Re: [ccp4bb] Weird MR result
Hmm - why should a translational peak not be along the 40 axis? Anyway othercell shows this Conversion of cell 40, 32, 101, 90, 101, 90 can give Laue groups C m m m 40.0 198.3 32.0 90.0 90.0 89.60.42 [h,h+2l,-k] Possible spacegroups: C 2 2 21 C 2 2 2 or C 1 2/m 1 40.0 198.3 32.0 90.0 90.0 89.60.42 [h,h+2l,-k] or C 1 2/m 1 198.3 40.0 32.0 90.0 90.0 90.40.42 [-h-2l,h,-k] or P 1 2/m 1 40.0 32.0 101.3 90.0 101.8 90.00.84 [-h,-k,h+l] That is so close to your input cell that twinning is a very likely option. What does thedata processing suggest - look at pointless or Xtriage or something Eleanor On 15 November 2013 18:18, Niu Tou niutou2...@gmail.com wrote: It may be helpful to add some information during index. HKL2000 could find four reasonable solutions: 40, 32, 101, 90, 101, 90 for P1 and P2 200, 40, 32, 90, 90, 90 for C2 and C222 It looks very strange to me since these two unit cells look differently, but during refinement the predicated spots are identical, and they produced similar quality data--at least from those output parameters. All solutions (including P21, C2221) have the 95% off origin peak and several minor ones. The 95% peak is at (0.5 0 0) on the 40 line, so if cut it into half, that dimension will be too small (20 only). HKL2000 also did not give any solution with one dimension as 20. Maybe I did not get a right index yet, I wonder any expert can tell something from these information? On Fri, Nov 15, 2013 at 6:41 AM, Melanie Vollmar melanie.voll...@sgc.ox.ac.uk wrote: Dear Niu, I had an interesting pseudo-translation case recently where my off-origin peak was located near the centre of the unit cell (fractions a=0.5, b=0.46, c=0.5) of a P222 symmetry. Processing and phasing in P222 looked reasonable and the model could be built. I had background density which I thought of as water. I got suspicious when I identified density for a helix which was near my build main chain but could not be joined and built or be accounted for by looking at symmetry mates. Moreover I got stuck in refinement with R/Rfree 25/30%. I could identify which part of the protein caused me the trouble on crystal packing and the appearance of the off-origin peak. In my case it was the C terminus. So I used a new construct with swapped purification tag (N to C terminus). This altered the peptide sequence for the C terminus and allowed the protein to pack nicely into I222. This turned my off-origin peak into a true symmetry operator. I also had reasonable processing and phasing results for P2 and C2. So besides the strength of your off-origin peak it may be off some use to look at the location. HTH Melanie From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Niu Tou [niutou2...@gmail.com] Sent: 14 November 2013 23:58 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Weird MR result Dear Phil, I used PHASER to do the task. I have double checked and both files have the same prefix, so they are from the same output. I have also checked the headers again, they have the same spacegroup. Actually I was trying to search for two different molecules but only one was found. The spacegeoup is P2 and I am quite sure it is not P21 from system absence. One possibility is that the space group was wrong, since there is a 95% off origin peak. There are several choices from data processing, P1, P2, C2 C222, all have this large off origin peak. I wonder if this 95% peak can tell some information? It will not surprise me if this result is incorrect, however how could these regular density be? Best, Niu On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey pjeff...@princeton.edu wrote: Hello Niu, 1. We need extra information. What program did you use ? What's the similarity (e.g. % identity) of your model. What's your space group ? Did you try ALL the space groups in your point group in ALL the permutations (e.g. in primitive orthorhombic there are 8 possibilities). 1a. My best guess on limited info is that you've got a partial solution in the wrong space group with only part of the molecules at their correct position. 2. I recently had a very unusual case where I could solve a structure in EITHER P41212 or P43212 with similar statistics, but that I would see interpenetrating electron density for a second, partial occupancy molecule no matter which of these space groups I tried (and it showed this when I expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, in retrospect, but we obtained a more friendly crystal form. I hope you don't have something like that, but it's possible. Phil Jeffrey Princeton On 11/14/13 5:22 PM, Niu Tou wrote: Dear All, I have a strange MR case which do not know how to interpret, I wonder if any one had similar experiences. The output model does not fit into the map at all, as shown in picture
[ccp4bb] AW: [ccp4bb] Weird MR result
Dear Niu, To me, it looks like random density. Since coot contours are based on sigma levels, you will always see features. I do not think you can do anything with your current map. As others have said, it is always a good idea to test ALL possible space groups, even if you are convinced it is P2. It only takes CPU time and, compared to trying to build in uninterpretable maps, very little time of yourself. Make sure to run the jobs in different directories, so the results do not get mixed up. The other thing to do would be to look at the diffraction images: are all spots sharp, or are some spots smeared? Are the spots with even L much stronger then the spots with odd L? Is your off-origin peak at c=0.5 (fractional) or at some random position? How many molecules do you expect based on a Matthews calculation? Are you sure the protein in the crystals is the protein you think it is? Since P2 is a very low-symmetry space group, the first thing I would do is to process the data in P1 and run Phaser in P1. In that case you do not have to worry about the space group etc. Once you get a solution, you can use Zanuda to find the correct space group. If you have a pseudo-translation (all L=odd reflections weak), you could also consider processing the data with the c-axis forced to be half the current length and running molecular replacement with that data. The solution will be approximate but can give you valuable information about the true packing. With an off-origin peak of 95% of the origin peak, the solution will not be far off. Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Niu Tou Gesendet: Freitag, 15. November 2013 00:58 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Weird MR result Dear Phil, I used PHASER to do the task. I have double checked and both files have the same prefix, so they are from the same output. I have also checked the headers again, they have the same spacegroup. Actually I was trying to search for two different molecules but only one was found. The spacegeoup is P2 and I am quite sure it is not P21 from system absence. One possibility is that the space group was wrong, since there is a 95% off origin peak. There are several choices from data processing, P1, P2, C2 C222, all have this large off origin peak. I wonder if this 95% peak can tell some information? It will not surprise me if this result is incorrect, however how could these regular density be? Best, Niu On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey pjeff...@princeton.edumailto:pjeff...@princeton.edu wrote: Hello Niu, 1. We need extra information. What program did you use ? What's the similarity (e.g. % identity) of your model. What's your space group ? Did you try ALL the space groups in your point group in ALL the permutations (e.g. in primitive orthorhombic there are 8 possibilities). 1a. My best guess on limited info is that you've got a partial solution in the wrong space group with only part of the molecules at their correct position. 2. I recently had a very unusual case where I could solve a structure in EITHER P41212 or P43212 with similar statistics, but that I would see interpenetrating electron density for a second, partial occupancy molecule no matter which of these space groups I tried (and it showed this when I expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, in retrospect, but we obtained a more friendly crystal form. I hope you don't have something like that, but it's possible. Phil Jeffrey Princeton On 11/14/13 5:22 PM, Niu Tou wrote: Dear All, I have a strange MR case which do not know how to interpret, I wonder if any one had similar experiences. The output model does not fit into the map at all, as shown in picture 1, however the map still looks good in part regions. From picture 2 we can see even clear alpha helix. I guess this could not be due to some random density, and I have tried to do MR with a irrelevant model without producing such kind of regular secondary structure. This data has a long c axis, and in most parts the density are still not interpretable. I do not know if this is a good starting point. Could any one give some suggestions? Many thanks! Best, Niu
Re: [ccp4bb] Weird MR result
The 95% off-origin peak in the Patterson might be telling you that the true space group has a centering operation that was missed, or the cell was doubled, in the indexing step (i.e. systematically absent spots are being indexed and integrated). If the zeros for systematically absent spots are replaced by noise, the origin-equivalent peak that should come up at 100% in the native Patterson can be reduced by something like 5%. Alternatively, you may have something extremely close to a centering operation, but not exactly crystallographic. To choose between these, you need to look at the original diffraction images to see whether there really are spots in the places that would be predicted to be absent if there were an exact centering operator or if the cell were half as long. Either way, you could probably get away with temporarily treating the translation corresponding to the Patterson peak as an exact crystallographic translation, process the data in the corresponding space group (which, at least, xtriage will tell you and maybe also pointless), and solve the molecular replacement problem in that space group. If you get a clear solution, then if the translation is non-crystallographic, you can worry later about how the exact symmetry is broken in the crystal. However, if the approach of using a smaller cell would work, I'm surprised that recent versions of Phaser that account for translational NCS would not also work. If you looked for two copies in one search, Phaser should have accounted for the tNCS implied by the Patterson peak. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +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 On 14 Nov 2013, at 23:58, Niu Tou niutou2...@gmail.com wrote: Dear Phil, I used PHASER to do the task. I have double checked and both files have the same prefix, so they are from the same output. I have also checked the headers again, they have the same spacegroup. Actually I was trying to search for two different molecules but only one was found. The spacegeoup is P2 and I am quite sure it is not P21 from system absence. One possibility is that the space group was wrong, since there is a 95% off origin peak. There are several choices from data processing, P1, P2, C2 C222, all have this large off origin peak. I wonder if this 95% peak can tell some information? It will not surprise me if this result is incorrect, however how could these regular density be? Best, Niu On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey pjeff...@princeton.edu wrote: Hello Niu, 1. We need extra information. What program did you use ? What's the similarity (e.g. % identity) of your model. What's your space group ? Did you try ALL the space groups in your point group in ALL the permutations (e.g. in primitive orthorhombic there are 8 possibilities). 1a. My best guess on limited info is that you've got a partial solution in the wrong space group with only part of the molecules at their correct position. 2. I recently had a very unusual case where I could solve a structure in EITHER P41212 or P43212 with similar statistics, but that I would see interpenetrating electron density for a second, partial occupancy molecule no matter which of these space groups I tried (and it showed this when I expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, in retrospect, but we obtained a more friendly crystal form. I hope you don't have something like that, but it's possible. Phil Jeffrey Princeton On 11/14/13 5:22 PM, Niu Tou wrote: Dear All, I have a strange MR case which do not know how to interpret, I wonder if any one had similar experiences. The output model does not fit into the map at all, as shown in picture 1, however the map still looks good in part regions. From picture 2 we can see even clear alpha helix. I guess this could not be due to some random density, and I have tried to do MR with a irrelevant model without producing such kind of regular secondary structure. This data has a long c axis, and in most parts the density are still not interpretable. I do not know if this is a good starting point. Could any one give some suggestions? Many thanks! Best, Niu
Re: [ccp4bb] Weird MR result
Dear Niu, I had an interesting pseudo-translation case recently where my off-origin peak was located near the centre of the unit cell (fractions a=0.5, b=0.46, c=0.5) of a P222 symmetry. Processing and phasing in P222 looked reasonable and the model could be built. I had background density which I thought of as water. I got suspicious when I identified density for a helix which was near my build main chain but could not be joined and built or be accounted for by looking at symmetry mates. Moreover I got stuck in refinement with R/Rfree 25/30%. I could identify which part of the protein caused me the trouble on crystal packing and the appearance of the off-origin peak. In my case it was the C terminus. So I used a new construct with swapped purification tag (N to C terminus). This altered the peptide sequence for the C terminus and allowed the protein to pack nicely into I222. This turned my off-origin peak into a true symmetry operator. I also had reasonable processing and phasing results for P2 and C2. So besides the strength of your off-origin peak it may be off some use to look at the location. HTH Melanie From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Niu Tou [niutou2...@gmail.com] Sent: 14 November 2013 23:58 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Weird MR result Dear Phil, I used PHASER to do the task. I have double checked and both files have the same prefix, so they are from the same output. I have also checked the headers again, they have the same spacegroup. Actually I was trying to search for two different molecules but only one was found. The spacegeoup is P2 and I am quite sure it is not P21 from system absence. One possibility is that the space group was wrong, since there is a 95% off origin peak. There are several choices from data processing, P1, P2, C2 C222, all have this large off origin peak. I wonder if this 95% peak can tell some information? It will not surprise me if this result is incorrect, however how could these regular density be? Best, Niu On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey pjeff...@princeton.edumailto:pjeff...@princeton.edu wrote: Hello Niu, 1. We need extra information. What program did you use ? What's the similarity (e.g. % identity) of your model. What's your space group ? Did you try ALL the space groups in your point group in ALL the permutations (e.g. in primitive orthorhombic there are 8 possibilities). 1a. My best guess on limited info is that you've got a partial solution in the wrong space group with only part of the molecules at their correct position. 2. I recently had a very unusual case where I could solve a structure in EITHER P41212 or P43212 with similar statistics, but that I would see interpenetrating electron density for a second, partial occupancy molecule no matter which of these space groups I tried (and it showed this when I expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, in retrospect, but we obtained a more friendly crystal form. I hope you don't have something like that, but it's possible. Phil Jeffrey Princeton On 11/14/13 5:22 PM, Niu Tou wrote: Dear All, I have a strange MR case which do not know how to interpret, I wonder if any one had similar experiences. The output model does not fit into the map at all, as shown in picture 1, however the map still looks good in part regions. From picture 2 we can see even clear alpha helix. I guess this could not be due to some random density, and I have tried to do MR with a irrelevant model without producing such kind of regular secondary structure. This data has a long c axis, and in most parts the density are still not interpretable. I do not know if this is a good starting point. Could any one give some suggestions? Many thanks! Best, Niu
Re: [ccp4bb] Weird MR result
It may be helpful to add some information during index. HKL2000 could find four reasonable solutions: 40, 32, 101, 90, 101, 90 for P1 and P2 200, 40, 32, 90, 90, 90 for C2 and C222 It looks very strange to me since these two unit cells look differently, but during refinement the predicated spots are identical, and they produced similar quality data--at least from those output parameters. All solutions (including P21, C2221) have the 95% off origin peak and several minor ones. The 95% peak is at (0.5 0 0) on the 40 line, so if cut it into half, that dimension will be too small (20 only). HKL2000 also did not give any solution with one dimension as 20. Maybe I did not get a right index yet, I wonder any expert can tell something from these information? On Fri, Nov 15, 2013 at 6:41 AM, Melanie Vollmar melanie.voll...@sgc.ox.ac.uk wrote: Dear Niu, I had an interesting pseudo-translation case recently where my off-origin peak was located near the centre of the unit cell (fractions a=0.5, b=0.46, c=0.5) of a P222 symmetry. Processing and phasing in P222 looked reasonable and the model could be built. I had background density which I thought of as water. I got suspicious when I identified density for a helix which was near my build main chain but could not be joined and built or be accounted for by looking at symmetry mates. Moreover I got stuck in refinement with R/Rfree 25/30%. I could identify which part of the protein caused me the trouble on crystal packing and the appearance of the off-origin peak. In my case it was the C terminus. So I used a new construct with swapped purification tag (N to C terminus). This altered the peptide sequence for the C terminus and allowed the protein to pack nicely into I222. This turned my off-origin peak into a true symmetry operator. I also had reasonable processing and phasing results for P2 and C2. So besides the strength of your off-origin peak it may be off some use to look at the location. HTH Melanie -- *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Niu Tou [ niutou2...@gmail.com] *Sent:* 14 November 2013 23:58 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Weird MR result Dear Phil, I used PHASER to do the task. I have double checked and both files have the same prefix, so they are from the same output. I have also checked the headers again, they have the same spacegroup. Actually I was trying to search for two different molecules but only one was found. The spacegeoup is P2 and I am quite sure it is not P21 from system absence. One possibility is that the space group was wrong, since there is a 95% off origin peak. There are several choices from data processing, P1, P2, C2 C222, all have this large off origin peak. I wonder if this 95% peak can tell some information? It will not surprise me if this result is incorrect, however how could these regular density be? Best, Niu On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey pjeff...@princeton.eduwrote: Hello Niu, 1. We need extra information. What program did you use ? What's the similarity (e.g. % identity) of your model. What's your space group ? Did you try ALL the space groups in your point group in ALL the permutations (e.g. in primitive orthorhombic there are 8 possibilities). 1a. My best guess on limited info is that you've got a partial solution in the wrong space group with only part of the molecules at their correct position. 2. I recently had a very unusual case where I could solve a structure in EITHER P41212 or P43212 with similar statistics, but that I would see interpenetrating electron density for a second, partial occupancy molecule no matter which of these space groups I tried (and it showed this when I expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, in retrospect, but we obtained a more friendly crystal form. I hope you don't have something like that, but it's possible. Phil Jeffrey Princeton On 11/14/13 5:22 PM, Niu Tou wrote: Dear All, I have a strange MR case which do not know how to interpret, I wonder if any one had similar experiences. The output model does not fit into the map at all, as shown in picture 1, however the map still looks good in part regions. From picture 2 we can see even clear alpha helix. I guess this could not be due to some random density, and I have tried to do MR with a irrelevant model without producing such kind of regular secondary structure. This data has a long c axis, and in most parts the density are still not interpretable. I do not know if this is a good starting point. Could any one give some suggestions? Many thanks! Best, Niu
Re: [ccp4bb] Weird MR result
Hello Niu, 1. We need extra information. What program did you use ? What's the similarity (e.g. % identity) of your model. What's your space group ? Did you try ALL the space groups in your point group in ALL the permutations (e.g. in primitive orthorhombic there are 8 possibilities). 1a. My best guess on limited info is that you've got a partial solution in the wrong space group with only part of the molecules at their correct position. 2. I recently had a very unusual case where I could solve a structure in EITHER P41212 or P43212 with similar statistics, but that I would see interpenetrating electron density for a second, partial occupancy molecule no matter which of these space groups I tried (and it showed this when I expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, in retrospect, but we obtained a more friendly crystal form. I hope you don't have something like that, but it's possible. Phil Jeffrey Princeton On 11/14/13 5:22 PM, Niu Tou wrote: Dear All, I have a strange MR case which do not know how to interpret, I wonder if any one had similar experiences. The output model does not fit into the map at all, as shown in picture 1, however the map still looks good in part regions. From picture 2 we can see even clear alpha helix. I guess this could not be due to some random density, and I have tried to do MR with a irrelevant model without producing such kind of regular secondary structure. This data has a long c axis, and in most parts the density are still not interpretable. I do not know if this is a good starting point. Could any one give some suggestions? Many thanks! Best, Niu
Re: [ccp4bb] Weird MR result
Hello Niu, Do you have pseudo translation. It could echo of another molecule that might be in correct orientation. Regards Garib On 14 Nov 2013, at 22:47, Phil Jeffrey pjeff...@princeton.edu wrote: Hello Niu, 1. We need extra information. What program did you use ? What's the similarity (e.g. % identity) of your model. What's your space group ? Did you try ALL the space groups in your point group in ALL the permutations (e.g. in primitive orthorhombic there are 8 possibilities). 1a. My best guess on limited info is that you've got a partial solution in the wrong space group with only part of the molecules at their correct position. 2. I recently had a very unusual case where I could solve a structure in EITHER P41212 or P43212 with similar statistics, but that I would see interpenetrating electron density for a second, partial occupancy molecule no matter which of these space groups I tried (and it showed this when I expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, in retrospect, but we obtained a more friendly crystal form. I hope you don't have something like that, but it's possible. Phil Jeffrey Princeton On 11/14/13 5:22 PM, Niu Tou wrote: Dear All, I have a strange MR case which do not know how to interpret, I wonder if any one had similar experiences. The output model does not fit into the map at all, as shown in picture 1, however the map still looks good in part regions. From picture 2 we can see even clear alpha helix. I guess this could not be due to some random density, and I have tried to do MR with a irrelevant model without producing such kind of regular secondary structure. This data has a long c axis, and in most parts the density are still not interpretable. I do not know if this is a good starting point. Could any one give some suggestions? Many thanks! Best, Niu Dr Garib N Murshudov MRC-LMB Francis Crick Avenue Cambridge CB2 0QH UK Web http://www.mrc-lmb.cam.ac.uk, http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
Re: [ccp4bb] Weird MR result
Dear Phil, I used PHASER to do the task. I have double checked and both files have the same prefix, so they are from the same output. I have also checked the headers again, they have the same spacegroup. Actually I was trying to search for two different molecules but only one was found. The spacegeoup is P2 and I am quite sure it is not P21 from system absence. One possibility is that the space group was wrong, since there is a 95% off origin peak. There are several choices from data processing, P1, P2, C2 C222, all have this large off origin peak. I wonder if this 95% peak can tell some information? It will not surprise me if this result is incorrect, however how could these regular density be? Best, Niu On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey pjeff...@princeton.eduwrote: Hello Niu, 1. We need extra information. What program did you use ? What's the similarity (e.g. % identity) of your model. What's your space group ? Did you try ALL the space groups in your point group in ALL the permutations (e.g. in primitive orthorhombic there are 8 possibilities). 1a. My best guess on limited info is that you've got a partial solution in the wrong space group with only part of the molecules at their correct position. 2. I recently had a very unusual case where I could solve a structure in EITHER P41212 or P43212 with similar statistics, but that I would see interpenetrating electron density for a second, partial occupancy molecule no matter which of these space groups I tried (and it showed this when I expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, in retrospect, but we obtained a more friendly crystal form. I hope you don't have something like that, but it's possible. Phil Jeffrey Princeton On 11/14/13 5:22 PM, Niu Tou wrote: Dear All, I have a strange MR case which do not know how to interpret, I wonder if any one had similar experiences. The output model does not fit into the map at all, as shown in picture 1, however the map still looks good in part regions. From picture 2 we can see even clear alpha helix. I guess this could not be due to some random density, and I have tried to do MR with a irrelevant model without producing such kind of regular secondary structure. This data has a long c axis, and in most parts the density are still not interpretable. I do not know if this is a good starting point. Could any one give some suggestions? Many thanks! Best, Niu
Re: [ccp4bb] Weird MR result
On Thursday, 14 November, 2013 18:58:27 Niu Tou wrote: Dear Phil, I used PHASER to do the task. I have double checked and both files have the same prefix, so they are from the same output. I have also checked the headers again, they have the same spacegroup. Actually I was trying to search for two different molecules but only one was found. The spacegeoup is P2 and I am quite sure it is not P21 from system absence. P21 is 100 times more common than P2. There are only 160 protein structures in P2 in all of the PDB So although it is of course possible for it to be P2, it is more likely from a priori expectations to be P21 with prohibited large intensities for the 0k0 relections. You definitely need to consider P21 as a possibility when running MR. Ethan One possibility is that the space group was wrong, since there is a 95% off origin peak. There are several choices from data processing, P1, P2, C2 C222, all have this large off origin peak. I wonder if this 95% peak can tell some information? It will not surprise me if this result is incorrect, however how could these regular density be? Best, Niu On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey pjeff...@princeton.eduwrote: Hello Niu, 1. We need extra information. What program did you use ? What's the similarity (e.g. % identity) of your model. What's your space group ? Did you try ALL the space groups in your point group in ALL the permutations (e.g. in primitive orthorhombic there are 8 possibilities). 1a. My best guess on limited info is that you've got a partial solution in the wrong space group with only part of the molecules at their correct position. 2. I recently had a very unusual case where I could solve a structure in EITHER P41212 or P43212 with similar statistics, but that I would see interpenetrating electron density for a second, partial occupancy molecule no matter which of these space groups I tried (and it showed this when I expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, in retrospect, but we obtained a more friendly crystal form. I hope you don't have something like that, but it's possible. Phil Jeffrey Princeton On 11/14/13 5:22 PM, Niu Tou wrote: Dear All, I have a strange MR case which do not know how to interpret, I wonder if any one had similar experiences. The output model does not fit into the map at all, as shown in picture 1, however the map still looks good in part regions. From picture 2 we can see even clear alpha helix. I guess this could not be due to some random density, and I have tried to do MR with a irrelevant model without producing such kind of regular secondary structure. This data has a long c axis, and in most parts the density are still not interpretable. I do not know if this is a good starting point. Could any one give some suggestions? Many thanks! Best, Niu
