 |
 |
Did you try ShelxE autotrace? At that resolution it should work nicely, or at least be able to distinguish between the two sequences.
D
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Keller, Jacob
Sent: 05 February 2015 15:49
To: ccp4bb
Subject: Re: [ccp4bb] Resolve Domain Sequence Ambiguities
Sorry--should have included a bit more info:
A huge caveat: data is tetartohedrally twinned, which makes everything an issue. But, I have managed to get Rfree down to ~32% in refmac with intensity-based twin refinement. I know--R's with de-twinning are illusory, but I still think it's solved, since I also can see anomalous signal in partial-model LLG maps from phaser at places predicted by the structure (and I don't think that anomalous info could be encoded in the MR phases (can it?)). So, that was a nice confirmatory moment...
Resolution is good, but cut off by detector limit on home system (set at max resolution w/o 2theta)
N 1/d^2 Dmid CCanom Nanom RCRanom CC1/2 NCC1/2 Rsplit CCfit CCanomfit $$ $$
1 0.0061 12.82 -0.018 938 0.982 0.998 989 0.028 1.000 0.001
2 0.0182 7.40 0.026 1831 1.026 0.998 1880 0.027 1.000 0.006
3 0.0304 5.73 0.062 2334 1.064 0.995 2385 0.032 1.000 0.010
4 0.0426 4.85 0.048 2806 1.049 0.995 2881 0.033 1.000 0.014
5 0.0547 4.27 0.036 3164 1.036 0.995 3243 0.034 1.000 0.019
6 0.0669 3.87 0.025 3524 1.026 0.994 3606 0.035 1.000 0.023
7 0.0791 3.56 0.011 3758 1.011 0.993 3873 0.038 1.000 0.027
8 0.0912 3.31 0.021 4111 1.021 0.993 4206 0.041 0.999 0.032
9 0.1034 3.11 -0.003 4340 0.997 0.991 4441 0.044 0.999 0.036
10 0.1155 2.94 -0.040 4602 0.961 0.989 4724 0.049 0.999 0.040
11 0.1277 2.80 0.050 4864 1.051 0.991 4968 0.048 0.999 0.045
12 0.1399 2.67 0.051 4996 1.052 0.988 5121 0.052 0.998 0.049
13 0.1520 2.56 0.073 5348 1.076 0.988 5469 0.053 0.997 0.053
14 0.1642 2.47 -0.009 5486 0.991 0.987 5611 0.057 0.996 0.058
15 0.1764 2.38 0.032 5698 1.032 0.985 5827 0.061 0.995 0.062
16 0.1885 2.30 0.091 5945 1.095 0.985 6067 0.063 0.993 0.066
17 0.2007 2.23 0.038 6002 1.039 0.985 6118 0.064 0.991 0.070
18 0.2128 2.17 0.086 6331 1.089 0.983 6445 0.068 0.987 0.075
19 0.2250 2.11 0.075 6411 1.078 0.983 6556 0.070 0.983 0.079
20 0.2372 2.05 0.097 6608 1.102 0.983 6756 0.070 0.977 0.083
21 0.2493 2.00 0.141 6712 1.152 0.981 6880 0.078 0.968 0.088
22 0.2615 1.96 0.104 6556 1.110 0.974 7126 0.093 0.957 0.092
23 0.2737 1.91 0.141 5595 1.152 0.953 7054 0.121 0.943 0.096
24 0.2858 1.87 0.149 4659 1.160 0.936 6652 0.151 0.923 0.101
25 0.2980 1.83 0.125 3630 1.133 0.909 5936 0.184 0.898 0.105
26 0.3101 1.80 0.138 2640 1.148 0.874 5118 0.219 0.866 0.109
27 0.3223 1.76 0.111 1793 1.116 0.851 4035 0.250 0.825 0.114
28 0.3345 1.73 0.040 1040 1.041 0.782 2857 0.305 0.776 0.118
29 0.3466 1.70 0.094 300 1.097 0.713 1474 0.371 0.717 0.122
30 0.3588 1.67 - 2 - 0.589 228 0.497 0.649 0.127
$$
Overall: 0.027 122024 1.027 0.997 138526 0.048
CCanom Nanom RCRanom CC1/2 NCC1/2 Rsplit CCfit CCanomfit
MR solution:
SOLU SET RFZ=3.9 TFZ=7.1 PAK=0 LLG=38 RFZ=3.7 TFZ=8.9 PAK=0 LLG=75 RFZ=4.2
TFZ=8.2 PAK=0 LLG=40 LLG=160 RFZ=3.2 TFZ=11.2 PAK=0 LLG=249 LLG=262 RFZ=4.2
TFZ=9.4 PAK=0 LLG=331 LLG=339 RFZ=4.1 TFZ=11.3 PAK=0 LLG=405 LLG=418 RFZ=3.9
TFZ=11.6 PAK=0 LLG=487 LLG=494 RFZ=4.2 TFZ=8.9 PAK=0 LLG=539 LLG=554 RFZ=3.3
TFZ=8.6 PAK=0 LLG=612 LLG=638 RFZ=3.1 TFZ=8.7 PAK=0 LLG=679 LLG=691 RFZ=2.6
TFZ=12.4 PAK=0 LLG=910 LLG=926 RFZ=3.0 TFZ=9.2 PAK=0 LLG=987 LLG=1001 RFZ=2.7
TFZ=9.8 PAK=3 LLG=1018 LLG=1043 RFZ=2.9 TFZ=9.1 PAK=5 LLG=1039
-----Original Message-----
From: [log in to unmask] [mailto:[log in to unmask]]
Sent: Thursday, February 05, 2015 10:28 AM
To: Keller, Jacob; [log in to unmask]
Subject: RE: Resolve Domain Sequence Ambiguities
Dear Jacob,
Are you sure your MR solution is correct? What is your resolution?
Best,
D
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Keller, Jacob
Sent: 05 February 2015 15:21
To: ccp4bb
Subject: [ccp4bb] Resolve Domain Sequence Ambiguities
Hi All,
I have 14 identical domains placed in my ASU with reasonable MR scores, but the problem is that there should really be 7+7 or 8+8 of domains A and B (which are structurally similar). Can anyone think of a great and easy way of resolving the ambiguity?
I was thinking potentially:
-change one domain to polyAla
-SA omit map of that one
-rebuild/refine
-iterate through all domains, noting scores
Seems it might be pretty low reliability and a fair amount of work though. Otherwise, could try to go back to a small SAD signal, use partial model phases to find HAs, then phase without the model, rebuild from there. Any thoughts or similar experiences?
JPK
*******************************************
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: [log in to unmask]
*******************************************
--
This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom