Re: [ccp4bb] Bulk solvent correction in Phaser MR LF
Hi, Bernhard, ok, sure, you are right ! Nevertheless, I would not be so desperate and categorical: you are right , at my knowledge also, there is currently NO known algorithm to take into account the flat mask bulk solvent contribution at the rotation step (maybe I am wrong?), however this does not mean it is impossible. The question is should it be done at all ? When do you the rotation search, you need to use mostly the highest resolution data, and it may be rather useful to remove the low-resolution data (see the tests described in Acta Cryst D51, 888-895, 1995; however, it looks like in practice nobody uses variable resolution for different MR steps). When you work at low resolution with envelopes, you do not care about bulk solvent correction since all this results indeed in a scale coefficient. There is a tiny (but not unusual) situation when one wants to do MR at the worse resolution of 9-12 A (worse in the sense that the maps show neither (already) molecular envelope nor (yet) clear structure. Suppose we could solve the MR problem - what we do then since the maps are so poor ? It is worthy in this case artificially lower the resolution ? I do not know... However, I agree, you question is fully valid and is interesting. All the best , Sacha De : hofkristall...@gmail.commailto:hofkristall...@gmail.com [hofkristall...@gmail.com] Envoyé : mercredi 4 février 2015 14:09 À : Alexandre OURJOUMTSEV; CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Objet : RE: [ccp4bb] Bulk solvent correction in Phaser MR LF Hi Sacha, I was imprecise. With unplaced I meant 'neither rotated nor translated'. Once you become post-rotationally SF based, you can in fact compute a F(env) whole inclusion should improve the TF score. What is not evident to me is how to use a mask and compute the Fs if the orientation (rotation) is yet to be determined? Thx, BR
Re: [ccp4bb] Bulk solvent correction in Phaser MR LF
Hi Sacha, I was imprecise. With unplaced I meant neither rotated nor translated. Once you become post-rotationally SF based, you can in fact compute a F(env) whole inclusion should improve the TF score. What is not evident to me is how to use a mask and compute the Fs if the orientation (rotation) is yet to be determined? Thx, BR From: Alexandre OURJOUMTSEV [mailto:sa...@igbmc.fr] Sent: Dienstag, 3. Februar 2015 22:19 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: RE:[ccp4bb] Bulk solvent correction in Phaser MR LF Dear Bernhard, For the unplaced model, it can only be a Babinet model to improve the scaling, This is not fully true, and the flat mask correction can be used as well. Please look : Fokine, A. Urzhumtsev, A.G. (2002) On the use of low resolution data for translation search in molecular replacement. Acta Cryst., A58, 72-74 Fokine, A., Capitani, G., Grütter, M.G. Urzhumtsev, A. (2003) Bulk-solvent correction for fast translation search in molecular replacement: service programs for AMoRe and CNS. J. Appl.Cryst., 36, 352-355. Best regards, Sacha Urzhumtsev _ De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Bernhard Rupp (Hofkristallrat a.D.) [hofkristall...@gmail.com] Envoyé : mardi 3 février 2015 14:49 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Bulk solvent correction in Phaser MR LF Hi Fellows, I cannot find the proper reference for the implementation of bulk solvent corrections in the Phaser Molecular replacement likelihood functions. For the unplaced model, it can only be a Babinet model to improve the scaling, and I believe that is implemented via a Babinet rescaled function for sigma A including the coordinate error. Can anybody help me where to find that? Thx, BR
Re: [ccp4bb] Bulk solvent correction in Phaser MR LF
Hi Bernhard, You're right, it's a Babinet-style correction to the SigmaA curve for the effect of neglecting bulk solvent in the model. We gave a formula in equation 19 of the main Phaser reference (McCoy et al., 2007), but actually we've changed the form of this since then. It looks like the equation wasn't given in the documentation, so I've just updated that: http://www.phaser.cimr.cam.ac.uk/index.php/Keywords#SOLPARAMETERS Best wishes, Randy Read On 3 Feb 2015, at 13:49, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Hi Fellows, I cannot find the proper reference for the implementation of bulk solvent corrections in the Phaser Molecular replacement likelihood functions. For the unplaced model, it can only be a Babinet model to improve the scaling, and I believe that is implemented via a Babinet rescaled function for sigma A including the coordinate error. Can anybody help me where to find that? Thx, BR -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
[ccp4bb] Bulk solvent correction in Phaser MR LF
Hi Fellows, I cannot find the proper reference for the implementation of bulk solvent corrections in the Phaser Molecular replacement likelihood functions. For the unplaced model, it can only be a Babinet model to improve the scaling, and I believe that is implemented via a Babinet rescaled function for sigma A including the coordinate error. Can anybody help me where to find that? Thx, BR
Re: [ccp4bb] Bulk solvent correction in Phaser MR LF
Dear Bernhard, For the unplaced model, it can only be a Babinet model to improve the scaling, This is not fully true, and the flat mask correction can be used as well. Please look : Fokine, A. Urzhumtsev, A.G. (2002) On the use of low resolution data for translation search in molecular replacement. Acta Cryst., A58, 72-74 Fokine, A., Capitani, G., Grütter, M.G. Urzhumtsev, A. (2003) Bulk-solvent correction for fast translation search in molecular replacement: service programs for AMoRe and CNS. J. Appl.Cryst., 36, 352-355. Best regards, Sacha Urzhumtsev De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Bernhard Rupp (Hofkristallrat a.D.) [hofkristall...@gmail.com] Envoyé : mardi 3 février 2015 14:49 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Bulk solvent correction in Phaser MR LF Hi Fellows, I cannot find the proper reference for the implementation of bulk solvent corrections in the Phaser Molecular replacement likelihood functions. For the unplaced model, it can only be a Babinet model to improve the scaling, and I believe that is implemented via a Babinet rescaled function for sigma A including the coordinate error. Can anybody help me where to find that? Thx, BR
Re: [ccp4bb] Bulk solvent
Dear Bernhard, I think, the main difference of an unmodelled part between the mask bulk solvent correction and the Babinet bulk solvent correction is, that the mask approach can use quite detailed structural information, whereas the Babinet approach uses only two additional scale factors. Let's illustrate this for a model with an unmodelled part: In the mask bulk solvent correction, the solvent mask fills the region outside the modelled part and thus lowers the local contrast of the unmodelled part. For the unmodelled part, it would be better if there wouldn't be any bulk solvent density (BUSTER allows this). Then, the superior scaling of the mask bulk solvent approach without reducing the local contrast should really help with the interpretation of the unmodelled part. However, masking out the unmodelled part shouldn't be too detailed, since the hole left in the bulk solvent mask will return as positive difference density and can be heavily biased towards the atoms that were used to exclude the solvent mask. I've seen this in the very old X-Plor, where setting the occupany to 0 of a part of the model took it out from the model's Fcalc but not from the solvent mask calculation, leading to positive difference density exactly around the omitted atoms + mask radius. Something like this could not happen with the Babinet approach, since it only affects overall scale factors. But here, the effect is quite counter-intuitive! If the unmodelled part is well ordered (but just missing), it's contribution will be missing from the model's Fcalc at all resolutions and thus will affect the overall scale factor of the model Fcalc, only, but not the additional Babinet scale factors. If the missing atoms are not accounted for in the overall scaling, this could decrease, or underestimate, the signal of the difference density everywhere, which is a general problem, but not specifically related to the Babinet solvent correction. If, however, the unmodelled part is less well ordered (which is the more common case), it's contribution will mainly affect the model's Fcalc at low resolution. If the overall scaling is dominated by the high resolution terms (which is usually the case), the unmodelled part will not have an effect on the overall scale factor of the model's Fcalc, leaving only the Fcalc at low resolution somewhat too low. Since lowering the model's Fcalc scale factor at low resolution is the main purpose of the Babinet solvent correction, this will lead to an _underestimation_ (!) of the Babinet bulk solvent contribution scale factor (ksol). This, in principle, should increase, or overestimate, the signal of the difference densities at low resolution, which might also help with interpretation of the unmodelled part. But all these scaling effects should be small, unless a substantial part of the model is missing. Best regards, Dirk. On 12.01.2015 11:09, Bernhard Rupp wrote: What still evades me is, why exactly is the Babinet immune to these effects of excluding/masking-out unmodelled parts? The Babinet correction is also a function of the MODELLED part, just the opposite sign. So an incomplete model de facto equals an over-estimated solvent. Is it just the high effective dampening of this correction (B ~200) as Pavel said that makes it less susceptible because the higher resolution reflections are less affected and therefore have a chance to correct/overcome the inadequate (implicit) masking? Best, BR *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Eleanor Dodson *Sent:* Sonntag, 11. Januar 2015 17:05 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Bulk solvent Yes. If the model is incomplete it is obviously not sensible to use the mask based solvent - you will tend to lose the unmodelled features. It also gives unrealistically low R factors for a crystal with high solvent content. However the best test would be to analyse maps and try to decide if when the different procedures work best.. A project for a student dissertation perhaps?? Eleanor On 9 January 2015 at 20:13, Roberts, Sue A - (suer) s...@email.arizona.edu mailto:s...@email.arizona.edu wrote: I always try both methods - usually there is little difference. However, For CueO (multicopper oxidase) where there are about 25 disordered (unseen) residues in a loop, using Babinet scaling instead of the default refmac scaling reduced the R factors by about 2% (both R and Rfree) and improved the quality of the maps substantially. From Dirk's comment, I'd guess this is because the mask-based solvent model is putting solvent where there is (disordered) protein, which is different from real bulk solvent. Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1306 E. University Blvd, Tucson, AZ 85721 Phone: 520 621 4168 tel:520%20621%204168 s...@email.arizona.edu mailto:s...@email.arizona.edu -Original Message
Re: [ccp4bb] Bulk solvent
On 12 Jan 2015, at 10:09, Bernhard Rupp b...@ruppweb.orgmailto:b...@ruppweb.org wrote: What still evades me is, why exactly is the Babinet immune to these effects of excluding/masking-out unmodelled parts? The Babinet correction is also a function of the MODELLED part, just the opposite sign. So an incomplete model de facto equals an over-estimated solvent. Is it just the high effective dampening of this correction (B ~200) as Pavel said that makes it less susceptible because the higher resolution reflections are less affected and therefore have a chance to correct/overcome the inadequate (implicit) masking? I have the feeling that this might be the case. More details on the two bulk-solvent correction methods available in Refmac (with formulae) are in Murshudov et al (2011) Acta Cryst D67, 355-367 - Section 2.4 Best wishes Roberto Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Sonntag, 11. Januar 2015 17:05 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Bulk solvent Yes. If the model is incomplete it is obviously not sensible to use the mask based solvent - you will tend to lose the unmodelled features. It also gives unrealistically low R factors for a crystal with high solvent content. However the best test would be to analyse maps and try to decide if when the different procedures work best.. A project for a student dissertation perhaps?? Eleanor On 9 January 2015 at 20:13, Roberts, Sue A - (suer) s...@email.arizona.edumailto:s...@email.arizona.edu wrote: I always try both methods - usually there is little difference. However, For CueO (multicopper oxidase) where there are about 25 disordered (unseen) residues in a loop, using Babinet scaling instead of the default refmac scaling reduced the R factors by about 2% (both R and Rfree) and improved the quality of the maps substantially. From Dirk's comment, I'd guess this is because the mask-based solvent model is putting solvent where there is (disordered) protein, which is different from real bulk solvent. Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1306 E. University Blvd, Tucson, AZ 85721 Phone: 520 621 4168tel:520%20621%204168 s...@email.arizona.edumailto:s...@email.arizona.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Armando Albert Sent: Friday, January 09, 2015 12:56 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Bulk solvent Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando Roberto A. Steiner, PhD Randall Division of Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk Phone 0044 20 78488216 Fax0044 20 78486435 Room 3.10A New Hunt's House Guy's Campus SE1 1UL London
Re: [ccp4bb] Bulk solvent
What still evades me is, why exactly is the Babinet immune to these effects of excluding/masking-out unmodelled parts? The Babinet correction is also a function of the MODELLED part, just the opposite sign. So an incomplete model de facto equals an over-estimated solvent. Is it just the high effective dampening of this correction (B ~200) as Pavel said that makes it less susceptible because the higher resolution reflections are less affected and therefore have a chance to correct/overcome the inadequate (implicit) masking? Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Sonntag, 11. Januar 2015 17:05 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Bulk solvent Yes. If the model is incomplete it is obviously not sensible to use the mask based solvent - you will tend to lose the unmodelled features. It also gives unrealistically low R factors for a crystal with high solvent content. However the best test would be to analyse maps and try to decide if when the different procedures work best.. A project for a student dissertation perhaps?? Eleanor On 9 January 2015 at 20:13, Roberts, Sue A - (suer) s...@email.arizona.edu wrote: I always try both methods - usually there is little difference. However, For CueO (multicopper oxidase) where there are about 25 disordered (unseen) residues in a loop, using Babinet scaling instead of the default refmac scaling reduced the R factors by about 2% (both R and Rfree) and improved the quality of the maps substantially. From Dirk's comment, I'd guess this is because the mask-based solvent model is putting solvent where there is (disordered) protein, which is different from real bulk solvent. Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1306 E. University Blvd, Tucson, AZ 85721 Phone: 520 621 4168 tel:520%20621%204168 s...@email.arizona.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Armando Albert Sent: Friday, January 09, 2015 12:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Bulk solvent Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando
Re: [ccp4bb] Bulk solvent
Dear Bernhard, further thinking about the Babinet scaling effects, I have to correct my conclusion in the last sentence: On 12.01.2015 14:21, Dirk Kostrewa wrote: If, however, the unmodelled part is less well ordered (which is the more common case), it's contribution will mainly affect the model's Fcalc at low resolution. If the overall scaling is dominated by the high resolution terms (which is usually the case), the unmodelled part will not have an effect on the overall scale factor of the model's Fcalc, leaving only the Fcalc at low resolution somewhat too low. Since lowering the model's Fcalc scale factor at low resolution is the main purpose of the Babinet solvent correction, this will lead to an _underestimation_ (!) of the Babinet bulk solvent contribution scale factor (ksol). This, in principle, should increase, or overestimate, the signal of the difference densities at low resolution, which might also help with interpretation of the unmodelled part. The underestimation of the Babinet bulk solvent scale factor is equivalent to an overestimation of the contrast between protein and solvent and should therefore lead to an overestimation of the Fcalc at low resolution. If scaling is still dominated by the high resolution terms, this should lead to a decrease, or underestimation, of the structure factor differences at low resolution, which would reduce the overall signal of the difference densities. But still, this will be an overall effect and not restricted to the location of the unmodelled part. Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Bulk solvent
the different procedures work best.. A project for a student dissertation perhaps?? Eleanor On 9 January 2015 at 20:13, Roberts, Sue A - (suer) s...@email.arizona.edu wrote: I always try both methods - usually there is little difference. However, For CueO (multicopper oxidase) where there are about 25 disordered (unseen) residues in a loop, using Babinet scaling instead of the default refmac scaling reduced the R factors by about 2% (both R and Rfree) and improved the quality of the maps substantially. From Dirk's comment, I'd guess this is because the mask-based solvent model is putting solvent where there is (disordered) protein, which is different from real bulk solvent. Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1306 E. University Blvd, Tucson, AZ 85721 Phone: 520 621 4168 s...@email.arizona.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Armando Albert Sent: Friday, January 09, 2015 12:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Bulk solvent Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando
Re: [ccp4bb] Bulk solvent
Yes. If the model is incomplete it is obviously not sensible to use the mask based solvent - you will tend to lose the unmodelled features. It also gives unrealistically low R factors for a crystal with high solvent content. However the best test would be to analyse maps and try to decide if when the different procedures work best.. A project for a student dissertation perhaps?? Eleanor On 9 January 2015 at 20:13, Roberts, Sue A - (suer) s...@email.arizona.edu wrote: I always try both methods - usually there is little difference. However, For CueO (multicopper oxidase) where there are about 25 disordered (unseen) residues in a loop, using Babinet scaling instead of the default refmac scaling reduced the R factors by about 2% (both R and Rfree) and improved the quality of the maps substantially. From Dirk's comment, I'd guess this is because the mask-based solvent model is putting solvent where there is (disordered) protein, which is different from real bulk solvent. Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1306 E. University Blvd, Tucson, AZ 85721 Phone: 520 621 4168 s...@email.arizona.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Armando Albert Sent: Friday, January 09, 2015 12:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Bulk solvent Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando
Re: [ccp4bb] Bulk solvent
A related/follow-on question, hopefully on the same topic: When mask-based solvent modeling leads to problems caused by calculation of an inappropriate mask (eg inclusion of disordered loops or inaccessible pockets as bulk-solvent volume) it seems that a feasible workaround is to (a) output the calculated mask via MSKOUT (b) edit it to remove spurious regions (c) calculate partial structure factors for the new solvent region using refmac's previous kSol, bSol estimates (d) include the partial structure factors in a second round of refinement by specifying SOLVENT NO, FPART and SCPART. However, this does not re-calculate kSol and bSol to reflect the modified mask. Is there a way to simply supply the mask to be used rather than have refmac calculate it ? Thanks, Alastair Fyfe On 01/11/2015 08:04 AM, Eleanor Dodson wrote: Yes. If the model is incomplete it is obviously not sensible to use the mask based solvent - you will tend to lose the unmodelled features. It also gives unrealistically low R factors for a crystal with high solvent content. However the best test would be to analyse maps and try to decide if when the different procedures work best.. A project for a student dissertation perhaps?? Eleanor On 9 January 2015 at 20:13, Roberts, Sue A - (suer) s...@email.arizona.edu wrote: I always try both methods - usually there is little difference. However, For CueO (multicopper oxidase) where there are about 25 disordered (unseen) residues in a loop, using Babinet scaling instead of the default refmac scaling reduced the R factors by about 2% (both R and Rfree) and improved the quality of the maps substantially. From Dirk's comment, I'd guess this is because the mask-based solvent model is putting solvent where there is (disordered) protein, which is different from real bulk solvent. Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1306 E. University Blvd, Tucson, AZ 85721 Phone: 520 621 4168 s...@email.arizona.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Armando Albert Sent: Friday, January 09, 2015 12:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Bulk solvent Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando
Re: [ccp4bb] Bulk solvent
Dear Alaistair, this sound a little like the SQUEEZE command in Platon (with dummies placed at the spurious regions), although I am not an expert about what SQUEEZE does in detail. If your structure is not too large, you could give it a try. The Polymerase is too large for Platon, but it works with insulin ;-) best, Tim On 01/11/2015 08:05 PM, Alastair Fyfe wrote: A related/follow-on question, hopefully on the same topic: When mask-based solvent modeling leads to problems caused by calculation of an inappropriate mask (eg inclusion of disordered loops or inaccessible pockets as bulk-solvent volume) it seems that a feasible workaround is to (a) output the calculated mask via MSKOUT (b) edit it to remove spurious regions (c) calculate partial structure factors for the new solvent region using refmac's previous kSol, bSol estimates (d) include the partial structure factors in a second round of refinement by specifying SOLVENT NO, FPART and SCPART. However, this does not re-calculate kSol and bSol to reflect the modified mask. Is there a way to simply supply the mask to be used rather than have refmac calculate it ? Thanks, Alastair Fyfe On 01/11/2015 08:04 AM, Eleanor Dodson wrote: Yes. If the model is incomplete it is obviously not sensible to use the mask based solvent - you will tend to lose the unmodelled features. It also gives unrealistically low R factors for a crystal with high solvent content. However the best test would be to analyse maps and try to decide if when the different procedures work best.. A project for a student dissertation perhaps?? Eleanor On 9 January 2015 at 20:13, Roberts, Sue A - (suer) s...@email.arizona.edu wrote: I always try both methods - usually there is little difference. However, For CueO (multicopper oxidase) where there are about 25 disordered (unseen) residues in a loop, using Babinet scaling instead of the default refmac scaling reduced the R factors by about 2% (both R and Rfree) and improved the quality of the maps substantially. From Dirk's comment, I'd guess this is because the mask-based solvent model is putting solvent where there is (disordered) protein, which is different from real bulk solvent. Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1306 E. University Blvd, Tucson, AZ 85721 Phone: 520 621 4168 s...@email.arizona.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Armando Albert Sent: Friday, January 09, 2015 12:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Bulk solvent Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] Bulk solvent
Dear Armando, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? in addition to Dirk's excellent comment: Babinet bulk-solvent model is fine at resolutions lower than 15-20Å while not so much at higher resolutions as demonstrated by Podjarny, A. D. Urzhumtsev, A.G. (1997). Methods Enzymol. 276,641-658). Pavel
Re: [ccp4bb] Bulk solvent
On 09.01.2015 08:56, Armando Albert wrote: Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando Dear Armando, yes: the mask bulk solvent correction depends on the proper calculation of a protein mask. The bulk solvent density is then assigned outside the protein mask. This mask calculation is based on one or two radii around the protein atoms and is always a compromise. Sometimes, the protein mask misses really empty cavities usually surrounded by hydrophobic residues, wrongly filling these cavities with bulk solvent density. This results in relatively large blobs with negative difference density. Sometimes, the protein mask covers narrow cavities really filled with bulk solvent electron density, which is then missing in the model. This results in positive difference densities, that are not easy to interpret. The Babinet bulk solvent correction only uses two parameters, is less effective in describing the contribution of the bulk solvent to the scattering, but is free of these artefacts. I use the Babinet bulk solvent correction sometimes as a control if I'm not sure about the origin of possibly important difference density peaks in narrow regions. Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Bulk solvent
Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando
Re: [ccp4bb] bulk solvent treatment inside protein cavities
Dear Allister Crow, in cases like these, I would recommend to apply the Babinet bulk solvent correction instead of the mask bulk solvent correction as a control (Refmac5 - Scaling - Use Babinet scaling; uncheck Calculcate the contribution from the solvent region). The Babinet bulk solvent correction only uses two overall scaling factors and is usually simple, robust and, in my experience, does not show any local difference density artefacts. The mask bulk solvent correction is more powerful, but, depending on the project and the various mask radii for generating and shrinking the mask, could produce false positive or negative difference density. To exclude these cases, you can always calculate the Babinet bulk solvent correction as a control. Best regards, Dirk. Am 16.04.12 12:37, schrieb Allister Crow: Board members, I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins. I am currently nearing the end of refinement of a protein structure at 2.8 A resolution. I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps. These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied. I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters). My questions are therefore: 1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6? 2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities? Best wishes, and thanks in advance for all your help, - Allister Crow -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] bulk solvent treatment inside protein cavities
On Tue, 2012-04-17 at 11:08 +0200, Dirk Kostrewa wrote: The mask bulk solvent correction is more powerful Just to note that sometimes Babinet solvent correction returns lower Rfree and thus may be preferred to mask (assuming that the Rfree is the only thing that matters). Beginning with 5.6.0078, you can also optimize the bulk solvent mask parameters http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html#Bulk_solvent This, imho, is not likely to remove the density artifacts, but is worth a try. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] bulk solvent treatment inside protein cavities
Dear Allister Could you please update refmac version. In the version you it seems that bulk solvent mask calculation has some problems. New version (at the moment) can be downloaded from this site: http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz There is a mac version also. regards Garib On 16 Apr 2012, at 11:37, Allister Crow wrote: Board members, I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins. I am currently nearing the end of refinement of a protein structure at 2.8 A resolution. I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps. These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied. I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters). My questions are therefore: 1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6? 2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities? Best wishes, and thanks in advance for all your help, - Allister Crow bulk_solvent_inside_cavities.png Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] bulk solvent treatment inside protein cavities
Oh dear - this is the version of Refmac in the latest ccp4 release - can this be updated on the web site as soon as possible ? Eleanor On 16 April 2012 12:02, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk wrote: Dear Allister Could you please update refmac version. In the version you it seems that bulk solvent mask calculation has some problems. New version (at the moment) can be downloaded from this site: http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/ refmac5.7_linux.tar.gzhttp://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz There is a mac version also. regards Garib On 16 Apr 2012, at 11:37, Allister Crow wrote: Board members, I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins. I am currently nearing the end of refinement of a protein structure at 2.8 A resolution. I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps. These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied. I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters). My questions are therefore: 1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6? 2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities? Best wishes, and thanks in advance for all your help, - Allister Crow bulk_solvent_inside_cavities.png Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk jen...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] bulk solvent treatment inside protein cavities
Dear Garib, Is there REFMAC option to output solvent mask information (e.g. Fmask and PHImask in mtz to check with Coot)? I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL). But I'm not sure that FC_ALL = FC + FMASK is correct or not. Keitaro 2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk: Dear Allister Could you please update refmac version. In the version you it seems that bulk solvent mask calculation has some problems. New version (at the moment) can be downloaded from this site: http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz There is a mac version also. regards Garib On 16 Apr 2012, at 11:37, Allister Crow wrote: Board members, I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins. I am currently nearing the end of refinement of a protein structure at 2.8 A resolution. I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps. These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied. I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters). My questions are therefore: 1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6? 2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities? Best wishes, and thanks in advance for all your help, - Allister Crow bulk_solvent_inside_cavities.png Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] bulk solvent treatment inside protein cavities
Yes there is. If you use command line (it is not available on the ccp4i yet). If you run with command lines refmac5 all others like hklin, xyzin etc mskout mask file name eof all options you want eof Then there will be a map and you can visualise it using coot. regards Garib On 16 Apr 2012, at 15:09, Keitaro Yamashita wrote: Dear Garib, Is there REFMAC option to output solvent mask information (e.g. Fmask and PHImask in mtz to check with Coot)? I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL). But I'm not sure that FC_ALL = FC + FMASK is correct or not. Keitaro 2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk: Dear Allister Could you please update refmac version. In the version you it seems that bulk solvent mask calculation has some problems. New version (at the moment) can be downloaded from this site: http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz There is a mac version also. regards Garib On 16 Apr 2012, at 11:37, Allister Crow wrote: Board members, I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins. I am currently nearing the end of refinement of a protein structure at 2.8 A resolution. I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps. These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied. I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters). My questions are therefore: 1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6? 2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities? Best wishes, and thanks in advance for all your help, - Allister Crow bulk_solvent_inside_cavities.png Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] bulk solvent treatment inside protein cavities
A follow up: In the new version there is FC_ALL_LS, PHIC_ALL_LS That should be FC_ALL_LS = FC + FMASK. I have not tried but if you can use vector difference map then it should be: FMASK = FC_ALL_LS - FC But it is after scaling. If you write out mask map then it is just 0 1 map (0 inside protein and 1 outside), except values are not 0 1 but 0 and some constant Regards Garib On 16 Apr 2012, at 15:09, Keitaro Yamashita wrote: Dear Garib, Is there REFMAC option to output solvent mask information (e.g. Fmask and PHImask in mtz to check with Coot)? I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL). But I'm not sure that FC_ALL = FC + FMASK is correct or not. Keitaro 2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk: Dear Allister Could you please update refmac version. In the version you it seems that bulk solvent mask calculation has some problems. New version (at the moment) can be downloaded from this site: http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz There is a mac version also. regards Garib On 16 Apr 2012, at 11:37, Allister Crow wrote: Board members, I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins. I am currently nearing the end of refinement of a protein structure at 2.8 A resolution. I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps. These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied. I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters). My questions are therefore: 1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6? 2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities? Best wishes, and thanks in advance for all your help, - Allister Crow bulk_solvent_inside_cavities.png Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] bulk solvent treatment inside protein cavities
Hi there! I think some of you have given my email for correspondence or CC, please I do not have to do anything related to your conversation so please delete my email address from your correspondence I shall be grateful THANKS REGARDS! Tallat Hussain Ghazi IT Manager / Head of Web Graphics Depts. ITSS (Pvt) Ltd. Email: tal...@itssols.com Website: www.itssols.com Mob: +92 (0)323 992 Tel: +92 (0)42 5694723-25 Fax: +92 (0)42 5694727 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keitaro Yamashita Sent: Monday, April 16, 2012 7:09 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] bulk solvent treatment inside protein cavities Dear Garib, Is there REFMAC option to output solvent mask information (e.g. Fmask and PHImask in mtz to check with Coot)? I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL). But I'm not sure that FC_ALL = FC + FMASK is correct or not. Keitaro 2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk: Dear Allister Could you please update refmac version. In the version you it seems that bulk solvent mask calculation has some problems. New version (at the moment) can be downloaded from this site: http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_l inux.tar.gz There is a mac version also. regards Garib On 16 Apr 2012, at 11:37, Allister Crow wrote: Board members, I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins. I am currently nearing the end of refinement of a protein structure at 2.8 A resolution. I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps. These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied. I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters). My questions are therefore: 1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6? 2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities? Best wishes, and thanks in advance for all your help, - Allister Crow bulk_solvent_inside_cavities.png Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] bulk solvent treatment inside protein cavities
Dear Garib, Thank you very much for your quick reply. I tried mskout option and the output looked almost the same as the map generated by FC_ALL - FC. By the way, when mskout option is specified, refmac stops before CGMAT cycles. Is there any way to do refinement with mskout option? I have not tried but if you can use vector difference map then it should be: FMASK = FC_ALL_LS - FC What is FC_ALL in the new version? Thanks, Keitaro 2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk: A follow up: In the new version there is FC_ALL_LS, PHIC_ALL_LS That should be FC_ALL_LS = FC + FMASK. I have not tried but if you can use vector difference map then it should be: FMASK = FC_ALL_LS - FC But it is after scaling. If you write out mask map then it is just 0 1 map (0 inside protein and 1 outside), except values are not 0 1 but 0 and some constant Regards Garib On 16 Apr 2012, at 15:09, Keitaro Yamashita wrote: Dear Garib, Is there REFMAC option to output solvent mask information (e.g. Fmask and PHImask in mtz to check with Coot)? I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL). But I'm not sure that FC_ALL = FC + FMASK is correct or not. Keitaro 2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk: Dear Allister Could you please update refmac version. In the version you it seems that bulk solvent mask calculation has some problems. New version (at the moment) can be downloaded from this site: http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz There is a mac version also. regards Garib On 16 Apr 2012, at 11:37, Allister Crow wrote: Board members, I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins. I am currently nearing the end of refinement of a protein structure at 2.8 A resolution. I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps. These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied. I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters). My questions are therefore: 1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6? 2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities? Best wishes, and thanks in advance for all your help, - Allister Crow bulk_solvent_inside_cavities.png Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] bulk solvent treatment inside protein cavities
Dear Ketaro At the moment mskout option is a signal that the program should stop. Obviously I can add an option to continue. However if you have mskout option it is likely that you want to check what is going on with the mask. If you want to compare starting and final mask then you could run refmac with mskout in the beginning and after refinement. If you need it urgently then I can add continuation of refinement with mskout option. FC_ALL is ML scaled FC+FMASK Sometime it may be different from least-squares scaled FC+FMASK regards Garib On 16 Apr 2012, at 16:01, Keitaro Yamashita wrote: Dear Garib, Thank you very much for your quick reply. I tried mskout option and the output looked almost the same as the map generated by FC_ALL - FC. By the way, when mskout option is specified, refmac stops before CGMAT cycles. Is there any way to do refinement with mskout option? I have not tried but if you can use vector difference map then it should be: FMASK = FC_ALL_LS - FC What is FC_ALL in the new version? Thanks, Keitaro 2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk: A follow up: In the new version there is FC_ALL_LS, PHIC_ALL_LS That should be FC_ALL_LS = FC + FMASK. I have not tried but if you can use vector difference map then it should be: FMASK = FC_ALL_LS - FC But it is after scaling. If you write out mask map then it is just 0 1 map (0 inside protein and 1 outside), except values are not 0 1 but 0 and some constant Regards Garib On 16 Apr 2012, at 15:09, Keitaro Yamashita wrote: Dear Garib, Is there REFMAC option to output solvent mask information (e.g. Fmask and PHImask in mtz to check with Coot)? I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL). But I'm not sure that FC_ALL = FC + FMASK is correct or not. Keitaro 2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk: Dear Allister Could you please update refmac version. In the version you it seems that bulk solvent mask calculation has some problems. New version (at the moment) can be downloaded from this site: http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz There is a mac version also. regards Garib On 16 Apr 2012, at 11:37, Allister Crow wrote: Board members, I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins. I am currently nearing the end of refinement of a protein structure at 2.8 A resolution. I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps. These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied. I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters). My questions are therefore: 1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6? 2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities? Best wishes, and thanks in advance for all your help, - Allister Crow bulk_solvent_inside_cavities.png Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] bulk solvent treatment inside protein cavities
Dear Garib, I think it is better if refmac outputs final solvent mask when mskout specified. If one just wanted to calculate the mask, NCYC 0 should be specified. I hope my suggestion would be accepted, but I'm not in a hurry. FC_ALL is ML scaled FC+FMASK Sometime it may be different from least-squares scaled FC+FMASK For what purpose is FC_ALL_LS written? Can I check something by comparing FC_ALLto FC_ALL_LS? I found somewhat large difference between FC_ALL_LS map and FC_ALL map in Se position. I used SAD function. What does it mean? Cheers, Keitaro 2012/4/17 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk: Dear Ketaro At the moment mskout option is a signal that the program should stop. Obviously I can add an option to continue. However if you have mskout option it is likely that you want to check what is going on with the mask. If you want to compare starting and final mask then you could run refmac with mskout in the beginning and after refinement. If you need it urgently then I can add continuation of refinement with mskout option. FC_ALL is ML scaled FC+FMASK Sometime it may be different from least-squares scaled FC+FMASK regards Garib On 16 Apr 2012, at 16:01, Keitaro Yamashita wrote: Dear Garib, Thank you very much for your quick reply. I tried mskout option and the output looked almost the same as the map generated by FC_ALL - FC. By the way, when mskout option is specified, refmac stops before CGMAT cycles. Is there any way to do refinement with mskout option? I have not tried but if you can use vector difference map then it should be: FMASK = FC_ALL_LS - FC What is FC_ALL in the new version? Thanks, Keitaro 2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk: A follow up: In the new version there is FC_ALL_LS, PHIC_ALL_LS That should be FC_ALL_LS = FC + FMASK. I have not tried but if you can use vector difference map then it should be: FMASK = FC_ALL_LS - FC But it is after scaling. If you write out mask map then it is just 0 1 map (0 inside protein and 1 outside), except values are not 0 1 but 0 and some constant Regards Garib On 16 Apr 2012, at 15:09, Keitaro Yamashita wrote: Dear Garib, Is there REFMAC option to output solvent mask information (e.g. Fmask and PHImask in mtz to check with Coot)? I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL). But I'm not sure that FC_ALL = FC + FMASK is correct or not. Keitaro 2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk: Dear Allister Could you please update refmac version. In the version you it seems that bulk solvent mask calculation has some problems. New version (at the moment) can be downloaded from this site: http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz There is a mac version also. regards Garib On 16 Apr 2012, at 11:37, Allister Crow wrote: Board members, I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins. I am currently nearing the end of refinement of a protein structure at 2.8 A resolution. I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps. These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied. I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters). My questions are therefore: 1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6? 2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities? Best wishes, and thanks in advance for all your help, - Allister Crow bulk_solvent_inside_cavities.png Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
