Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map
Dear Paul, Thank you Regards Devbrat On Thu, Jun 6, 2024, 8:53 AM Paul Emsley wrote: > > On 06/06/2024 04:00, Devbrat Kumar wrote: > > > -- > Dear Paul, > > Thank you for your response. I wanted to compare a Coulomb potential map > to an electron density map. Before aligning these maps, I need to bring > them to similar parameters, which requires rescaling one map to match the > other. After that, I can proceed with density subtraction. > > I hope this clarifies my query. Sorry for any confusion. > Thank you again. > Regards > Devbrat > > > On Wed, Jun 5, 2024, 7:56 PM Paul Emsley > wrote: > >> >> On 05/06/2024 07:00, Devbrat Kumar wrote: >> >> >> -- >> >> Hello Everyone, >> >> Hello Devbrat, >> >> I have a query regarding the resampling of cryoEM density to match >> crystal density to obtain a density difference map. Specifically, I am >> trying to determine if it is feasible to resample a cryoEM map with an XRD >> density map. However, each time I attempt this, the resampling output >> provides an arbitrary ASU resample map, resulting in a significant loss of >> major density. >> >> I have been using Coot and Chimera for this process but have not achieved >> the desired outcome. Please guide me or suggest how to move forward with >> this. My goal is to create an accurate final density difference map. >> >> >> It is not clear to me exactly what the problem is. >> >> In Coot speak, "resampling" is (merely) changing the grid sampling so >> that the map appears (typically) on a finer grid. >> >> I don't think that this is what you want. >> >> You want is, I think, "Transform Map by LSQ Model-fit" and if that is >> what you used, then I can't help until I am more clear about what you think >> has gone wrong. >> >> Regards, >> >> Paul. >> >> Ah, OK, so you want to *rescale* not resample. The tool (in our world) to > do that is EMDA (available in CCPEM). > > Paul. > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Resampling CryoEM Density map to XRD Density map for Difference Map
Dear Paul, Thank you for your response. I wanted to compare a Coulomb potential map to an electron density map. Before aligning these maps, I need to bring them to similar parameters, which requires rescaling one map to match the other. After that, I can proceed with density subtraction. I hope this clarifies my query. Sorry for any confusion. Thank you again. Regards Devbrat On Wed, Jun 5, 2024, 7:56 PM Paul Emsley wrote: > > On 05/06/2024 07:00, Devbrat Kumar wrote: > > > -- > > Hello Everyone, > > Hello Devbrat, > > I have a query regarding the resampling of cryoEM density to match crystal > density to obtain a density difference map. Specifically, I am trying to > determine if it is feasible to resample a cryoEM map with an XRD density > map. However, each time I attempt this, the resampling output provides an > arbitrary ASU resample map, resulting in a significant loss of major > density. > > I have been using Coot and Chimera for this process but have not achieved > the desired outcome. Please guide me or suggest how to move forward with > this. My goal is to create an accurate final density difference map. > > > It is not clear to me exactly what the problem is. > > In Coot speak, "resampling" is (merely) changing the grid sampling so that > the map appears (typically) on a finer grid. > > I don't think that this is what you want. > > You want is, I think, "Transform Map by LSQ Model-fit" and if that is what > you used, then I can't help until I am more clear about what you think has > gone wrong. > > Regards, > > Paul. > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Resampling CryoEM Density map to XRD Density map for Difference Map
Dear Jon I will keep this in mind while working on it. Thank you. Regards Devbrat On Wed, Jun 5, 2024, 7:11 PM Jon Cooper < 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > Another factor might be that ccpem uses a different axis order to gemmi > and ccp4 ;-0 > > Best wishes, Jon Cooper. > jon.b.coo...@protonmail.com > > Sent from Proton Mail Android > > > Original Message > On 05/06/2024 12:51, Guillaume Gaullier wrote: > > With a cryoEM map, it's easier to do the rigid-body fitting of step 2 in > real space (this is trivial to do interactively in ChimeraX) rather than by > MR. > -- > *From:* CCP4 bulletin board on behalf of Eleanor > Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> > *Sent:* Wednesday, June 5, 2024 1:39:56 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map > for Difference Map > > Hmm - rather tricky! I would do an MR search with the crystal model v the > EM density, > Steps would be: > 1) convert EM density to "structure factors". - there are tools which do > this .. > 1a) You need to go back to ccp4i - program sfall to read map to generate > SFs from map - then cad or sftools to add a fake SigF column > 2) Solve MR search with the model v these "structure factors" using them > as Fobs > 3) Calculate the structure factors from the MR positiooned model and get > the difference map.. > > > On Wed, 5 Jun 2024 at 11:46, Martin Malý wrote: > >> Dear Devbrat, >> >> I am now playing with a similar problem but I don't have a simple >> solution for you as I'm also quite stuck. You can check these software >> tools which involve some scripting in Python (NumPy, SciPy) and C++: >> >> EMDA (for cryoEM maps, included in CCP-EM) >> https://gitlab.com/ccpem/emda >> https://doi.org/10.1016/j.jsb.2021.107826 >> >> Gemmi (mainly for crystallography, included in CCP4) >> https://gemmi.readthedocs.io/en/latest/grid.html >> >> Maybe there are also some relevant features in CCTBX (included in CCP4 >> and Phenix). >> >> Cheers, >> Martin >> >> On 05/06/2024 07:00, Devbrat Kumar wrote: >> >> Hello Everyone, >> >> Greetings! >> >> I have a query regarding the resampling of cryoEM density to match >> crystal density to obtain a density difference map. Specifically, I am >> trying to determine if it is feasible to resample a cryoEM map with an XRD >> density map. However, each time I attempt this, the resampling output >> provides an arbitrary ASU resample map, resulting in a significant loss of >> major density. >> >> I have been using Coot and Chimera for this process but have not achieved >> the desired outcome. Please guide me or suggest how to move forward with >> this. My goal is to create an accurate final density difference map. >> >> Thank you in advance for your help. >> *Warm Regards-* >> *Devbrat Kumar* >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner > igen avsändaren och vet att innehållet är säkert. > CAUTION: Do not click on links or open attachments unless you recognise > the sender and know the content is safe. > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör > det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal > data. For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Resampling CryoEM Density map to XRD Density map for Difference Map
Dear Guillaume I will keep that in mind while trying. Thank you Regards Devbrat On Wed, Jun 5, 2024, 5:21 PM Guillaume Gaullier < guillaume.gaull...@kemi.uu.se> wrote: > With a cryoEM map, it's easier to do the rigid-body fitting of step 2 in > real space (this is trivial to do interactively in ChimeraX) rather than by > MR. > -- > *From:* CCP4 bulletin board on behalf of Eleanor > Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> > *Sent:* Wednesday, June 5, 2024 1:39:56 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map > for Difference Map > > Hmm - rather tricky! I would do an MR search with the crystal model v the > EM density, > Steps would be: > 1) convert EM density to "structure factors". - there are tools which do > this .. > 1a) You need to go back to ccp4i - program sfall to read map to generate > SFs from map - then cad or sftools to add a fake SigF column > 2) Solve MR search with the model v these "structure factors" using them > as Fobs > 3) Calculate the structure factors from the MR positiooned model and get > the difference map.. > > > On Wed, 5 Jun 2024 at 11:46, Martin Malý wrote: > >> Dear Devbrat, >> >> I am now playing with a similar problem but I don't have a simple >> solution for you as I'm also quite stuck. You can check these software >> tools which involve some scripting in Python (NumPy, SciPy) and C++: >> >> EMDA (for cryoEM maps, included in CCP-EM) >> https://gitlab.com/ccpem/emda >> https://doi.org/10.1016/j.jsb.2021.107826 >> >> Gemmi (mainly for crystallography, included in CCP4) >> https://gemmi.readthedocs.io/en/latest/grid.html >> >> Maybe there are also some relevant features in CCTBX (included in CCP4 >> and Phenix). >> >> Cheers, >> Martin >> >> On 05/06/2024 07:00, Devbrat Kumar wrote: >> >> Hello Everyone, >> >> Greetings! >> >> I have a query regarding the resampling of cryoEM density to match >> crystal density to obtain a density difference map. Specifically, I am >> trying to determine if it is feasible to resample a cryoEM map with an XRD >> density map. However, each time I attempt this, the resampling output >> provides an arbitrary ASU resample map, resulting in a significant loss of >> major density. >> >> I have been using Coot and Chimera for this process but have not achieved >> the desired outcome. Please guide me or suggest how to move forward with >> this. My goal is to create an accurate final density difference map. >> >> Thank you in advance for your help. >> *Warm Regards-* >> *Devbrat Kumar* >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner > igen avsändaren och vet att innehållet är säkert. > CAUTION: Do not click on links or open attachments unless you recognise > the sender and know the content is safe. > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör > det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal > data. For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Resampling CryoEM Density map to XRD Density map for Difference Map
Hello Eleanor, Thank you for your consistent response to my inquiry. I will follow your suggestions and willl tell you the updates. Regards Devbrat On Wed, Jun 5, 2024, 5:10 PM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > Hmm - rather tricky! I would do an MR search with the crystal model v the > EM density, > Steps would be: > 1) convert EM density to "structure factors". - there are tools which do > this .. > 1a) You need to go back to ccp4i - program sfall to read map to generate > SFs from map - then cad or sftools to add a fake SigF column > 2) Solve MR search with the model v these "structure factors" using them > as Fobs > 3) Calculate the structure factors from the MR positiooned model and get > the difference map.. > > > On Wed, 5 Jun 2024 at 11:46, Martin Malý wrote: > >> Dear Devbrat, >> >> I am now playing with a similar problem but I don't have a simple >> solution for you as I'm also quite stuck. You can check these software >> tools which involve some scripting in Python (NumPy, SciPy) and C++: >> >> EMDA (for cryoEM maps, included in CCP-EM) >> https://gitlab.com/ccpem/emda >> https://doi.org/10.1016/j.jsb.2021.107826 >> >> Gemmi (mainly for crystallography, included in CCP4) >> https://gemmi.readthedocs.io/en/latest/grid.html >> >> Maybe there are also some relevant features in CCTBX (included in CCP4 >> and Phenix). >> >> Cheers, >> Martin >> >> On 05/06/2024 07:00, Devbrat Kumar wrote: >> >> Hello Everyone, >> >> Greetings! >> >> I have a query regarding the resampling of cryoEM density to match >> crystal density to obtain a density difference map. Specifically, I am >> trying to determine if it is feasible to resample a cryoEM map with an XRD >> density map. However, each time I attempt this, the resampling output >> provides an arbitrary ASU resample map, resulting in a significant loss of >> major density. >> >> I have been using Coot and Chimera for this process but have not achieved >> the desired outcome. Please guide me or suggest how to move forward with >> this. My goal is to create an accurate final density difference map. >> >> Thank you in advance for your help. >> *Warm Regards-* >> *Devbrat Kumar* >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Resampling CryoEM Density map to XRD Density map for Difference Map
Hello Martin, Thank you for your email and I will look into it. Regards Devbrat On Wed, Jun 5, 2024, 4:16 PM Martin Malý wrote: > Dear Devbrat, > > I am now playing with a similar problem but I don't have a simple solution > for you as I'm also quite stuck. You can check these software tools which > involve some scripting in Python (NumPy, SciPy) and C++: > > EMDA (for cryoEM maps, included in CCP-EM) > https://gitlab.com/ccpem/emda > https://doi.org/10.1016/j.jsb.2021.107826 > > Gemmi (mainly for crystallography, included in CCP4) > https://gemmi.readthedocs.io/en/latest/grid.html > > Maybe there are also some relevant features in CCTBX (included in CCP4 and > Phenix). > > Cheers, > Martin > > On 05/06/2024 07:00, Devbrat Kumar wrote: > > Hello Everyone, > > Greetings! > > I have a query regarding the resampling of cryoEM density to match crystal > density to obtain a density difference map. Specifically, I am trying to > determine if it is feasible to resample a cryoEM map with an XRD density > map. However, each time I attempt this, the resampling output provides an > arbitrary ASU resample map, resulting in a significant loss of major > density. > > I have been using Coot and Chimera for this process but have not achieved > the desired outcome. Please guide me or suggest how to move forward with > this. My goal is to create an accurate final density difference map. > > Thank you in advance for your help. > *Warm Regards-* > *Devbrat Kumar* > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
[ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map
Hello Everyone, Greetings! I have a query regarding the resampling of cryoEM density to match crystal density to obtain a density difference map. Specifically, I am trying to determine if it is feasible to resample a cryoEM map with an XRD density map. However, each time I attempt this, the resampling output provides an arbitrary ASU resample map, resulting in a significant loss of major density. I have been using Coot and Chimera for this process but have not achieved the desired outcome. Please guide me or suggest how to move forward with this. My goal is to create an accurate final density difference map. Thank you in advance for your help. *Warm Regards-* *Devbrat Kumar* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Multi-lattice crystal data processing strategy for structure solution
Dear Prof John Thank you for your valuable time and insight. I will do as you have suggested. *Warm Regards-* *Devbrat Kumar* On Wed, Nov 15, 2023 at 11:28 PM John Bacik < b45abf420e1f-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi Devbrat, here are a couple of other things to try: > > - When screening crystals use rastering to find regions of the sample > where multiple lattices may be less problematic. If multiple lattices are > observed, often regions on the crystal(s) close to the edge will not be as > affected by twinning/multiple lattices. Also try using fine slicing if you > are not already. > > - Try using AlphaFold to generate a model for the MR template. > > All the best, > John > > On Wednesday, November 15, 2023 at 06:10:06 AM CST, Phil Evans < > p...@mrc-lmb.cam.ac.uk> wrote: > > > Is the space group really P2? P21 is MUCH more common > Phil > > > On 14 Nov 2023, at 15:55, Devbrat Kumar wrote: > > > > sed data were integrated with the data reduction tool AIMLESS in the > CCP4i2 suite. > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Multi-lattice crystal data processing strategy for structure solution
Dear Prof Gerard Thank you for your in-depth analysis of the possibilities I am facing. The image slicing was at 0.1 degrees. *Warm Regards-* *Devbrat Kumar* On Wed, Nov 15, 2023 at 5:21 PM Gerard Bricogne wrote: > Dear Devbrat, > > With the unit-cell geometry you have, namely a very long axis and two > much shorter ones, you have to be exceedingly careful about how the data > are > collected, and in particular about the crystal orientation and image width. > > If the long axis can be brought close to being parallel to the > rotation > axis - either because the crystal morphology tends to make this happen or > (better) because you can use a multi-axis goniometer to orient it that way > - > the images will have rows of closely-spaced spots that should be resolvable > if the detector is placed far enough. If on the other hand the long axis is > at a large angle to the rotation axis, there will be image ranges where > that > axis gets close to being parallel to the beam, so that the separation of > reflections along that long axis (in fact, along the short reciprocal axis) > will depends on their angular distance. Unless the image width is small > enough, there will be overlap of the spots for consecutive reflections > along > that short reciprocal axis. Indexing diagnostics may then give an > impression > that there is more than one lattice, but most of all, because two distinct > reflexions may overlap into a single spot, many integrated intensities will > be corrupted. > > Perhaps this is not the case, but out of curiosity: what is the > angular > width of your images? > > > With best wishes, > > Gerard. > > -- > On Tue, Nov 14, 2023 at 09:25:30PM +0530, Devbrat Kumar wrote: > > Hello everyone, > > > > The issue with the crystal is its multi-lattice nature; even the > truncated > > protein, which has been crystallized, exhibits multi-lattice > > characteristics (detectable only after XRD). > > > > I have multiple native and selenium datasets with similar unit cell > > parameters. (One axis is excessively long.) The XRD images were processed > > using XDS in the P2 spacegroup, with unit cell parameters as follows: a = > > 27.75 Å, b = 293.9 Å, c = 34.6 Å, and β = 113°. The XDS-processed data > were > > integrated with the data reduction tool AIMLESS in the CCP4i2 suite. In > > CRANK2, the Estimation of Matthews coefficient (Program used: GCX) > > suggested the presence of monomer NCS with a solvent content of 63.6%. > The > > FA estimation and substructure detection were performed by SHELXC, which > > detected a very weak signal below 3.4 Å. Substructure determination was > > carried out using SHELXD, yielding a maximum figure of merit of 27.8 > after > > 640 trials and suggesting 11 atoms in the substructure with an occupancy > of > > at least 25%. Phasing and substructure refinement were conducted using > the > > BP3 program, resulting in an FOM of 0.2. During hand determination, the > > programs suggested combined DM (density modification) FOM and phasing CLD > > score for hand one as 6.0 and for hand two as 4.783375. The tool didn't > > choose the hand because the value is less than the threshold. Density > > modification with Fourier recycling suggests that the final FOM for hand > > one and hand two is 0.428 and 0.482, respectively, while REFMAC5 gives > the > > R factor and Rfree factor as 0.4262 and 0.4912. > > > > One of the MR templates (model with balbes) works(For MR, Identity with > the > > PDB template is 21%), but R & Rfree are stuck at 33 & 37 for the 2.7 > > Angstrom cut-off (the total resolution in the dataset is 2 Angstrom). > The R > > & Rfree is not decreasing for the dataset. I have played with detector > > distances for spot resolution, but at one pHi the spots have merged as a > > single spot, while at 90 degrees will give us the streak of spots. > > > > Looking forward to hearing from you regarding dataset processing ideas > for > > multi-lattice crystals(Native & Se dataset) and structure solution > strategy. > > > > Thank you. > > Regards > > Devbrat > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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
Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution
Dear Professor, Thank you for your valuable suggestions. I have attempted to investigate the NCS operator, but it seems to be a monomer. Nevertheless, I will reconsider your suggestion regarding this matter. I employed the concept of using high-resolution data (2 Angstroms) without cutoff for model building and refinement cycling, along with phases from MR (2.7 Angstroms). I will revisit this process. I will follow your advice for the peak search. If I cannot find any leads, I hope to seek your guidance. Thank you again for your support. *Warm Regards-* *Devbrat Kumar* On Wed, Nov 15, 2023 at 4:38 PM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > You seem pretty near to having solved your structure! > Ignoring the data problems.. > > Extra steps I might have used. > 1) Self rotation function. (in CCP4I2 the task is under data analysis ..) > Does it suggest a NCS operator? > If so is this a two fold? which might mean you have a dimer.. > > > 2) Now you have a reasonable R factor try extending the resolution. the > refinement program will weight down the high resolution less reliable data > but the extra information might marginally improve the maps. > > 3) Use the calculated phases to run an anomalous map - REFMAC will produce > the appropriate coefficients and you can display the map in COOT. > Do a peaksearch and you should of course see the sites SHELX found.. > But sometimes you get peaks over S atoms and that makes you pretty > confident that the sequence there is correct. > > > > On Wed, 15 Nov 2023 at 10:42, Kay Diederichs < > kay.diederi...@uni-konstanz.de> wrote: > >> Hello Devbrat, >> >> your project is difficult and there is no magic bullet to solve its >> problems. Your approach is good because it always pays off to process >> the data carefully. >> In this respect, let me make a few comments. >> 1) you don't say why you call the diffraction patterns "multi-lattice". >> What exactly do you mean by that? Non-merohedral >> twinning? How many lattices superimposed and visible on all frames? Can >> they be separately indexed by XDS >> (see https://wiki.uni-konstanz.de/xds/index.php/Indexing)? >> 2) "XDS processing" _is_ integrating; what AIMLESS does is called scaling. >> 3) what do you mean by "monomer NCS"? NCS implies two or more copies of >> the same molecule in the asymmetric unit. >> These copies often form dimers, trimers, tetramers, ... by making >> more-or-less strong and specific interactions. >> 4) you've advanced amazingly far and it sounds to me that with a >> combination of your refined MR model with the SAD data you >> should be able to improve your solution. Look up the MR-SAD pipeline (for >> SAD after MR and for model rebuilding using anomalous >> data) of Crank2. >> >> If you want me to take a look at your raw data, upload the best datasets >> (native and SeMet) to a cloud service and send me the link. >> >> Good luck, >> Kay >> >> On Tue, 14 Nov 2023 21:25:30 +0530, Devbrat Kumar >> wrote: >> >> >Hello everyone, >> > >> >The issue with the crystal is its multi-lattice nature; even the >> truncated >> >protein, which has been crystallized, exhibits multi-lattice >> >characteristics (detectable only after XRD). >> > >> >I have multiple native and selenium datasets with similar unit cell >> >parameters. (One axis is excessively long.) The XRD images were processed >> >using XDS in the P2 spacegroup, with unit cell parameters as follows: a = >> >27.75 Å, b = 293.9 Å, c = 34.6 Å, and β = 113°. The XDS-processed data >> were >> >integrated with the data reduction tool AIMLESS in the CCP4i2 suite. In >> >CRANK2, the Estimation of Matthews coefficient (Program used: GCX) >> >suggested the presence of monomer NCS with a solvent content of 63.6%. >> The >> >FA estimation and substructure detection were performed by SHELXC, which >> >detected a very weak signal below 3.4 Å. Substructure determination was >> >carried out using SHELXD, yielding a maximum figure of merit of 27.8 >> after >> >640 trials and suggesting 11 atoms in the substructure with an occupancy >> of >> >at least 25%. Phasing and substructure refinement were conducted using >> the >> >BP3 program, resulting in an FOM of 0.2. During hand determination, the >> >programs suggested combined DM (density modification) FOM and phasing CLD >> >score for hand one as 6.0 and for hand two as 4.783375. The tool didn't >> >choose the hand because the value is
Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution
Hello Professor Kay Thank you for your in-depth and valuable suggestions. 1. I used to observe multiple spots at one Phi, and at 90 degrees, I would find a streak of spots. The crystal used to be spade-shaped. The spots are visible in a count of 8 (matching the total number of crystal lattices). 2. I tried MR-SAD, but couldn't find the selenium substructure at the Sulpher position of the sequence. 3. I will follow your suggestion to read about XDS and conduct the integration using XDS. 4. If I do not find any leads, I will email you the dataset. *Warm Regards-* *Devbrat * On Wed, Nov 15, 2023 at 4:12 PM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Hello Devbrat, > > your project is difficult and there is no magic bullet to solve its > problems. Your approach is good because it always pays off to process > the data carefully. > In this respect, let me make a few comments. > 1) you don't say why you call the diffraction patterns "multi-lattice". > What exactly do you mean by that? Non-merohedral > twinning? How many lattices superimposed and visible on all frames? Can > they be separately indexed by XDS > (see https://wiki.uni-konstanz.de/xds/index.php/Indexing)? > 2) "XDS processing" _is_ integrating; what AIMLESS does is called scaling. > 3) what do you mean by "monomer NCS"? NCS implies two or more copies of > the same molecule in the asymmetric unit. > These copies often form dimers, trimers, tetramers, ... by making > more-or-less strong and specific interactions. > 4) you've advanced amazingly far and it sounds to me that with a > combination of your refined MR model with the SAD data you > should be able to improve your solution. Look up the MR-SAD pipeline (for > SAD after MR and for model rebuilding using anomalous > data) of Crank2. > > If you want me to take a look at your raw data, upload the best datasets > (native and SeMet) to a cloud service and send me the link. > > Good luck, > Kay > > On Tue, 14 Nov 2023 21:25:30 +0530, Devbrat Kumar > wrote: > > >Hello everyone, > > > >The issue with the crystal is its multi-lattice nature; even the truncated > >protein, which has been crystallized, exhibits multi-lattice > >characteristics (detectable only after XRD). > > > >I have multiple native and selenium datasets with similar unit cell > >parameters. (One axis is excessively long.) The XRD images were processed > >using XDS in the P2 spacegroup, with unit cell parameters as follows: a = > >27.75 Å, b = 293.9 Å, c = 34.6 Å, and β = 113°. The XDS-processed data > were > >integrated with the data reduction tool AIMLESS in the CCP4i2 suite. In > >CRANK2, the Estimation of Matthews coefficient (Program used: GCX) > >suggested the presence of monomer NCS with a solvent content of 63.6%. The > >FA estimation and substructure detection were performed by SHELXC, which > >detected a very weak signal below 3.4 Å. Substructure determination was > >carried out using SHELXD, yielding a maximum figure of merit of 27.8 after > >640 trials and suggesting 11 atoms in the substructure with an occupancy > of > >at least 25%. Phasing and substructure refinement were conducted using the > >BP3 program, resulting in an FOM of 0.2. During hand determination, the > >programs suggested combined DM (density modification) FOM and phasing CLD > >score for hand one as 6.0 and for hand two as 4.783375. The tool didn't > >choose the hand because the value is less than the threshold. Density > >modification with Fourier recycling suggests that the final FOM for hand > >one and hand two is 0.428 and 0.482, respectively, while REFMAC5 gives the > >R factor and Rfree factor as 0.4262 and 0.4912. > > > >One of the MR templates (model with balbes) works(For MR, Identity with > the > >PDB template is 21%), but R & Rfree are stuck at 33 & 37 for the 2.7 > >Angstrom cut-off (the total resolution in the dataset is 2 Angstrom). The > R > >& Rfree is not decreasing for the dataset. I have played with detector > >distances for spot resolution, but at one pHi the spots have merged as a > >single spot, while at 90 degrees will give us the streak of spots. > > > >Looking forward to hearing from you regarding dataset processing ideas for > >multi-lattice crystals(Native & Se dataset) and structure solution > strategy. > > > >Thank you. > >Regards > >Devbrat > > > > > > > >To unsubscribe from the CCP4BB list, click the following link: > >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > &
Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution
Dear Professor Phil Thank you for highlighting and providing input. Yes, The space group is P21. *Warm Regards-* *Devbrat Kumar* On Wed, Nov 15, 2023 at 5:39 PM Phil Evans wrote: > Is the space group really P2? P21 is MUCH more common > Phil > > > On 14 Nov 2023, at 15:55, Devbrat Kumar wrote: > > > > sed data were integrated with the data reduction tool AIMLESS in the > CCP4i2 suite. > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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/
[ccp4bb] Multi-lattice crystal data processing strategy for structure solution
Hello everyone, The issue with the crystal is its multi-lattice nature; even the truncated protein, which has been crystallized, exhibits multi-lattice characteristics (detectable only after XRD). I have multiple native and selenium datasets with similar unit cell parameters. (One axis is excessively long.) The XRD images were processed using XDS in the P2 spacegroup, with unit cell parameters as follows: a = 27.75 Å, b = 293.9 Å, c = 34.6 Å, and β = 113°. The XDS-processed data were integrated with the data reduction tool AIMLESS in the CCP4i2 suite. In CRANK2, the Estimation of Matthews coefficient (Program used: GCX) suggested the presence of monomer NCS with a solvent content of 63.6%. The FA estimation and substructure detection were performed by SHELXC, which detected a very weak signal below 3.4 Å. Substructure determination was carried out using SHELXD, yielding a maximum figure of merit of 27.8 after 640 trials and suggesting 11 atoms in the substructure with an occupancy of at least 25%. Phasing and substructure refinement were conducted using the BP3 program, resulting in an FOM of 0.2. During hand determination, the programs suggested combined DM (density modification) FOM and phasing CLD score for hand one as 6.0 and for hand two as 4.783375. The tool didn't choose the hand because the value is less than the threshold. Density modification with Fourier recycling suggests that the final FOM for hand one and hand two is 0.428 and 0.482, respectively, while REFMAC5 gives the R factor and Rfree factor as 0.4262 and 0.4912. One of the MR templates (model with balbes) works(For MR, Identity with the PDB template is 21%), but R & Rfree are stuck at 33 & 37 for the 2.7 Angstrom cut-off (the total resolution in the dataset is 2 Angstrom). The R & Rfree is not decreasing for the dataset. I have played with detector distances for spot resolution, but at one pHi the spots have merged as a single spot, while at 90 degrees will give us the streak of spots. Looking forward to hearing from you regarding dataset processing ideas for multi-lattice crystals(Native & Se dataset) and structure solution strategy. Thank you. Regards Devbrat To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
