Re: [ccp4bb] Mixed oligomeric states in crystallo
Hi, To my knowledge, the structure of the rhizavidin-biotin complex contains a hexamer and a monomer, where the monomer forms a dimer using symmetry operations. PDB id: 3ew2. Best, Orly On Fri, Jan 31, 2020, 17:33 Kluenemann, Thomas < thomas.kluenem...@helmholtz-hzi.de> wrote: > Dear all, > > > > We recently solved a the structure of a small c-type cytochrome. We > observed, that of the eleven chains in the asymmetric unit ten form 3D > domain swapped dimers by exchanging an α-helix. The eleventh chain is > present as a monomer. Based on the anomalous iron signal and the chain > tracing we are sure that no chain was missed. > > I tried to find other examples in the PDB, were one crystal is made of > different homo- or heterooligomers. I only found proteins with partial > occupied peptide binding sites, which is not what I am looking for. Does > anyone know of a case were the presence of different homo- or > heterooligomers is required to form the crystal? > > > > Best regards, > > Thomas Klünemann > > > > > > -- > > Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 > Braunschweig | www.helmholtz-hzi.de > > Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von > Messling > Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für > Wissenschaft und Kultur > Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel > Gesellschaft mit beschränkter Haftung (GmbH) > Sitz der Gesellschaft: Braunschweig > Handelsregister: Amtsgericht Braunschweig, HRB 477 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Generating symmetry mates using python
Hi all, I am a crystallographer currently employing computational methods as well as experimental crystallography. I am trying to generate symmetry mates in python (working with pandas dataframes), in order to analyze inter-sub-unit interactions. To do so I am trying to use the info in "REMARK 290 CRYSTALLOGRAPHIC SYMMETRY" and manually (using numpy) perform a matrix multiplication with the relevant translation (xyz*rotation + translation). For some reason this doesn't work consistently and I feel I need to use the info in CRYST1 to obtain the unit cell and multiplication matrix. Here I ran into trouble with extracting the correct symmetry operations based on each space group. I found spglib but it doesn't quite solve the problem. I also tried opening PyMol through the command and generating symmetry mates this way. It worked on a few files but failed quite quickly (segmentation fault) and was also very slow. Can anyone suggest a useful solution, preferably clear to use and/or well documented? Or even have a python script/code they can share for this? Best regards, Orly -- Orly Avraham, Ph.D. Postdoctoral fellow The lab of Prof. Oded Livnah and the lab of Prof. Ora Schueler-Furman The Hebrew University of Jerusalem Israel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Generating symmetry mates using python
Hi, Thank you all for your help! Of course coot works perfectly and also PISA is useful, not I am not sure both can be employed in a high-throuput manner for hundreds of structures. I looked at gemmi but am not familiar with python-mmdb, so I will take a look at that. Thank you Zhijie for the script and the explanation! I will take a look at it when I'm back in the lab. Thanks again everyone for your help and have a great weekend, Orly On Sat, Jan 11, 2020, 03:11 Zhijie Li wrote: > Hi Orly, > > REMARK 290 should be the easiest way for generating symmetry mates. Other > routes are just going to give you the same results. As Jonathan already > pointed out, the symm ops do not garantee that the symm copies are close to > each other. The most simple-minded solution to this problem would be > simply generating 3x3x3 unit cells so that the unit cell in center will be > complete. An upgrade to this is to compute the center of mass of the > symmetry copies in each of the 3x3c3 cells and find which one is closest to > the orignal 1555 copy. Just for fun, I wrote a little python script that > does this (attached). In this script for unit cell translation and > calculating center-center distances, I converted the Cartesian coordinates > to fractional coords first. Then after the translation,I used the inverse > of the SCALE1 matrix to get the shifted Cartesian coords. This way I don't > need to read wikipedia on geometry . But as noted in the script the > distances should better be calculated in Cartesian. > > Zhijie > > ---------- > *From:* CCP4 bulletin board on behalf of orly > avraham > *Sent:* Friday, January 10, 2020 3:30 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Generating symmetry mates using python > > Hi all, > > I am a crystallographer currently employing computational methods as well > as experimental crystallography. > I am trying to generate symmetry mates in python (working with pandas > dataframes), in order to analyze inter-sub-unit interactions. To do so I am > trying to use the info in "REMARK 290 CRYSTALLOGRAPHIC SYMMETRY" and > manually (using numpy) perform a matrix multiplication with the relevant > translation (xyz*rotation + translation). > For some reason this doesn't work consistently and I feel I need to use > the info in CRYST1 to obtain the unit cell and multiplication matrix. Here > I ran into trouble with extracting the correct symmetry operations based on > each space group. I found spglib but it doesn't quite solve the problem. > I also tried opening PyMol through the command and generating symmetry > mates this way. It worked on a few files but failed quite quickly > (segmentation fault) and was also very slow. > Can anyone suggest a useful solution, preferably clear to use and/or well > documented? Or even have a python script/code they can share for this? > > Best regards, > Orly > > -- > > Orly Avraham, Ph.D. > Postdoctoral fellow > The lab of Prof. Oded Livnah > and the lab of Prof. Ora Schueler-Furman > The Hebrew University of Jerusalem > Israel > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Generating symmetry mates using python
Hi Tristan, Thank you very much!! I will continue with my exploration and I am grateful for all the assistance. Best regards, Orly On Sun, Jan 12, 2020 at 11:18 PM Tristan Croll wrote: > (sending again because it seems the message board server gets a little > confused by Python files as attachments). > > Hi Orly, > > Turns out I didn't have a pre-baked method for this specific task, but > the method defined in the attached file works - although you'll > undoubtedly want to adapt it to your specific purposes. To play around > with it, download and install ChimeraX 0.91, then install Clipper with > "toolshed install clipper" on its command line. Then, you can open the > ChimeraX interactive Python shell with Tools/General/Shell. This comes > with the top-level ChimeraX session object pre-loaded with the variable > name "session". Copy-paste the method definition in to that, and you'll > be ready to explore. You can also run Python files with "open xxx.py" on > the command line or on starting ChimeraX with "chimerax xxx.py" - in > either case, these will also have the session object automatically > available. > > Best regards, > > Tristan > > On 2020-01-12 19:54, orly avraham wrote: > > Hi Tristan, > > > > I am looking into all the options listed, yet would still highly > > appreciate any additional resources! > > If you would be kind enough to share an example script that would be > > great. > > > > Best, > > Orly > > > > On Sun, Jan 12, 2020 at 9:12 PM Tristan Croll wrote: > > > >> Just to add to the already-excellent list of replies, this can also > >> be done quite straightforwardly with the Clipper plugin in ChimeraX. > >> I’d be happy to provide an example script if you want one. > >> > >> Best regards, > >> > >> Tristan > >> > >> On 12 Jan 2020, at 18:54, orly avraham > >> wrote: > >> > >> Hi Marcin, > >> > >> Thank you very much for your detailed reply! > >> You pointed out many special cases that I wouldn't have thought of. > >> Indeed an existing solution is highly preferred, and I appreciate > >> you pointing out several available libraries. I came across Gemmi > >> and I will give it another look, and I will examine the additional > >> resources you mentioned as well. > >> > >> Best regards, > >> Orly Avraham > >> > >> On Sun, Jan 12, 2020 at 5:59 PM Marcin Wojdyr > >> wrote: > >> Hi Zhijie, > >> > >> it's good and instructive to implement such things from the ground > >> up, > >> but there are many special cases that one would be discovering while > >> testing this procedure, so if the time is limited it may be better > >> to > >> use an existing solution. > >> > >> For instance, here one may find out that using the SCALE1 record > >> doesn't give the sufficient accuracy. In the example in your script > >> you have 6 significant digits in the unit cell lengths in CRYST1, > >> but > >> only 4 significant digits in SCALE1. (The accuracy of SCALE1 is > >> problematic in general; sometimes it needs to be manually removed > >> when > >> a program reads it in preference to CRYST1.) > >> > >> Then one may find out that the 3x3x3 supercell is not sufficient. If > >> the molecule is far from the origin, symmetry operations send it far > >> away. For example, 5M3H annotates (in the mmCIF format) hydrogen > >> bond > >> between 1_555 and 2_11516 - the symmetry mate is shifted 16 unit > >> cells > >> in the z direction. Since you already use fractional coordinates in > >> your script you could tell directly from the center-of-mass > >> coordinates how many unit cells it should be shifted. Say, you have > >> x=3.1, so to shift it near the origin you shift it by 3 unit cells > >> along x. > >> > >> But even if all the molecules are shifted near the origin, the 3x3x3 > >> cell is still not sufficient to find contacts. > >> See 3NWH – a homo-4-mer in P2 (4 x 2 chains per unit cell). Here > >> it in > >> its unit cell, colored by the chain id: > >> https://gemmi.readthedocs.io/en/latest/_images/3nwh.png > >> Or 5XG2 – a monomer in P21. Two copies of the chain are > >> rainbow-colored here: > >> https://gemmi.readthedocs.io/en/latest/_images/5xg2.png > >> These chains span over more than 4 unit cells in one direction. One > >> could use big
Re: [ccp4bb] Generating symmetry mates using python
Hi Tristan, I am looking into all the options listed, yet would still highly appreciate any additional resources! If you would be kind enough to share an example script that would be great. Best, Orly On Sun, Jan 12, 2020 at 9:12 PM Tristan Croll wrote: > Just to add to the already-excellent list of replies, this can also be > done quite straightforwardly with the Clipper plugin in ChimeraX. I’d be > happy to provide an example script if you want one. > > Best regards, > > Tristan > > > > > On 12 Jan 2020, at 18:54, orly avraham > wrote: > > Hi Marcin, > > Thank you very much for your detailed reply! > You pointed out many special cases that I wouldn't have thought of. > Indeed an existing solution is highly preferred, and I appreciate you > pointing out several available libraries. I came across Gemmi and I will > give it another look, and I will examine the additional resources you > mentioned as well. > > Best regards, > Orly Avraham > > On Sun, Jan 12, 2020 at 5:59 PM Marcin Wojdyr wrote: > >> Hi Zhijie, >> >> it's good and instructive to implement such things from the ground up, >> but there are many special cases that one would be discovering while >> testing this procedure, so if the time is limited it may be better to >> use an existing solution. >> >> For instance, here one may find out that using the SCALE1 record >> doesn't give the sufficient accuracy. In the example in your script >> you have 6 significant digits in the unit cell lengths in CRYST1, but >> only 4 significant digits in SCALE1. (The accuracy of SCALE1 is >> problematic in general; sometimes it needs to be manually removed when >> a program reads it in preference to CRYST1.) >> >> Then one may find out that the 3x3x3 supercell is not sufficient. If >> the molecule is far from the origin, symmetry operations send it far >> away. For example, 5M3H annotates (in the mmCIF format) hydrogen bond >> between 1_555 and 2_11516 - the symmetry mate is shifted 16 unit cells >> in the z direction. Since you already use fractional coordinates in >> your script you could tell directly from the center-of-mass >> coordinates how many unit cells it should be shifted. Say, you have >> x=3.1, so to shift it near the origin you shift it by 3 unit cells >> along x. >> >> But even if all the molecules are shifted near the origin, the 3x3x3 >> cell is still not sufficient to find contacts. >> See 3NWH – a homo-4-mer in P2 (4 x 2 chains per unit cell). Here it in >> its unit cell, colored by the chain id: >> https://gemmi.readthedocs.io/en/latest/_images/3nwh.png >> Or 5XG2 – a monomer in P21. Two copies of the chain are rainbow-colored >> here: >> https://gemmi.readthedocs.io/en/latest/_images/5xg2.png >> These chains span over more than 4 unit cells in one direction. One >> could use big enough supercell, but it'd be slow. I suppose that even >> using a 3x3x3 supercell is slow. The alternative is to do the distance >> calculation in fractional coordinates modulo 1. >> >> Then you needs to consider atoms on special positions. If you apply >> symmetry operations to an atom on a 4-fold symmetry axis you get 4 >> atoms in the same place. So this needs to be handled. The atom may not >> be exactly on the axis, because the refinement program may not >> constrain its position. So the symmetry operations should produce, I >> think, 4 alternative locations of the same atom. But you could also >> have an atom near the symmetry axis bonded to its symmetry mate - then >> the symmetry operations should produce different atoms. So the >> procedure requires a cut-off distance or a heuristics to distinguish >> the two cases. >> >> Then, if you'd like to expand non-crystallographic symmetry from the >> MTRIX records - this is another complication. And so on... >> >> So I'd recommend using one of many available programs for finding >> contacts or interactions. If none of them is suitable - then try >> crystallographic libraries. >> I didn't document yet how to find the contacts using gemmi, but I'll >> do it in the coming weeks (or months). Cctbx and clipper are other >> (more mature) libraries worth checking. >> >> Best wishes, >> Marcin >> >> >> On Sat, 11 Jan 2020 at 02:11, Zhijie Li wrote: >> > >> > Hi Orly, >> > >> > REMARK 290 should be the easiest way for generating symmetry mates. >> Other routes are just going to give you the same results. As Jonathan >> already pointed out, the symm ops do not garantee that the symm copies are >> clos
Re: [ccp4bb] Generating symmetry mates using python
Hi Marcin, Thank you very much for your detailed reply! You pointed out many special cases that I wouldn't have thought of. Indeed an existing solution is highly preferred, and I appreciate you pointing out several available libraries. I came across Gemmi and I will give it another look, and I will examine the additional resources you mentioned as well. Best regards, Orly Avraham On Sun, Jan 12, 2020 at 5:59 PM Marcin Wojdyr wrote: > Hi Zhijie, > > it's good and instructive to implement such things from the ground up, > but there are many special cases that one would be discovering while > testing this procedure, so if the time is limited it may be better to > use an existing solution. > > For instance, here one may find out that using the SCALE1 record > doesn't give the sufficient accuracy. In the example in your script > you have 6 significant digits in the unit cell lengths in CRYST1, but > only 4 significant digits in SCALE1. (The accuracy of SCALE1 is > problematic in general; sometimes it needs to be manually removed when > a program reads it in preference to CRYST1.) > > Then one may find out that the 3x3x3 supercell is not sufficient. If > the molecule is far from the origin, symmetry operations send it far > away. For example, 5M3H annotates (in the mmCIF format) hydrogen bond > between 1_555 and 2_11516 - the symmetry mate is shifted 16 unit cells > in the z direction. Since you already use fractional coordinates in > your script you could tell directly from the center-of-mass > coordinates how many unit cells it should be shifted. Say, you have > x=3.1, so to shift it near the origin you shift it by 3 unit cells > along x. > > But even if all the molecules are shifted near the origin, the 3x3x3 > cell is still not sufficient to find contacts. > See 3NWH – a homo-4-mer in P2 (4 x 2 chains per unit cell). Here it in > its unit cell, colored by the chain id: > https://gemmi.readthedocs.io/en/latest/_images/3nwh.png > Or 5XG2 – a monomer in P21. Two copies of the chain are rainbow-colored > here: > https://gemmi.readthedocs.io/en/latest/_images/5xg2.png > These chains span over more than 4 unit cells in one direction. One > could use big enough supercell, but it'd be slow. I suppose that even > using a 3x3x3 supercell is slow. The alternative is to do the distance > calculation in fractional coordinates modulo 1. > > Then you needs to consider atoms on special positions. If you apply > symmetry operations to an atom on a 4-fold symmetry axis you get 4 > atoms in the same place. So this needs to be handled. The atom may not > be exactly on the axis, because the refinement program may not > constrain its position. So the symmetry operations should produce, I > think, 4 alternative locations of the same atom. But you could also > have an atom near the symmetry axis bonded to its symmetry mate - then > the symmetry operations should produce different atoms. So the > procedure requires a cut-off distance or a heuristics to distinguish > the two cases. > > Then, if you'd like to expand non-crystallographic symmetry from the > MTRIX records - this is another complication. And so on... > > So I'd recommend using one of many available programs for finding > contacts or interactions. If none of them is suitable - then try > crystallographic libraries. > I didn't document yet how to find the contacts using gemmi, but I'll > do it in the coming weeks (or months). Cctbx and clipper are other > (more mature) libraries worth checking. > > Best wishes, > Marcin > > > On Sat, 11 Jan 2020 at 02:11, Zhijie Li wrote: > > > > Hi Orly, > > > > REMARK 290 should be the easiest way for generating symmetry mates. > Other routes are just going to give you the same results. As Jonathan > already pointed out, the symm ops do not garantee that the symm copies are > close to each other. The most simple-minded solution to this problem would > be simply generating 3x3x3 unit cells so that the unit cell in center will > be complete. An upgrade to this is to compute the center of mass of the > symmetry copies in each of the 3x3c3 cells and find which one is closest to > the orignal 1555 copy. Just for fun, I wrote a little python script that > does this (attached). In this script for unit cell translation and > calculating center-center distances, I converted the Cartesian coordinates > to fractional coords first. Then after the translation,I used the inverse > of the SCALE1 matrix to get the shifted Cartesian coords. This way I don't > need to read wikipedia on geometry . But as noted in the script the > distances should better be calculated in Cartesian. > > > > Zhijie > > > > > > From: CCP4 bulletin boar
Re: [ccp4bb] Looking for method to find similar oligomeric arrangement
Hi Andy, Are you familiar with ProtCID? http://dunbrack2.fccc.edu/ProtCiD/Default.aspx Might be relevant. Best, Orly On Sun, Jun 21, 2020 at 12:02 AM Andrew Lovering wrote: > Dear colleagues, > > > I have a structure of a simple, common fold (hth, dna-binding) that I > believe has oligomerized in a different way to that observed for any > members of the superfamily that I can reasonably analyze. > > > So if I run fold comparison analysis (e.g. DALI) it will find similar > structures on the monomeric level but what I really want is it to find hth > structures that place each monomer in a similar position to the monomers of > our tetramer.this seems harder to do > > [literature searches are slow and all yield tetramers dissimilar in nature > to ours] > > > I can of course "cheat" and turn our tetramer into a monomer (e.g. give > the four chains the same chain ID but different residue ranges) but in > something like DALI this would only get a hit to anything approximating the > tetramer with a single chain protein? (I tried, this seems to be so) > > > I hope its easier than I'm making out and would love to be enlightened! > > Best > > Andy > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Orly Avraham, Ph.D. Postdoctoral fellow The lab of Prof. Oded Livnah and the lab of Prof. Ora Schueler-Furman The Hebrew University of Jerusalem Israel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] off-topic: structural motif / domain comparison
You might also find use in databases such as pfam, ecod, cath, scop. Orly On Fri, Aug 6, 2021, 09:43 Sam Tang wrote: > Dear all > > Sorry for an off-topic question here. I wonder if anyone may be aware of > any search program which allows one to 'blast' a protein domain just like > we 'blast' a protein sequence? For example I have an epitope in hand and > would like to find out whether this also exists in other proteins. Most > programs I accessed are based on sequence similarity but is there any > program which searches a structure against a database of structures? > > BRs > > Sam > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] High-order oligomers vs robust crystals - references?
Hi, I think this paper might be useful for digging into oligomerization and crystallization: https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.201806092 I'm not sure they discuss prokaryotes but do have many interesting ideas. Best, Orly On Fri, Nov 12, 2021 at 7:20 PM Edwin Pozharski wrote: > One could use PISA to get a rough distribution of oligomerization states > of proteins in the PDB and compare bacterial vs mammalian... there always > will be a question though of whether any bias is inherent in proteins or > driven by crystallizability itself. > > Personally, I always though that bacterial proteins crystallize better > because they express better and are more stable. All of this is hand > waiving on my part, of course. > > --- > I don't know why the sacrifice didn't work. The science seemed so solid. > Julien XIII, Lord of the Lemurs > > On Fri, Nov 12, 2021 at 9:52 AM Frank von Delft < > frank.vonde...@cmd.ox.ac.uk> wrote: > >> Hello all >> >> Two decades ago, I remember (!) much talk about a reason that bacterial >> proteins crystallize "more easily" is that they tend to come as >> oligomers (dimers and up), and that this internal symmetry made them >> happier to crystallize. >> >> Did anybody ever publish hard evidence? Or even, is there a primary >> citation for the idea? >> >> Thanks >> Frank >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Orly Avraham, Ph.D. Postdoctoral fellow The lab of Prof. Ora Schueler-Furman The Hebrew University of Jerusalem Israel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
