you were to grow the crystals using the floating drop method, to prevent contact with the plate materials, would the crystals form a bipyramidal habit? Or do you see crystals in the current drop that have the same habit but are not in contact with the plate materials? Scott -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul Paukstelis Sent: Monday, June 01, 2015 11:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine which direction the screw axis is going with respect to top and the base of the pyramidal crystals (right image) so I can gauge how/why the crystals grow this way based on the cell contents. Thanks in advance. --paul
Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents
Yes, but where is the screw axis in that UFO? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harry Powell Sent: Monday, June 01, 2015 12:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents Hi Sorry about this, it's been a hard day and it's the first thing I thought of when I saw the pics of crystals... Brits of a certain age may be reminded of Gerry Anderson's UFOs... [UFO.jpg] On 1 Jun 2015, at 17:20, Paul Paukstelis wrote: I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine which direction the screw axis is going with respect to top and the base of the pyramidal crystals (right image) so I can gauge how/why the crystals grow this way based on the cell contents. Thanks in advance. --paul [cid:image002.png@01D09C70.632CE060] Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents
Hi Paul, If you have access to diffractometer equipped with a 4-circle goniometer, you should be able to index the faces of the crystals. All you need to do is collect some images to index the lattice and determine the orientation matrix. Most instruments have software that allows one to then orient specific faces or crystallographic directions relative to various directions of the instrument (eg. camera, phi axis, direct beam, etc). So after indexing, you could then orient the [001] direction of the crystal towards the camera to determine if this is the top or the base. You can also determine the direction of the a/b axes [100] and [010] relative to the crystal and index the other faces. If you can also measure the interfacial angles, this may help you to confirm the indices. If you do this for a number of samples, is the top face always the [001] direction or is it the [00-1] direction for other crystals? Assuming that you are growing these crystals by hanging drop, my guess is that the base is in contact with the coverslip during growth and you observe this half pyramid habit. If you were to grow the crystals using the floating drop method, to prevent contact with the plate materials, would the crystals form a bipyramidal habit? Or do you see crystals in the current drop that have the same habit but are not in contact with the plate materials? Scott -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul Paukstelis Sent: Monday, June 01, 2015 11:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine which direction the screw axis is going with respect to top and the base of the pyramidal crystals (right image) so I can gauge how/why the crystals grow this way based on the cell contents. Thanks in advance. --paul
Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents
I would have thought that what the indexing routine defined as [001] vs [00-1] would be essentially random as one would obtain the equivalent indexing in 622 in both up and down alignment of the crystallographic a/b/c axes with respect to crystal morphology. Phil Jeffrey Princeton On 6/1/15 1:44 PM, Scott Lovell wrote: Hi Paul, If you have access to diffractometer equipped with a 4-circle goniometer, you should be able to index the faces of the crystals. All you need to do is collect some images to index the lattice and determine the orientation matrix. Most instruments have software that allows one to then orient specific faces or crystallographic directions relative to various directions of the instrument (eg. camera, phi axis, direct beam, etc). So after indexing, you could then orient the [001] direction of the crystal towards the camera to determine if this is the top or the base. You can also determine the direction of the a/b axes [100] and [010] relative to the crystal and index the other faces. If you can also measure the interfacial angles, this may help you to confirm the indices. If you do this for a number of samples, is the top face always the [001] direction or is it the [00-1] direction for other crystals? Assuming that you are growing these crystals by hanging drop, my guess is that the base is in contact with the coverslip during growth and you observe this half pyramid habit. If you were to grow the crystals using the floating drop method, to prevent contact with the plate materials, would the crystals form a bipyramidal habit? Or do you see crystals in the current drop that have the same habit but are not in contact with the plate materials? Scott -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul Paukstelis Sent: Monday, June 01, 2015 11:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine which direction the screw axis is going with respect to top and the base of the pyramidal crystals (right image) so I can gauge how/why the crystals grow this way based on the cell contents. Thanks in advance. --paul
Re: [ccp4bb] [phenixbb] Allignment of multiple structures
Dear Jens J. Birktoft, lsqman from the Uppsala Software Factory (USF) is very flexible in terms of atom selection etc. and it is scriptable. You may need to choose one reference structure amongst your coordinates, though. Best wishes, Tim On Mon, Jun 01, 2015 at 03:53:54PM -0400, jens j birktoft wrote: I apologize if this question this question has been asked before but I still need help finding an answer to the following. I am looking for a program/web-server that will calculate the superposition of multiple structures (non-protein!) Thanks -- +++ Jens J. Birktoft Structural DNA Nanotechnology Department of Chemistry New York University e-mail: jens.kn...@gmail.com; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++ ___ phenixbb mailing list pheni...@phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-le...@phenix-online.org -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] [phenixbb] Allignment of multiple structures
THESEUS should be able to do it rather easily. You can email me offlist if you need some guidance. On Jun 1, 2015, at 3:53 PM, jens j birktoft birkt...@nyu.edu wrote: I apologize if this question this question has been asked before but I still need help finding an answer to the following. I am looking for a program/web-server that will calculate the superposition of multiple structures (non-protein!) Thanks -- +++ Jens J. Birktoft Structural DNA Nanotechnology Department of Chemistry New York University e-mail: jens.kn...@gmail.com; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++ ___ phenixbb mailing list pheni...@phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-le...@phenix-online.org
Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents
Is it possible to distinguish P64 from P62 without having basically solved the structure? Given that it is P64, is the +ive direction of the c axis arbitrary? A left-hand helix is left hand either way you point it, and the molecules in the asymmetric units could be pointing the opposite way. Clearly the lattice is symmetric, so you could start out with either orientation and end up solving the structure. Phaser offers to try both enantiomers, but not to try with rotating the lattice to reverse the c axis in case you got that wrong. I too would first guess that the truncated base is where it ran into the glass, and the flat tip may be where it hit the air-water interface; the basic morphology being hexagonal bipyramid. Unless there are dozens of crystals with the same habit. eab On 06/01/2015 03:45 PM, Roberts, Sue A - (suer) wrote: Can't you break the ambiguity if there is significant anomalous signal? So, you'd need to have collected data from a protein crystal with SeMet, or a heavy atom, or near the S edge, and know the orientation of the crystal w.r.t. the direction of the unique crystal axis (for instance from face indexing.) Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1306 E. University Blvd, Tucson, AZ 85721 Phone: 520 621 4168 s...@email.arizona.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Jeffrey Sent: Monday, June 01, 2015 12:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents I would have thought that what the indexing routine defined as [001] vs [00-1] would be essentially random as one would obtain the equivalent indexing in 622 in both up and down alignment of the crystallographic a/b/c axes with respect to crystal morphology. Phil Jeffrey Princeton On 6/1/15 1:44 PM, Scott Lovell wrote: Hi Paul, If you have access to diffractometer equipped with a 4-circle goniometer, you should be able to index the faces of the crystals. All you need to do is collect some images to index the lattice and determine the orientation matrix. Most instruments have software that allows one to then orient specific faces or crystallographic directions relative to various directions of the instrument (eg. camera, phi axis, direct beam, etc). So after indexing, you could then orient the [001] direction of the crystal towards the camera to determine if this is the top or the base. You can also determine the direction of the a/b axes [100] and [010] relative to the crystal and index the other faces. If you can also measure the interfacial angles, this may help you to confirm the indices. If you do this for a number of samples, is the top face always the [001] direction or is it the [00-1] direction for other crystals? Assuming that you are growing these crystals by hanging drop, my guess is that the base is in contact with the coverslip during growth and you observe this half pyramid habit. If you were to grow the crystals using the floating drop method, to prevent contact with the plate materials, would the crystals form a bipyramidal habit? Or do you see crystals in the current drop that have the same habit but are not in contact with the plate materials? Scott -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul Paukstelis Sent: Monday, June 01, 2015 11:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine which direction the screw axis is going with respect to top and the base of the pyramidal crystals (right image) so I can gauge how/why the crystals grow this way based on the cell contents. Thanks in advance. --paul
Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents
All the crystals are unipyramidal, regardless of how they are grown. The crystal habit seems to be dictated by the arrangement of the molecules in the unit cell. The structure is solved, so this is really an exercise in trying to figure out if what we see in the crystal packing can explain the morphology. --paul On 06/01/2015 04:25 PM, Edward A. Berry wrote: Is it possible to distinguish P64 from P62 without having basically solved the structure? Given that it is P64, is the +ive direction of the c axis arbitrary? A left-hand helix is left hand either way you point it, and the molecules in the asymmetric units could be pointing the opposite way. Clearly the lattice is symmetric, so you could start out with either orientation and end up solving the structure. Phaser offers to try both enantiomers, but not to try with rotating the lattice to reverse the c axis in case you got that wrong. I too would first guess that the truncated base is where it ran into the glass, and the flat tip may be where it hit the air-water interface; the basic morphology being hexagonal bipyramid. Unless there are dozens of crystals with the same habit. eab On 06/01/2015 03:45 PM, Roberts, Sue A - (suer) wrote: Can't you break the ambiguity if there is significant anomalous signal? So, you'd need to have collected data from a protein crystal with SeMet, or a heavy atom, or near the S edge, and know the orientation of the crystal w.r.t. the direction of the unique crystal axis (for instance from face indexing.) Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1306 E. University Blvd, Tucson, AZ 85721 Phone: 520 621 4168 s...@email.arizona.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Jeffrey Sent: Monday, June 01, 2015 12:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents I would have thought that what the indexing routine defined as [001] vs [00-1] would be essentially random as one would obtain the equivalent indexing in 622 in both up and down alignment of the crystallographic a/b/c axes with respect to crystal morphology. Phil Jeffrey Princeton On 6/1/15 1:44 PM, Scott Lovell wrote: Hi Paul, If you have access to diffractometer equipped with a 4-circle goniometer, you should be able to index the faces of the crystals. All you need to do is collect some images to index the lattice and determine the orientation matrix. Most instruments have software that allows one to then orient specific faces or crystallographic directions relative to various directions of the instrument (eg. camera, phi axis, direct beam, etc). So after indexing, you could then orient the [001] direction of the crystal towards the camera to determine if this is the top or the base. You can also determine the direction of the a/b axes [100] and [010] relative to the crystal and index the other faces. If you can also measure the interfacial angles, this may help you to confirm the indices. If you do this for a number of samples, is the top face always the [001] direction or is it the [00-1] direction for other crystals? Assuming that you are growing these crystals by hanging drop, my guess is that the base is in contact with the coverslip during growth and you observe this half pyramid habit. If you were to grow the crystals using the floating drop method, to prevent contact with the plate materials, would the crystals form a bipyramidal habit? Or do you see crystals in the current drop that have the same habit but are not in contact with the plate materials? Scott -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul Paukstelis Sent: Monday, June 01, 2015 11:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine which direction the screw axis is going with respect to top and the base of the pyramidal crystals (right image) so I can gauge how/why the crystals grow this way based on the cell contents. Thanks in advance. --paul
Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents
Dear Paul, could you check if the crystals are optically active and find out which way they rotate the polarisation of light? I am not sure how to deduce the screw direction from this, I would first try to determine an angle... Best, Tim On Mon, Jun 01, 2015 at 04:41:41PM -0400, Paul Paukstelis wrote: All the crystals are unipyramidal, regardless of how they are grown. The crystal habit seems to be dictated by the arrangement of the molecules in the unit cell. The structure is solved, so this is really an exercise in trying to figure out if what we see in the crystal packing can explain the morphology. --paul On 06/01/2015 04:25 PM, Edward A. Berry wrote: Is it possible to distinguish P64 from P62 without having basically solved the structure? Given that it is P64, is the +ive direction of the c axis arbitrary? A left-hand helix is left hand either way you point it, and the molecules in the asymmetric units could be pointing the opposite way. Clearly the lattice is symmetric, so you could start out with either orientation and end up solving the structure. Phaser offers to try both enantiomers, but not to try with rotating the lattice to reverse the c axis in case you got that wrong. I too would first guess that the truncated base is where it ran into the glass, and the flat tip may be where it hit the air-water interface; the basic morphology being hexagonal bipyramid. Unless there are dozens of crystals with the same habit. eab On 06/01/2015 03:45 PM, Roberts, Sue A - (suer) wrote: Can't you break the ambiguity if there is significant anomalous signal? So, you'd need to have collected data from a protein crystal with SeMet, or a heavy atom, or near the S edge, and know the orientation of the crystal w.r.t. the direction of the unique crystal axis (for instance from face indexing.) Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1306 E. University Blvd, Tucson, AZ 85721 Phone: 520 621 4168 s...@email.arizona.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Jeffrey Sent: Monday, June 01, 2015 12:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents I would have thought that what the indexing routine defined as [001] vs [00-1] would be essentially random as one would obtain the equivalent indexing in 622 in both up and down alignment of the crystallographic a/b/c axes with respect to crystal morphology. Phil Jeffrey Princeton On 6/1/15 1:44 PM, Scott Lovell wrote: Hi Paul, If you have access to diffractometer equipped with a 4-circle goniometer, you should be able to index the faces of the crystals. All you need to do is collect some images to index the lattice and determine the orientation matrix. Most instruments have software that allows one to then orient specific faces or crystallographic directions relative to various directions of the instrument (eg. camera, phi axis, direct beam, etc). So after indexing, you could then orient the [001] direction of the crystal towards the camera to determine if this is the top or the base. You can also determine the direction of the a/b axes [100] and [010] relative to the crystal and index the other faces. If you can also measure the interfacial angles, this may help you to confirm the indices. If you do this for a number of samples, is the top face always the [001] direction or is it the [00-1] direction for other crystals? Assuming that you are growing these crystals by hanging drop, my guess is that the base is in contact with the coverslip during growth and you observe this half pyramid habit. If you were to grow the crystals using the floating drop method, to prevent contact with the plate materials, would the crystals form a bipyramidal habit? Or do you see crystals in the current drop that have the same habit but are not in contact with the plate materials? Scott -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul Paukstelis Sent: Monday, June 01, 2015 11:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine which direction the screw axis is going with respect to top and the base of the pyramidal crystals (right image) so I can gauge how/why the crystals grow this way based on the cell contents. Thanks in advance. --paul -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key
Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents
You need: a) to have an image of your crystal mounted on the goniometer in orientation, in which the axis of interest (6-fold) is perpendicular to the beam. You should know the system well enough to relate the coordinate system of the crystal on this image to the beam-gravity coordinate system. b) you collect in this orientation diffracion image(s) sufficient for indexing c) index the lattice and chose hexagonal lattice and refine parameters d) then you collect data set from the crystal so you can solve the structure in this coordinate system. Because space group is polar, there are always two non-equivalent choices for the coordinate system and you cannot replace one with another. The critical step is performed after (c) and depends on software -- I describe here HKL2000. On the image oriented according to (a) check where are the positive and negative values of hexagonal index (l index - use zoom window). HKL2000 present the diffraction image of the detector from the perspective of an incident beam. Therefore, you would need to correlate positive and negative values of indices with the optical image coordinate system from (a). Remember that optical axis (of the camera imaging a crystal) may not be along the beam. The structure solution will provide you with the direction of axis c. D. I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine which direction the screw axis is going with respect to top and the base of the pyramidal crystals (right image) so I can gauge how/why the crystals grow this way based on the cell contents. Thanks in advance. --paul Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-9577 (phone) *** 214-645-6353 (fax)
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