Re: [ccp4bb] real real-space-refinement
On 31/07/2020 20:33, James Holton wrote: But, if you real really want to do real real-space, then I suppose coot is doing that? I'm actually not sure. If by "real-space refinement" you mean the same thing as described by Bob Diamond [1], then no, the sum of the squared difference between the calculated and "observed" density is not what is minimized in Coot. Paul. [1]"A real-space refinement procedure for proteins" R.Diamond (1971) Acta Cryst A27 436-452. 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] real real-space-refinement
Dear Thierry, - Le 31 Juil 20, à 21:58, Fischmann, Thierry <22f7fda0a875-dmarc-requ...@jiscmail.ac.uk> a écrit : > Jim wrote: > “ technically, not in Phenix either. The real-space refinement in Phenix > simply > picks peaks in the density and then pulls nearby atoms toward them. . Like a > black hole gobbling up nearby planets (snip)” > Do you have a reference to support this assertion The methodology of the "dirty but very fast" real space refinement in Phenix is described in detail in the article : Afonine, P.V.et al. (2018) "Real-space refinement in PHENIX for cryo-EM and crystallography". Acta Cryst ., D 74 , 531-544. The articel contains also arguments for such kind of procedure, its advantages (the principal goal and advantage is a very high speed) and obvious limitations (one of them mentioned by James). > Hopefully someone from the Phenix team will give some clarifications. But the > statement above indicates that Phenix is capable of performing real space > refinement by some other means than the “black hole approach” Sorry, here I cannot comment. Best regards, Sacha Urzhumtsev 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] real real-space-refinement
The isolde suggestion already made is an excellent one. The hardest part of that is getting the right version of chimeraX working. But, once you've done that its pretty straightforward. Hopefully not for too much longer. All going well, ISOLDE 1.0 (to work in ChimeraX 1.0) should be out this week. On 2020-07-31 20:33, James Holton wrote: Not in CCP4, no. And, technically, not in Phenix either. The real-space refinement in Phenix simply picks peaks in the density and then pulls nearby atoms toward them. Like a black hole gobbling up nearby planets. It took me a while to realize that! If you manage to turn off geometry restraints (as I eventually did) all the atoms end up on top of each other. Might seem like a horrible idea, but for poor resolution data and reasonably good geometry restraints it has a high radius of convergence and is incredibly fast when compared to "real real-space refinement". Refining against map voxels directly is a very very slow process. But, if you real really want to do real real-space, then I suppose coot is doing that? I'm actually not sure. The isolde suggestion already made is an excellent one. The hardest part of that is getting the right version of chimeraX working. But, once you've done that its pretty straightforward. One program that has not been mentioned, but does "real real" space refinement is: "rsref" https://chapman.missouri.edu/wp-content/uploads/sites/2/software/rsref/html/rsref_doc.html It is not too hard to install and use. I can't say I've gotten results appreciably different from reciprocal-space refinement, and that led me to ask myself why exactly I thought it would be different. The Fourier transform is symmetric after all. But I do expect that if you have unmodeled regions, such as big, spiky metals, or large tracts of disordered, ropy stuff, then localizing the refinement could be beneficial. Now, of course, you can also do localized refinement in reciprocal space by just smoothing out parts of the map that are "uninteresting". The vast area of noise around the protein in a cryoEM map, for example, is perhaps a candidate for noise suppression. The only trick is how to suppress noise without creating systematic error. For example, if your model does not have "bulk solvent" then this area will be modeled as vacuum, but if you simply set the map voxel values to 0.00, you will have effectively created more bulk solvent, not eliminated it. This is because 0.00 is usually the average voxel value, not the "vacuum level". Then there is the "edge" between the modified and unmodified areas. Unless you smooth it in some way this edge will be very sharp and therefore have significant Fourier coefficients at a wide range of resolutions. So, if you are not careful, your "noise suppression" can create a lot more error than it eliminates. As for what to do? The scale factor given to the "bulk solvent" model is perhaps the best value to use to replace the "bulk" solvent region. The bulk solvent mask itself, ranging from 0 to 1, might also be a reasonable weighting function for combining your original map with a single-valued map. That is, don't change the protein, but flatten the solvent. You can get this map out of refmac using the MSKOUT feature. You then smooth it in reciprocal space by applying refmac's best-fit solvent B factor using sfall and fft, then finally scale it with mapmask. I should admit, however, that I have not tried this in a while. Let me know if it works! HTH -James Holton MAD Scientist On 7/29/2020 8:20 AM, Schreuder, Herman /DE wrote: Dear BB, I would like to do a real real-space-refinement of a protein against a cryo-EM map; not the mtz-based Refmac approach. A quick internet search produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how to do this using ccp4 programs, or has someone a Coot script to do this? Thank you for your help! Herman - 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 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] real real-space-refinement
Jim wrote: "technically, not in Phenix either. The real-space refinement in Phenix simply picks peaks in the density and then pulls nearby atoms toward them. . Like a black hole gobbling up nearby planets (snip)" Do you have a reference to support this assertion? "It took me a while to realize that! If you manage to turn off geometry restraints (as I eventually did) all the atoms end up on top of each other." As expected if no bond distance is enforced, unless you have very high resolution to the point that density for each atom becomes discrete. Since that is very unlikely to be your case your observation: does not prove anything about how Phenix works. >From phenix.refine documentation: "Coordinates can be refined using: * (snip) * individual coordinate refinement in real-space using a combination of gradient-driven (LBFGS) minimization and local torsion-angle grid searches" Hopefully someone from the Phenix team will give some clarifications. But the statement above indicates that Phenix is capable of performing real space refinement by some other means than the "black hole approach". Thierry Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. 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] real real-space-refinement
Not in CCP4, no. And, technically, not in Phenix either. The real-space refinement in Phenix simply picks peaks in the density and then pulls nearby atoms toward them. Like a black hole gobbling up nearby planets. It took me a while to realize that! If you manage to turn off geometry restraints (as I eventually did) all the atoms end up on top of each other. Might seem like a horrible idea, but for poor resolution data and reasonably good geometry restraints it has a high radius of convergence and is incredibly fast when compared to "real real-space refinement". Refining against map voxels directly is a very very slow process. But, if you real really want to do real real-space, then I suppose coot is doing that? I'm actually not sure. The isolde suggestion already made is an excellent one. The hardest part of that is getting the right version of chimeraX working. But, once you've done that its pretty straightforward. One program that has not been mentioned, but does "real real" space refinement is: "rsref" https://chapman.missouri.edu/wp-content/uploads/sites/2/software/rsref/html/rsref_doc.html It is not too hard to install and use. I can't say I've gotten results appreciably different from reciprocal-space refinement, and that led me to ask myself why exactly I thought it would be different. The Fourier transform is symmetric after all. But I do expect that if you have unmodeled regions, such as big, spiky metals, or large tracts of disordered, ropy stuff, then localizing the refinement could be beneficial. Now, of course, you can also do localized refinement in reciprocal space by just smoothing out parts of the map that are "uninteresting". The vast area of noise around the protein in a cryoEM map, for example, is perhaps a candidate for noise suppression. The only trick is how to suppress noise without creating systematic error. For example, if your model does not have "bulk solvent" then this area will be modeled as vacuum, but if you simply set the map voxel values to 0.00, you will have effectively created more bulk solvent, not eliminated it. This is because 0.00 is usually the average voxel value, not the "vacuum level". Then there is the "edge" between the modified and unmodified areas. Unless you smooth it in some way this edge will be very sharp and therefore have significant Fourier coefficients at a wide range of resolutions. So, if you are not careful, your "noise suppression" can create a lot more error than it eliminates. As for what to do? The scale factor given to the "bulk solvent" model is perhaps the best value to use to replace the "bulk" solvent region. The bulk solvent mask itself, ranging from 0 to 1, might also be a reasonable weighting function for combining your original map with a single-valued map. That is, don't change the protein, but flatten the solvent. You can get this map out of refmac using the MSKOUT feature. You then smooth it in reciprocal space by applying refmac's best-fit solvent B factor using sfall and fft, then finally scale it with mapmask. I should admit, however, that I have not tried this in a while. Let me know if it works! HTH -James Holton MAD Scientist On 7/29/2020 8:20 AM, Schreuder, Herman /DE wrote: Dear BB, I would like to do a real real-space-refinement of a protein against a cryo-EM map; not the mtz-based Refmac approach. A quick internet search produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how to do this using ccp4 programs, or has someone a Coot script to do this? Thank you for your help! Herman 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] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
To paraphrase from our 2018 Acta Cryst D74(6) paper: “There has been debate as to whether refinement should be performed in real space or reciprocal space; both approaches have advantages and disadvantages. In real space, refinement can be performed locally, which has advantages for computational speed and parallelisation. [Update: Refmac now has the option to perform “local refinement”, which means focusing on just a localised region in order to speed things up – this option is available from within the CCP-EM interface.] Refinement in reciprocal space allows accounting for errors in Fourier coefficients more accurately. And, although errors in neighbouring Fourier coefficients are correlated, they are less correlated than between proximal points in real space. Furthermore, the degree to which errors are correlated will depend on the nature of the underlying data (i.e. on the reconstruction methods). There is a common misconception that the original data are in real space. Reconstructions are typically performed in Fourier space using the projection-slice theorem, before the reconstructed maps are subsequently calculated in real space. Alternatively, 3D reconstruction may be performed in real space using back-projection, noting that this results in a large correlation radius of errors in real space. The procedures in real and reciprocal space are mathematically equivalent; in both cases refinement should be equivalent (apart from details of implementation). The community would benefit from clarification about best practice on this controversial topic, thus proper analysis will be required in future." Indeed, until works have been published on the objective comparative analysis of the performance of real vs reciprocal space refinement of models against cryo-EM maps, it seems premature to sit too strongly on one side of the fence or the other. Until then, I'd recommend people to try different tools and use what works best for them, without too much preconception. Regards, Rob Dr Rob Nicholls Senior Investigator Scientist MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH > On 30 Jul 2020, at 13:28, Schreuder, Herman /DE > wrote: > > Hi everybody, > > Thank you very much for the many tips! I discovered that in Coot by clicking > on the N- and C-terminus of a protein chain, one can indeed run a real-space > refinement on the complete chain and the same is true for a rigid body fit. > However, subsequent refinement with Refmac did not converge, so it looks like > I still have to go manually through the chains. ☹ > Still on my to do list are: > - test Isolde > - test Main > - test the wiggle-fit option in Coot. > > Although the Refmac procedure consisting of converting the cryo-EM map into > structure factors and running a "crystallographic" refinement on it seems to > work, in my opinion the future will be a robust real-space refinement on the > cryo-EM map itself, instead of a refinement on derived structure factors. > However, this is my personal opinion. > > Best regards, > Herman > > -Ursprüngliche Nachricht- > Von: CCP4 bulletin board Im Auftrag von Tom Burnley - > UKRI STFC > Gesendet: Mittwoch, 29. Juli 2020 18:51 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement > > EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk > > > > Hi Herman, > > > There is lots of information on CCP-EM's modelling tools here: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ccpem.ac.uk_training_icknield-5F2019_icknield-5F2019.php=DwIFAg=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=aaxzRy8JT0AM0_MqNvU2fr6IB4wIbkY8SsgvQkYcw_w=D5VOMK2Fz8AOV1PCvJpD9tm914KUxJlsRNRWXYPb7tI= > > > This includes a tutorial on Refmac. As you note this is done in reciprocal > space but the CCP-EM pipeline handles conversions from MRC to MTZ format (and > runs Refmac via CCP4). > > > All the best, > > > Tom > > ________ > From: CCP4 bulletin board on behalf of Boaz Shaanan > > Sent: 29 July 2020 16:31:46 > To: ccp4bb > Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement > > Hi, > Try searching ccp-em. > Boaz > > Boaz Shaanan, Ph.D. > Department of Life Sciences > Ben Gurion University of the Negev > Beer Sheva > Israel > > On Jul 29, 2020 18:29, "Schreuder, Herman /DE" > wrote: > Coot does it, but if one wants to do it for a complete protein, it is a lot > of clicking. On the other hand, I have not tried to just select the N- and > C-terminus for real-space refinement to see what happens. I would prefe
[ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
Thank you. I think I will then first try to optimize the weight and then increase the cycles. Herman -Ursprüngliche Nachricht- Von: Tom Burnley - UKRI STFC Gesendet: Donnerstag, 30. Juli 2020 14:35 An: ccp4bb@jiscmail.ac.uk; Schreuder, Herman /DE Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement EXTERNAL : Real sender is tom.burn...@stfc.ac.uk Hi Herman, Just a couple of tips for Refmac... 1) increase number of cycles - we find some cases require a lot of cycles, more than you may be used from MX refinement. 2) optimise weight - this is important and at present the autoweighting option is not as reliable for EM refinement as MX. You could run these in parallel whilst exploring the other very nice tools suggested ! Cheers, Tom From: CCP4 bulletin board on behalf of Schreuder, Herman /DE Sent: 30 July 2020 13:28:00 To: ccp4bb Subject: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement Hi everybody, Thank you very much for the many tips! I discovered that in Coot by clicking on the N- and C-terminus of a protein chain, one can indeed run a real-space refinement on the complete chain and the same is true for a rigid body fit. However, subsequent refinement with Refmac did not converge, so it looks like I still have to go manually through the chains. ☹ Still on my to do list are: - test Isolde - test Main - test the wiggle-fit option in Coot. Although the Refmac procedure consisting of converting the cryo-EM map into structure factors and running a "crystallographic" refinement on it seems to work, in my opinion the future will be a robust real-space refinement on the cryo-EM map itself, instead of a refinement on derived structure factors. However, this is my personal opinion. Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board Im Auftrag von Tom Burnley - UKRI STFC Gesendet: Mittwoch, 29. Juli 2020 18:51 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk Hi Herman, There is lots of information on CCP-EM's modelling tools here: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ccpem.ac.uk_training_icknield-5F2019_icknield-5F2019.php=DwIFAg=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=aaxzRy8JT0AM0_MqNvU2fr6IB4wIbkY8SsgvQkYcw_w=D5VOMK2Fz8AOV1PCvJpD9tm914KUxJlsRNRWXYPb7tI= This includes a tutorial on Refmac. As you note this is done in reciprocal space but the CCP-EM pipeline handles conversions from MRC to MTZ format (and runs Refmac via CCP4). All the best, Tom From: CCP4 bulletin board on behalf of Boaz Shaanan Sent: 29 July 2020 16:31:46 To: ccp4bb Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement Hi, Try searching ccp-em. Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Jul 29, 2020 18:29, "Schreuder, Herman /DE" wrote: Coot does it, but if one wants to do it for a complete protein, it is a lot of clicking. On the other hand, I have not tried to just select the N- and C-terminus for real-space refinement to see what happens. I would prefer to have some script to do it. Best, Herman Von: Eleanor Dodson Gesendet: Mittwoch, 29. Juli 2020 17:23 An: Schreuder, Herman /DE Cc: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement EXTERNAL : Real sender is eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk> Wont coot do that? Eleanor On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE mailto:herman.schreu...@sanofi.com>> wrote: Dear BB, I would like to do a real real-space-refinement of a protein against a cryo-EM map; not the mtz-based Refmac approach. A quick internet search produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how to do this using ccp4 programs, or has someone a Coot script to do this? Thank you for your help! Herman To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwIFAg=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=aaxzRy8JT0AM0_MqNvU2fr6IB4wIbkY8SsgvQkYcw_w=oaC9nUo2Fbh2pGf7qGeQPpoRSR8vFBLjOxlTLJRAxcU=<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=Ch0pjy23vd6uA_krOf8kvGcBAXoSM6A4B64IAhROL4g=12CS6Fb_HI-kbl4I1FebLJB9l_zTdFKUTIGdO53-Ar8=> _
Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
Hi Herman, Just a couple of tips for Refmac... 1) increase number of cycles - we find some cases require a lot of cycles, more than you may be used from MX refinement. 2) optimise weight - this is important and at present the autoweighting option is not as reliable for EM refinement as MX. You could run these in parallel whilst exploring the other very nice tools suggested ! Cheers, Tom From: CCP4 bulletin board on behalf of Schreuder, Herman /DE Sent: 30 July 2020 13:28:00 To: ccp4bb Subject: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement Hi everybody, Thank you very much for the many tips! I discovered that in Coot by clicking on the N- and C-terminus of a protein chain, one can indeed run a real-space refinement on the complete chain and the same is true for a rigid body fit. However, subsequent refinement with Refmac did not converge, so it looks like I still have to go manually through the chains. ☹ Still on my to do list are: - test Isolde - test Main - test the wiggle-fit option in Coot. Although the Refmac procedure consisting of converting the cryo-EM map into structure factors and running a "crystallographic" refinement on it seems to work, in my opinion the future will be a robust real-space refinement on the cryo-EM map itself, instead of a refinement on derived structure factors. However, this is my personal opinion. Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board Im Auftrag von Tom Burnley - UKRI STFC Gesendet: Mittwoch, 29. Juli 2020 18:51 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk Hi Herman, There is lots of information on CCP-EM's modelling tools here: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ccpem.ac.uk_training_icknield-5F2019_icknield-5F2019.php=DwIFAg=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=aaxzRy8JT0AM0_MqNvU2fr6IB4wIbkY8SsgvQkYcw_w=D5VOMK2Fz8AOV1PCvJpD9tm914KUxJlsRNRWXYPb7tI= This includes a tutorial on Refmac. As you note this is done in reciprocal space but the CCP-EM pipeline handles conversions from MRC to MTZ format (and runs Refmac via CCP4). All the best, Tom From: CCP4 bulletin board on behalf of Boaz Shaanan Sent: 29 July 2020 16:31:46 To: ccp4bb Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement Hi, Try searching ccp-em. Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Jul 29, 2020 18:29, "Schreuder, Herman /DE" wrote: Coot does it, but if one wants to do it for a complete protein, it is a lot of clicking. On the other hand, I have not tried to just select the N- and C-terminus for real-space refinement to see what happens. I would prefer to have some script to do it. Best, Herman Von: Eleanor Dodson Gesendet: Mittwoch, 29. Juli 2020 17:23 An: Schreuder, Herman /DE Cc: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement EXTERNAL : Real sender is eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk> Wont coot do that? Eleanor On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE mailto:herman.schreu...@sanofi.com>> wrote: Dear BB, I would like to do a real real-space-refinement of a protein against a cryo-EM map; not the mtz-based Refmac approach. A quick internet search produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how to do this using ccp4 programs, or has someone a Coot script to do this? Thank you for your help! Herman To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwIFAg=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=aaxzRy8JT0AM0_MqNvU2fr6IB4wIbkY8SsgvQkYcw_w=oaC9nUo2Fbh2pGf7qGeQPpoRSR8vFBLjOxlTLJRAxcU=<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=Ch0pjy23vd6uA_krOf8kvGcBAXoSM6A4B64IAhROL4g=12CS6Fb_HI-kbl4I1FebLJB9l_zTdFKUTIGdO53-Ar8=> To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwIFAg=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=aaxzRy8JT0AM0_MqNvU2fr6IB4wIbkY8SsgvQkYcw_w=oaC9nUo2Fbh2pGf7qGeQPpoRSR8vFBLjOxlTLJRAxcU= To unsubscribe from the CCP4BB list, click the following link: ht
[ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
Hi everybody, Thank you very much for the many tips! I discovered that in Coot by clicking on the N- and C-terminus of a protein chain, one can indeed run a real-space refinement on the complete chain and the same is true for a rigid body fit. However, subsequent refinement with Refmac did not converge, so it looks like I still have to go manually through the chains. ☹ Still on my to do list are: - test Isolde - test Main - test the wiggle-fit option in Coot. Although the Refmac procedure consisting of converting the cryo-EM map into structure factors and running a "crystallographic" refinement on it seems to work, in my opinion the future will be a robust real-space refinement on the cryo-EM map itself, instead of a refinement on derived structure factors. However, this is my personal opinion. Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board Im Auftrag von Tom Burnley - UKRI STFC Gesendet: Mittwoch, 29. Juli 2020 18:51 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk Hi Herman, There is lots of information on CCP-EM's modelling tools here: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ccpem.ac.uk_training_icknield-5F2019_icknield-5F2019.php=DwIFAg=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=aaxzRy8JT0AM0_MqNvU2fr6IB4wIbkY8SsgvQkYcw_w=D5VOMK2Fz8AOV1PCvJpD9tm914KUxJlsRNRWXYPb7tI= This includes a tutorial on Refmac. As you note this is done in reciprocal space but the CCP-EM pipeline handles conversions from MRC to MTZ format (and runs Refmac via CCP4). All the best, Tom From: CCP4 bulletin board on behalf of Boaz Shaanan Sent: 29 July 2020 16:31:46 To: ccp4bb Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement Hi, Try searching ccp-em. Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Jul 29, 2020 18:29, "Schreuder, Herman /DE" wrote: Coot does it, but if one wants to do it for a complete protein, it is a lot of clicking. On the other hand, I have not tried to just select the N- and C-terminus for real-space refinement to see what happens. I would prefer to have some script to do it. Best, Herman Von: Eleanor Dodson Gesendet: Mittwoch, 29. Juli 2020 17:23 An: Schreuder, Herman /DE Cc: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement EXTERNAL : Real sender is eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk> Wont coot do that? Eleanor On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE mailto:herman.schreu...@sanofi.com>> wrote: Dear BB, I would like to do a real real-space-refinement of a protein against a cryo-EM map; not the mtz-based Refmac approach. A quick internet search produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how to do this using ccp4 programs, or has someone a Coot script to do this? Thank you for your help! Herman To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwIFAg=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=aaxzRy8JT0AM0_MqNvU2fr6IB4wIbkY8SsgvQkYcw_w=oaC9nUo2Fbh2pGf7qGeQPpoRSR8vFBLjOxlTLJRAxcU=<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=Ch0pjy23vd6uA_krOf8kvGcBAXoSM6A4B64IAhROL4g=12CS6Fb_HI-kbl4I1FebLJB9l_zTdFKUTIGdO53-Ar8=> To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwIFAg=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=aaxzRy8JT0AM0_MqNvU2fr6IB4wIbkY8SsgvQkYcw_w=oaC9nUo2Fbh2pGf7qGeQPpoRSR8vFBLjOxlTLJRAxcU= To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwIFAg=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=aaxzRy8JT0AM0_MqNvU2fr6IB4wIbkY8SsgvQkYcw_w=oaC9nUo2Fbh2pGf7qGeQPpoRSR8vFBLjOxlTLJRAxcU= This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innova
Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
Hello, Have you tried ISOLDE? Interactive MDFF is really powerful both for fixing models with poor geometry and for improving fit to the map. There is a good tutorial for refinement of a model against a cryoEM map with ISOLDE: https://isolde.cimr.cam.ac.uk/static/isolde/doc/tutorials/intro/cryo_intro/cryo_intro.html I hope this helps, Guillaume > On 29 Jul 2020, at 17:29, Schreuder, Herman /DE > wrote: > > > Coot does it, but if one wants to do it for a complete protein, it is a lot > of clicking. On the other hand, I have not tried to just select the N- and > C-terminus for real-space refinement to see what happens. I would prefer to > have some script to do it. > Best, Herman > > Von: Eleanor Dodson > Gesendet: Mittwoch, 29. Juli 2020 17:23 > An: Schreuder, Herman /DE > Cc: CCP4BB@JISCMAIL.AC.UK > Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement > > EXTERNAL : Real sender is eleanor.dod...@york.ac.uk > > > > Wont coot do that? > Eleanor > > On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE > wrote: > Dear BB, > > I would like to do a real real-space-refinement of a protein against a > cryo-EM map; not the mtz-based Refmac approach. A quick internet search > produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how > to do this using ccp4 programs, or has someone a Coot script to do this? > > Thank you for your help! > Herman > > 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 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] real real-space-refinement
Would the stepped refinement protocol in Coot do what you want? It does a real space refinement for every residue automatically. Cheers Christian On Wed, Jul 29, 2020 at 5:20 PM Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Dear BB, > > > > I would like to do a real real-space-refinement of a protein against a > cryo-EM map; not the mtz-based Refmac approach. A quick internet search > produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how > to do this using ccp4 programs, or has someone a Coot script to do this? > > > > Thank you for your help! > > Herman > > -- > > 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] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
Hi Herman, There is lots of information on CCP-EM's modelling tools here: https://www.ccpem.ac.uk/training/icknield_2019/icknield_2019.php This includes a tutorial on Refmac. As you note this is done in reciprocal space but the CCP-EM pipeline handles conversions from MRC to MTZ format (and runs Refmac via CCP4). All the best, Tom From: CCP4 bulletin board on behalf of Boaz Shaanan Sent: 29 July 2020 16:31:46 To: ccp4bb Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement Hi, Try searching ccp-em. Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Jul 29, 2020 18:29, "Schreuder, Herman /DE" wrote: Coot does it, but if one wants to do it for a complete protein, it is a lot of clicking. On the other hand, I have not tried to just select the N- and C-terminus for real-space refinement to see what happens. I would prefer to have some script to do it. Best, Herman Von: Eleanor Dodson Gesendet: Mittwoch, 29. Juli 2020 17:23 An: Schreuder, Herman /DE Cc: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement EXTERNAL : Real sender is eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk> Wont coot do that? Eleanor On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE mailto:herman.schreu...@sanofi.com>> wrote: Dear BB, I would like to do a real real-space-refinement of a protein against a cryo-EM map; not the mtz-based Refmac approach. A quick internet search produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how to do this using ccp4 programs, or has someone a Coot script to do this? Thank you for your help! Herman To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=Ch0pjy23vd6uA_krOf8kvGcBAXoSM6A4B64IAhROL4g=12CS6Fb_HI-kbl4I1FebLJB9l_zTdFKUTIGdO53-Ar8=> 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 email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. Opinions, conclusions or other information in this message and attachments that are not related directly to UKRI business are solely those of the author and do not represent the views of UKRI. 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] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
Hi, Try searching ccp-em. Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Jul 29, 2020 18:29, "Schreuder, Herman /DE" wrote: Coot does it, but if one wants to do it for a complete protein, it is a lot of clicking. On the other hand, I have not tried to just select the N- and C-terminus for real-space refinement to see what happens. I would prefer to have some script to do it. Best, Herman Von: Eleanor Dodson Gesendet: Mittwoch, 29. Juli 2020 17:23 An: Schreuder, Herman /DE Cc: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement EXTERNAL : Real sender is eleanor.dod...@york.ac.uk Wont coot do that? Eleanor On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE <herman.schreu...@sanofi.com> wrote: Dear BB, I would like to do a real real-space-refinement of a protein against a cryo-EM map; not the mtz-based Refmac approach. A quick internet search produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how to do this using ccp4 programs, or has someone a Coot script to do this? Thank you for your help! Herman 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
Coot does it, but if one wants to do it for a complete protein, it is a lot of clicking. On the other hand, I have not tried to just select the N- and C-terminus for real-space refinement to see what happens. I would prefer to have some script to do it. Best, Herman Von: Eleanor Dodson Gesendet: Mittwoch, 29. Juli 2020 17:23 An: Schreuder, Herman /DE Cc: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement EXTERNAL : Real sender is eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk> Wont coot do that? Eleanor On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE mailto:herman.schreu...@sanofi.com>> wrote: Dear BB, I would like to do a real real-space-refinement of a protein against a cryo-EM map; not the mtz-based Refmac approach. A quick internet search produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how to do this using ccp4 programs, or has someone a Coot script to do this? Thank you for your help! Herman To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=Ch0pjy23vd6uA_krOf8kvGcBAXoSM6A4B64IAhROL4g=12CS6Fb_HI-kbl4I1FebLJB9l_zTdFKUTIGdO53-Ar8=> 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] real real-space-refinement
Wont coot do that? Eleanor On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Dear BB, > > > > I would like to do a real real-space-refinement of a protein against a > cryo-EM map; not the mtz-based Refmac approach. A quick internet search > produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how > to do this using ccp4 programs, or has someone a Coot script to do this? > > > > Thank you for your help! > > Herman > > -- > > 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/
[ccp4bb] real real-space-refinement
Dear BB, I would like to do a real real-space-refinement of a protein against a cryo-EM map; not the mtz-based Refmac approach. A quick internet search produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how to do this using ccp4 programs, or has someone a Coot script to do this? Thank you for your help! Herman 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/
