fix 180-degree ideal angles #65
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GaribMurshudov
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GaribMurshudov
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I could not check all of them. I trust they are correct
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Do the changes include C=C=C type of cases (it does include S=C=N cases, I believe) |
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I only checked ideal bond angle values in the monomer library. Now I checked =C= cases and triple bonds, and corrected 9N9 C2H DR8. |
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Do I need to approve again |
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It's not needed. I would like to wait a few days or a week to allow for someone (including me) to test the branch before merging. |
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Here is the list of updated monomers 051 06U 06V 06W 07M 09B 09F 09G 0B6 0C5 0CG 0E1 0FN 0JA 0KL 0KR 0L3 0L4 0L5 0L6 0L7 0LB 0LC 0LI 0N6 0R0 0R5 0R6 0R7 0R8 0RI 0S2 0S3 0T3 0TM 0U9 0V0 0V2 0V3 0V6 0VM 0VN 0WB 0WC 0X6 0XP 0Y4 0YV 10J 10N 10O 10Q 10V 10W 11F 13V 13W 14Q 185 18G 18H 196 198 1A2 1AD 1AK 1B1 1BB 1DJ 1EV 1FA 1FS 1H5 1H6 1H7 1H8 1HG 1HH 1HJ 1HL 1HM 1HO 1HQ 1HX 1J5 1JS 1JY 1L4 1LG 1M6 1OB 1OY 1Q3 1QA 1QZ 1R0 1RE 1SU 1SW 1TS 1UZ 1W1 1W2 1WL 1WM 1WN 1X2 1XP 1YV 1ZW 25U 27F 28B 29T 2C5 2CW 2D6 2EJ 2FF 2GN 2GT 2H2 2HT 2HY 2IC 2KW 2LG 2M7 2N6 2NI 2O7 2OL 2OO 2OQ 2P6 2QQ 2RS 2RT 2S6 2S7 2S9 2SF 2SZ 2T2 2TC 2TE 2TF 2TG 2TJ 2U8 2VK 2VT 2VU 2WQ 2XK 2Y2 2YX 30J 30X 328 32A 32H 32J 32V 33G 33H 34I 34N 3AJ 3B6 3BX 3CF 3CQ 3DX 3E8 3FD 3FE 3GO 3HH 3HK 3IF 3IU 3JB 3LL 3LQ 3M8 3MN 3NR 3OB 3OJ 3OQ 3OS 3P3 3PZ 3QH 3QV 3RQ 3RR 3SC 3T4 3UJ 3UZ 3VF 3W4 3W5 3WF 3X7 3XK 3XL 3XW 3XY 422 42A 43C 43D 43W 45F 45W 45Z 46X 46Y 47W 486 48M 49O 4CF 4CX 4CY 4DS 4DZ 4EJ 4F6 4HK 4HN 4HV 4K0 4KT 4LC 4N9 4TR 4TZ 4U9 4VS 4VT 4W4 4W6 4XO 4YM 4ZC 50D 50F 50P 51D 51E 51Y 52V 53R 53S 53T 53V 54L 55V 58E 58H 58O 58P 58Q 58R 599 5AG 5BZ 5CN 5DR 5DW 5EL 5EM 5EN 5EP 5FB 5JO 5L5 5MT 5N1 5N2 5OK 5P2 5P8 5PC 5Q7 5Q8 5QE 5QF 5QG 5QM 5RA 5RV 5RY 5S6 5TA 5TC 5TD 5U5 5UY 5WA 5WB 5Y2 5Y3 5Y4 5Z1 603 60S 60U 60V 60W 60Y 639 65B 65C 66J 67G 67T 68E 68J 68P 68R 68T 697 69D 6AJ 6BC 6CN 6CY 6DC 6DR 6E6 6E8 6FM 6FN 6FQ 6FV 6IC 6K2 6KE 6L2 6LJ 6M3 6NR 6O2 6QQ 6RF 6RJ 6RL 6RV 6TS 6VP 6X9 6XK 6YC 6YF 6Z0 6Z3 6Z6 6ZP 70M 71G 72F 72Q 738 741 743 75E 75J 75M 76C 76Z 772 775 778 77C 77T 77U 79A 79B 79D 79H 79V 7AC 7AX 7AY 7BK 7BP 7BR 7BW 7BX 7CI 7CP 7DQ 7DR 7DY 7E4 7EE 7GK 7H2 7II 7K4 7KA 7LK 7N1 7NB 7OE 7PP 7S4 7TM 7TO 7TQ 7TR 7UR 7XN 7Z0 80V 81V 85A 85E 85K 85T 86D 877 893 89I 8A0 8A3 8A6 8AO 8AU 8B0 8B3 8BY 8D0 8EV 8EY 8F1 8F7 8FD 8FS 8G1 8GN 8GQ 8H8 8HE 8HN 8KM 8KP 8M8 8MY 8NH 8Q2 8Q8 8QE 8QV 8R2 8S1 8SW 8TK 8TN 8TS 8U6 8U9 8UC 8UF 8UL 8UN 8UO 8UR 8UU 8UY 8V6 8VL 8WC 8Y5 8Y8 8YC 8YZ 8Z1 91R 91T 928 92F 92T 93J 93N 94Q 954 956 96D 97A 97E 97L 97X 98Z 99S 9DR 9EL 9EU 9FC 9FG 9HY 9J1 9JG 9JM 9JP 9K7 9KD 9KG 9LJ 9N2 9N5 9N9 9OG 9OJ 9P7 9PM 9S0 9SS 9TX 9U5 9U9 9VG 9VS 9X4 9ZJ A1Y A3H A3J A3K A3N A3Q A3Y A42 A4J A4K A54 A5F A7E A7Z A86 A8O A91 ABZ AC7 ADB AIA AJG AKS AOB AOC AQ4 AS7 AT6 AX1 AXD AZ6 AZI AZJ AZO B14 B1X B46 B4Y B5G B5R B66 B6T B6W B7H B7K B7Q B7V B9M B9T BC1 BC4 BDQ BFV BG0 BGJ BH0 BJD BJS BJV BJZ BMV BNE BTJ BWE BWI BYV C0J C0M C0T C16 C1V C2H C2W C3E C51 C7T C8W C8Y C90 CB3 CCT CCX CF7 CFJ CHR CIO CLJ CMD CNI CNU CO2 CRJ CU4 CWK CXD CZ3 D1F D1J D1M D2R D32 D4B D77 D88 D8B D8V DA4 DB0 DB8 DGZ DH3 DJZ DKK DKW DLN DO9 DQS DR8 DS5 DU6 DUV DWG DWJ DWP DWS DX7 DX8 DYR DZ6 DZC E1B E56 E5S E6Z E7M E94 E9Q E9W EA7 EB6 ED1 ED2 ED4 ED5 ED7 EDU EDV EE5 EE7 EEU EEV EFZ EI8 EJK EJP EK7 EKB ELW ELZ EM6 EMH EMV EOW EP5 EQO ER4 ERP EU4 EUB EUR F0H F1Z F2K F2U F3F F6M F7D F7J F7M F86 F87 F8Y F9D F9Y FB9 FC4 FCS FD9 FDU FEW FFR FFZ FGF FMD FNV FNZ FOJ FPT FRG FTE FTH FTI FTL FU6 FVQ FY7 FY9 FYL FYO FYX FYZ FZF FZL FZO FZR G0U G45 G4W G57 G5C G5X G6F G6Y G7V G8J G90 G93 G96 G98 G9Q GAS GC6 GCC GCF GDI GG1 GGK GHK GI8 GJ2 GK3 GKK GTU GUC GVS GWB GWI GWJ GX6 GYW H0U H10 H2K H2Q H2Z H3C H3K H41 H4H H4K H4L H4O H4R H5K H6D H6K H6R H76 H8A H8N H8Z H94 H9H H9V H9Y HDJ HHZ HJ4 HJ5 HK4 HK5 HKI HKM HNV HNW HO4 HOR HQP HR0 HRE HSI HV4 HWN I09 I14 I15 I20 I21 I32 I5I I6X I9H IA7 IB1 IC3 IEO IET IGM IHE IHI IHJ IIB IK4 IS8 IT5 ITY IUL IUY IVU IY1 IZ9 IZO J0C J20 J32 J47 J5M J5N J5V J7G J7J J8F J8L J8O J8R J8U J93 J9D JAD JBA JBW JCK JD2 JD7 JD8 JDH JE8 JEB JEE JEH JEK JEQ JEU JEW JF8 JFB JFT JGG JGZ JJD JJS JJV JJX JK3 JKS JLJ JMD JMN JNY JOY JQ8 JQB JQT JT6 JU2 JUO JUS JWM JWP JWV JX2 JXQ JXT JY2 JY5 JYB JZZ K1H K1Q K1Z K28 K2H K2K K2W K38 K3B K3E K3H K3K K3N K3W K51 K5A K6Y K75 K7F K9W K9Z KA4 KA7 KA8 KAQ KBT KBZ KDV KDW KEZ KFS KHC KK6 KKL KLY KM7 KMN KMV KR1 KRJ KRL KRP KRV KVC KVD KWG KWJ KWZ KX1 KZJ KZP L52 L53 L59 L6P L6V LCQ LG7 LGB LIR LJV LJY LK4 LKB LKM LKT LKY LMY LNH LNY LNZ LPG LPH LQA LQF LQG LR7 LS8 LTQ LTS LY7 LZB LZC LZM M06 M14 M22 M2H M3A M3D M3V M4P M4R M5D M5V M6A M6B M6E M6F M6G M6V M7D M83 M8K M9A M9J M9Y MB9 MBX MFZ MG9 MIL MJP MLG MQ0 MRA MS4 MSD MTC N05 N22 N37 N48 N75 N7F N9G NDR NEX NH8 NJ8 NO7 NOG NQE NQH NQK NQN NQQ NR8 NSE NTG NWJ NXG NXV NXW O17 O1H O22 O38 O44 O6G O6J O6M O6Y O71 O75 O7P OAJ OAV ODG OFD OG1 OLW OMJ ONY ORG ORH OS2 OS3 OUM OWW OXW OYZ OZ5 OZJ P0V P29 P2O P32 P3K P43 P44 P45 P4Z P51 P54 P55 P5U P63 P6J P74 P76 P8M P8V P94 P96 PAK PB9 PCE PDU PFG PID PK0 PPB PQ0 PU1 PU9 PUZ PV5 PWJ PWV PZ2 PZ5 PZK PZL Q0E Q0H Q0M Q0N Q0Q Q0T Q0W Q1G Q1T Q4H Q55 Q5D Q5J Q5W Q62 Q6G Q82 Q9H Q9K Q9N QA1 QAF QAG QB8 QBE QEJ QKM QL2 QL8 QLH QLN QLR QLZ QMV QNZ QO1 QS1 QSD QWJ QYK QYW QZ3 QZE QZV QZZ R0G R26 R2A R2Q R4Y R5D R5W R62 R8D R8E R9Q RAU RCF RCH RHP RLJ RLL RMA RN8 RQV RRA RS7 RSA RSZ RTH RTJ RUM RVZ RWY RXJ RXS RXV RYA RYM RYS RZA RZS S0P S0Y S1V S30 S33 S38 S6J S6L S6S S6W S8B S8W S8Z S92 SBN SCN SEF SJM SJY SK6 SKK SL4 SLK SNQ SOV SSJ SWJ SXJ SY1 T22 T27 T3C T3E T4D T4Q T4W T6Q T7Z T98 T9J T9K T9N TEI TF1 TH4 TI9 TJF TNN TO1 TPB TQM TR4 TUW TVV TW2 TWE TWH TWK TX6 TXM TZ0 U06 U08 U0G U0K U0N U0Q U0T U3Z U49 U64 U66 U6B U75 U7Q UC9 UF4 UFS UGJ UGM UGP UH1 UK4 UKW ULD ULS UMV UMY UNI UNS UO4 UOM UOP UTB UTY UUJ UWM UXM UYS V0Y V1S V3D V7Y VAO VBD VBG VBM VFC VFN VFT VGQ VGW VH5 VH8 VHB VHK VHN VHQ VHZ VJ2 VJ5 VJE VK2 VK7 VOY VP7 VPS VRV VSI VSY VT2 VTA VW1 W2A W2C W3M W4M W4P W8P WCV WGV WHD WHU WHY WJV WK7 WKD WL4 WOW WPS WQ4 WYD X01 X0D X0Q X0R X2S X2V X52 XCN XCV XE4 XEA XEY XF1 XFD XFS XHM XHY XI1 XIH XJS XKY XNV XP0 XPF XT0 XT3 XTK XTV XY3 XZN Y11 Y14 Y3G YG1 YG7 YH2 YLA YM7 YM8 YNC YP1 YPE YPF YSH YSO YSY YTJ YW2 YWZ ZBF ZDG ZG7 ZH2 ZH4 ZHK ZOO ZVY ZVZ ZZ5 ZZE ZZM |
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@drlemmus would it be possible to do some tests? We would like to minimise the number of probems before release |
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Yes, I will do some testing. |
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The angle esd is set to 3 degrees. Is this because the observed values really had a high variance or is this a fallback? |
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Yes, it must be. I will ask @flong-mrc today |
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CO2.cif is a nice example. That went from 179.682 +- 1.50 to 180 +- 3.00. That may make it less straight. |
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I think with new treatment 180 degrees in servalcat you may find this angle will be more straight than before. There is a problem in standard harmonic restraints, 180 is a singular point. That was the main cause of non-straightness |
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In addition, I should mention that compiling statistics for 180 degrees is also tricky. For metalCoord we use symmetrised von Mises distribution. @flong-mrc does not use this as far as I know. Observed angles cannot be more than 180 degrees. They will always be < 180. Therefore, average value will be biased. I will talk to @flong-mrc about this today. |
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I will merge this, but I think the sigma value should be revised later, based on the analysis using the symmetrised von Mises distribution. |
The ideal angles in several monomers, which should be 180 degrees, were found to be incorrect. They have been updated using Acedrg 326 (rev 384). I think now this branch is ready for testing.