Re: [COOT] problems of version 0.6
I tried today the new version (-0.6) and see some problems. In general it helps if you can give revision numbers as things move quickly (especially in the pre-releases). 1. Simple mutate for nucleotides. The program makes Gr, Cr etc. in DNA (should be Gd, Cd etc). And it does not mutate to thymine at all, because there is no Tr. Where can I say that it's a DNA? Not entirely sure what happens there. Maybe Paul knows more. 2. Where is pukka puckers...?? They got (temporarily!?) removed (hidden) due to some problems. If you still keen in using them (no warranties) use the scripting function: Scheme: (pukka-puckers? imol) Python: pukka_puckers_qm(imol) My wish list: I am waiting for a version where users can reprogram keys. I would like to use only one-button keys, so that I could use only one hand (or better, one finger) when fitting. This is already in place (although you cannot change the internally assigned button). For some scheme examples: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Example_11:_Paul_Emsley.27s_Key_Bindings or in python: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Example_1:_Bernhard_Lohkamp.27s_Key_Bindings Hope this helps, B *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487673 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] problems of version 0.6
Leonid Cherney wrote: I tried today the new version (-0.6) and see some problems. 1. Simple mutate for nucleotides. The program makes Gr, Cr etc. in DNA (should be Gd, Cd etc). And it does not mutate to thymine at all, because there is no Tr. Where can I say that it's a DNA? This has been fixed up recently - or so I believe. Please let us know the revision number. The output of $ coot --version is useful for us. 2. Where is pukka puckers...?? withdrawn due to a coding error. It should be straightforward to fix, but as yet has not been. Paul.
[COOT] merge water chains
Hi all, I am not sure but If I remember correctly Bernhard mentioned on the last CCP4 study weekend in Nottingham that Coot is able to merge the different water chains, generated through repeated refinement runs, in one. If this function exist, how can I use it? Thanks in advance for your help. Christian -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319
[COOT] RSR exploding RNA
Hi all, I am refining a structure that contains RNA. I've added hydrogens in the riding positions to help with maintaining proper geometry during refinement. However, when I go to adjust the model between refinements in coot using Real Space Refine (or even Regularize for that matter) the RNA explodes with atoms going every which way. This didn't happen before I had added in hydrogens (with Molprobity via Reduce). Also, when I Real Space Refine residues from the protein portion, the heavy atoms (C, O, N) behave normally while about half of the riding hydrogens go wandering off. Any particular reason why this might be happening? some (possibly) relevant info: Platform: Mac PPC-quad running Leopard 10.5.6 Coot 0.6-pre-1 (revision 1941) installed via fink examples of both protein and RNA from my PDB file: ATOM 4982 CB ARG D 289 16.348 55.471 6.150 1.00 50.50 AC ATOM 4983 CG ARG D 289 16.157 54.082 6.707 1.00 49.59 AC ATOM 4984 CD ARG D 289 15.289 53.235 5.789 1.00 45.31 AC ATOM 4985 NE ARG D 289 14.871 52.005 6.459 1.00 70.28 AN ATOM 4986 CZ ARG D 289 13.948 51.167 5.994 1.00 68.12 AC ATOM 4987 NH1 ARG D 289 13.333 51.422 4.845 1.00 57.79 AN ATOM 4988 NH2 ARG D 289 13.635 50.075 6.683 1.00 58.77 AN ATOM 4989 C ARG D 289 17.626 55.916 8.282 1.00 63.79 AC ATOM 4990 O ARG D 289 17.124 55.238 9.181 1.00 77.16 AO ATOM 4991 H ARG D 289 17.427 57.565 5.656 0.00 71.69 AH ATOM 4992 HA ARG D 289 15.928 56.857 7.608 0.00 59.59 AH ATOM 4993 HB2 ARG D 289 15.511 55.741 5.741 0.00 52.02 AH ATOM 4994 HB3 ARG D 289 17.041 55.423 5.474 0.00 52.02 AH ATOM 4995 HG2 ARG D 289 17.021 53.649 6.795 0.00 49.34 AH ATOM 4996 HG3 ARG D 289 15.720 54.140 7.572 0.00 49.34 AH ATOM 4997 HD2 ARG D 289 14.495 53.735 5.544 0.00 44.19 AH ATOM 4998 HD3 ARG D 289 15.795 52.996 4.997 0.00 44.19 AH ATOM 4999 HE ARG D 289 15.296 51.784 7.302 0.00 71.47 AH ATOM 5000 HH11 ARG D 289 13.533 52.129 4.398 0.00 56.48 AH ATOM 5001 HH12 ARG D 289 12.737 50.879 4.547 0.00 56.48 AH ATOM 5002 HH21 ARG D 289 14.031 49.907 7.428 0.00 59.45 AH ATOM 5003 HH22 ARG D 289 13.039 49.533 6.382 0.00 59.45 AH ATOM 8005 PAr E 18 -9.125 47.764 17.588 1.00 42.70 P ATOM 8006 OP1 Ar E 18 -10.280 48.637 17.912 1.00 56.33 O ATOM 8007 OP2 Ar E 18 -7.986 48.283 16.807 1.00 44.20 O ATOM 8008 O5' Ar E 18 -8.438 47.153 18.884 1.00 45.30 O ATOM 8009 C5' Ar E 18 -9.198 46.485 19.855 1.00 41.29 C ATOM 8010 C4' Ar E 18 -8.249 46.040 20.947 1.00 41.68 C ATOM 8011 O4' Ar E 18 -7.335 45.058 20.393 1.00 43.54 O ATOM 8012 C1' Ar E 18 -6.142 45.087 21.145 1.00 39.98 C ATOM 8013 N9 Ar E 18 -5.085 45.353 20.198 1.00 36.77 N ATOM 8014 C8 Ar E 18 -5.218 45.960 18.981 1.00 40.28 C ATOM 8015 N7 Ar E 18 -4.088 46.077 18.329 1.00 33.42 N ATOM 8016 C5 Ar E 18 -3.170 45.501 19.188 1.00 36.92 C ATOM 8017 C4 Ar E 18 -3.763 45.050 20.351 1.00 39.55 C ATOM 8018 N3 Ar E 18 -3.176 44.445 21.399 1.00 39.05 N ATOM 8019 C2 Ar E 18 -1.869 44.309 21.175 1.00 49.05 C ATOM 8020 N1 Ar E 18 -1.153 44.693 20.098 1.00 55.85 N ATOM 8021 C6 Ar E 18 -1.786 45.304 19.067 1.00 50.71 C ATOM 8022 N6 Ar E 18 -1.121 45.704 17.978 1.00 47.54 N ATOM 8023 C2' Ar E 18 -6.302 46.174 22.196 1.00 39.53 C ATOM 8024 O2' Ar E 18 -6.816 45.637 23.390 1.00 45.42 O ATOM 8025 C3' Ar E 18 -7.295 47.092 21.504 1.00 43.28 C ATOM 8026 O3' Ar E 18 -7.903 48.019 22.406 1.00 47.60 O ATOM 8027 H5' Ar E 18 -9.636 45.704 19.455 0.00 40.96 H ATOM 8028 H5'' Ar E 18 -9.872 47.091 20.226 0.00 40.96 H ATOM 8029 H4' Ar E 18 -8.758 45.636 21.681 0.00 37.61 H ATOM 8030 H3' Ar E 18 -6.856 47.571 20.770 0.00 42.61 H ATOM 8031 H2' Ar E 18 -5.451 46.634 22.354 0.00 41.95 H ATOM 8032 HO2' Ar E 18 -6.956 44.674 23.272 0.00 45.81 H ATOM 8033 HO3' Ar E 18 -7.578 48.090 23.328 0.00 44.87 H ATOM 8034 H1' Ar
Re: [COOT] RSR exploding RNA
Chris, The hydrogens are at 0 occupancy so their positions are not refined...the other atoms at non-zero occupancy do move leaving the Hs behind..set the hydrogens to non-zero occupancy (eg. 0.01). HTH, Iain CK wrote: Hi all, I am refining a structure that contains RNA. I've added hydrogens in the riding positions to help with maintaining proper geometry during refinement. However, when I go to adjust the model between refinements in coot using Real Space Refine (or even Regularize for that matter) the RNA explodes with atoms going every which way. This didn't happen before I had added in hydrogens (with Molprobity via Reduce). Also, when I Real Space Refine residues from the protein portion, the heavy atoms (C, O, N) behave normally while about half of the riding hydrogens go wandering off. Any particular reason why this might be happening? some (possibly) relevant info: Platform: Mac PPC-quad running Leopard 10.5.6 Coot 0.6-pre-1 (revision 1941) installed via fink examples of both protein and RNA from my PDB file: ATOM 4982 CB ARG D 289 16.348 55.471 6.150 1.00 50.50 AC ATOM 4983 CG ARG D 289 16.157 54.082 6.707 1.00 49.59 AC ATOM 4984 CD ARG D 289 15.289 53.235 5.789 1.00 45.31 AC ATOM 4985 NE ARG D 289 14.871 52.005 6.459 1.00 70.28 AN ATOM 4986 CZ ARG D 289 13.948 51.167 5.994 1.00 68.12 AC ATOM 4987 NH1 ARG D 289 13.333 51.422 4.845 1.00 57.79 AN ATOM 4988 NH2 ARG D 289 13.635 50.075 6.683 1.00 58.77 AN ATOM 4989 C ARG D 289 17.626 55.916 8.282 1.00 63.79 AC ATOM 4990 O ARG D 289 17.124 55.238 9.181 1.00 77.16 AO ATOM 4991 H ARG D 289 17.427 57.565 5.656 0.00 71.69 AH ATOM 4992 HA ARG D 289 15.928 56.857 7.608 0.00 59.59 AH ATOM 4993 HB2 ARG D 289 15.511 55.741 5.741 0.00 52.02 AH ATOM 4994 HB3 ARG D 289 17.041 55.423 5.474 0.00 52.02 AH ATOM 4995 HG2 ARG D 289 17.021 53.649 6.795 0.00 49.34 AH ATOM 4996 HG3 ARG D 289 15.720 54.140 7.572 0.00 49.34 AH ATOM 4997 HD2 ARG D 289 14.495 53.735 5.544 0.00 44.19 AH ATOM 4998 HD3 ARG D 289 15.795 52.996 4.997 0.00 44.19 AH ATOM 4999 HE ARG D 289 15.296 51.784 7.302 0.00 71.47 AH ATOM 5000 HH11 ARG D 289 13.533 52.129 4.398 0.00 56.48 AH ATOM 5001 HH12 ARG D 289 12.737 50.879 4.547 0.00 56.48 AH ATOM 5002 HH21 ARG D 289 14.031 49.907 7.428 0.00 59.45 AH ATOM 5003 HH22 ARG D 289 13.039 49.533 6.382 0.00 59.45 AH ATOM 8005 PAr E 18 -9.125 47.764 17.588 1.00 42.70 P ATOM 8006 OP1 Ar E 18 -10.280 48.637 17.912 1.00 56.33 O ATOM 8007 OP2 Ar E 18 -7.986 48.283 16.807 1.00 44.20 O ATOM 8008 O5' Ar E 18 -8.438 47.153 18.884 1.00 45.30 O ATOM 8009 C5' Ar E 18 -9.198 46.485 19.855 1.00 41.29 C ATOM 8010 C4' Ar E 18 -8.249 46.040 20.947 1.00 41.68 C ATOM 8011 O4' Ar E 18 -7.335 45.058 20.393 1.00 43.54 O ATOM 8012 C1' Ar E 18 -6.142 45.087 21.145 1.00 39.98 C ATOM 8013 N9 Ar E 18 -5.085 45.353 20.198 1.00 36.77 N ATOM 8014 C8 Ar E 18 -5.218 45.960 18.981 1.00 40.28 C ATOM 8015 N7 Ar E 18 -4.088 46.077 18.329 1.00 33.42 N ATOM 8016 C5 Ar E 18 -3.170 45.501 19.188 1.00 36.92 C ATOM 8017 C4 Ar E 18 -3.763 45.050 20.351 1.00 39.55 C ATOM 8018 N3 Ar E 18 -3.176 44.445 21.399 1.00 39.05 N ATOM 8019 C2 Ar E 18 -1.869 44.309 21.175 1.00 49.05 C ATOM 8020 N1 Ar E 18 -1.153 44.693 20.098 1.00 55.85 N ATOM 8021 C6 Ar E 18 -1.786 45.304 19.067 1.00 50.71 C ATOM 8022 N6 Ar E 18 -1.121 45.704 17.978 1.00 47.54 N ATOM 8023 C2' Ar E 18 -6.302 46.174 22.196 1.00 39.53 C ATOM 8024 O2' Ar E 18 -6.816 45.637 23.390 1.00 45.42 O ATOM 8025 C3' Ar E 18 -7.295 47.092 21.504 1.00 43.28 C ATOM 8026 O3' Ar E 18 -7.903 48.019 22.406 1.00 47.60 O ATOM 8027 H5' Ar E 18 -9.636 45.704 19.455 0.00 40.96 H ATOM 8028 H5'' Ar E 18 -9.872 47.091 20.226 0.00 40.96 H ATOM 8029 H4' Ar E 18 -8.758 45.636 21.681 0.00 37.61 H ATOM 8030 H3' Ar E 18 -6.856 47.571 20.770 0.00 42.61 H ATOM 8031 H2' Ar E 18 -5.451 46.634 22.354 0.00 41.95 H ATOM 8032
Re: [COOT] RSR exploding RNA
Also, does the resolution of your data warrant including the hydrogens in the model ? Can you actually see them ? You can add them in their riding positions, which may help stablise your refinement, but not write them out to the coordinate file (uncheck and output to coordinate file in the GUI). Iain CK wrote: Hi all, I am refining a structure that contains RNA. I've added hydrogens in the riding positions to help with maintaining proper geometry during refinement. However, when I go to adjust the model between refinements in coot using Real Space Refine (or even Regularize for that matter) the RNA explodes with atoms going every which way. This didn't happen before I had added in hydrogens (with Molprobity via Reduce). Also, when I Real Space Refine residues from the protein portion, the heavy atoms (C, O, N) behave normally while about half of the riding hydrogens go wandering off. Any particular reason why this might be happening? some (possibly) relevant info: Platform: Mac PPC-quad running Leopard 10.5.6 Coot 0.6-pre-1 (revision 1941) installed via fink examples of both protein and RNA from my PDB file: ATOM 4982 CB ARG D 289 16.348 55.471 6.150 1.00 50.50 AC ATOM 4983 CG ARG D 289 16.157 54.082 6.707 1.00 49.59 AC ATOM 4984 CD ARG D 289 15.289 53.235 5.789 1.00 45.31 AC ATOM 4985 NE ARG D 289 14.871 52.005 6.459 1.00 70.28 AN ATOM 4986 CZ ARG D 289 13.948 51.167 5.994 1.00 68.12 AC ATOM 4987 NH1 ARG D 289 13.333 51.422 4.845 1.00 57.79 AN ATOM 4988 NH2 ARG D 289 13.635 50.075 6.683 1.00 58.77 AN ATOM 4989 C ARG D 289 17.626 55.916 8.282 1.00 63.79 AC ATOM 4990 O ARG D 289 17.124 55.238 9.181 1.00 77.16 AO ATOM 4991 H ARG D 289 17.427 57.565 5.656 0.00 71.69 AH ATOM 4992 HA ARG D 289 15.928 56.857 7.608 0.00 59.59 AH ATOM 4993 HB2 ARG D 289 15.511 55.741 5.741 0.00 52.02 AH ATOM 4994 HB3 ARG D 289 17.041 55.423 5.474 0.00 52.02 AH ATOM 4995 HG2 ARG D 289 17.021 53.649 6.795 0.00 49.34 AH ATOM 4996 HG3 ARG D 289 15.720 54.140 7.572 0.00 49.34 AH ATOM 4997 HD2 ARG D 289 14.495 53.735 5.544 0.00 44.19 AH ATOM 4998 HD3 ARG D 289 15.795 52.996 4.997 0.00 44.19 AH ATOM 4999 HE ARG D 289 15.296 51.784 7.302 0.00 71.47 AH ATOM 5000 HH11 ARG D 289 13.533 52.129 4.398 0.00 56.48 AH ATOM 5001 HH12 ARG D 289 12.737 50.879 4.547 0.00 56.48 AH ATOM 5002 HH21 ARG D 289 14.031 49.907 7.428 0.00 59.45 AH ATOM 5003 HH22 ARG D 289 13.039 49.533 6.382 0.00 59.45 AH ATOM 8005 PAr E 18 -9.125 47.764 17.588 1.00 42.70 P ATOM 8006 OP1 Ar E 18 -10.280 48.637 17.912 1.00 56.33 O ATOM 8007 OP2 Ar E 18 -7.986 48.283 16.807 1.00 44.20 O ATOM 8008 O5' Ar E 18 -8.438 47.153 18.884 1.00 45.30 O ATOM 8009 C5' Ar E 18 -9.198 46.485 19.855 1.00 41.29 C ATOM 8010 C4' Ar E 18 -8.249 46.040 20.947 1.00 41.68 C ATOM 8011 O4' Ar E 18 -7.335 45.058 20.393 1.00 43.54 O ATOM 8012 C1' Ar E 18 -6.142 45.087 21.145 1.00 39.98 C ATOM 8013 N9 Ar E 18 -5.085 45.353 20.198 1.00 36.77 N ATOM 8014 C8 Ar E 18 -5.218 45.960 18.981 1.00 40.28 C ATOM 8015 N7 Ar E 18 -4.088 46.077 18.329 1.00 33.42 N ATOM 8016 C5 Ar E 18 -3.170 45.501 19.188 1.00 36.92 C ATOM 8017 C4 Ar E 18 -3.763 45.050 20.351 1.00 39.55 C ATOM 8018 N3 Ar E 18 -3.176 44.445 21.399 1.00 39.05 N ATOM 8019 C2 Ar E 18 -1.869 44.309 21.175 1.00 49.05 C ATOM 8020 N1 Ar E 18 -1.153 44.693 20.098 1.00 55.85 N ATOM 8021 C6 Ar E 18 -1.786 45.304 19.067 1.00 50.71 C ATOM 8022 N6 Ar E 18 -1.121 45.704 17.978 1.00 47.54 N ATOM 8023 C2' Ar E 18 -6.302 46.174 22.196 1.00 39.53 C ATOM 8024 O2' Ar E 18 -6.816 45.637 23.390 1.00 45.42 O ATOM 8025 C3' Ar E 18 -7.295 47.092 21.504 1.00 43.28 C ATOM 8026 O3' Ar E 18 -7.903 48.019 22.406 1.00 47.60 O ATOM 8027 H5' Ar E 18 -9.636 45.704 19.455 0.00 40.96 H ATOM 8028 H5'' Ar E 18 -9.872 47.091 20.226 0.00 40.96 H ATOM 8029 H4' Ar E 18 -8.758 45.636 21.681 0.00 37.61 H ATOM 8030 H3' Ar E 18 -6.856 47.571 20.770 0.00 42.61
Re: [COOT] RSR exploding RNA
On May 5, 2009, at 3:16 PM, CK wrote: Hi all, I am refining a structure that contains RNA. I've added hydrogens in the riding positions to help with maintaining proper geometry during refinement. However, when I go to adjust the model between refinements in coot using Real Space Refine (or even Regularize for that matter) the RNA explodes with atoms going every which way. This didn't happen before I had added in hydrogens (with Molprobity via Reduce). Also, when I Real Space Refine residues from the protein portion, the heavy atoms (C, O, N) behave normally while about half of the riding hydrogens go wandering off. Any particular reason why this might be happening? Hydrogen can be quite explosive. Have you tried helium? But seriously, if the program you used to hydrogenate uses a nomenclature that coot/refmac doesn't expect, this could happen. Also the zero occupancy might be the culprit. However you mentioned that without hydrogens it was hard to maintain proper geometry. This might be a cause for concern, or re-examination of the structure and its density.
Re: [COOT] RSR exploding RNA
I think perhaps I should clarify what I've been doing. I've been refining my structure using phenix.refine and had reached a fairly satisfactory point with suitably low R-factors (21/25) and very reasonable RMSDs for bonds and angles. At this point I ran my structure through the molprobity server to take a closer look at geometry and clashes. As going through the entire clash list by hand can be very tedious I wanted to see if adding hydrogens in the riding positions and refining again would help alleviate some of the clashes, which it did. Note, the refinements have been stable both before and after the addition of the riding hydrogens. with no significant changes in R- factors or geometry RMSDs. Also, the hydrogens are explicitly excluded from Fcalc during refinement as the resolution of the data would not warrant their inclusion. So now at this point I'm simply trying to make some minor adjustments to the model using RSR in coot and have happened upon the exploding RNA residue / wandering hydrogen phenomenon. I have tried changing the occupancy of the hydrogens to various values (0.01-1.0) using the Residue Info menu option but it has no effect on RSR and is not likely the culprit. I'll next try the changing the nomenclature to see if that fixes the problem. -Chris On May 5, 2009, at 3:59 PM, William G. Scott wrote: On May 5, 2009, at 3:16 PM, CK wrote: Hi all, I am refining a structure that contains RNA. I've added hydrogens in the riding positions to help with maintaining proper geometry during refinement. However, when I go to adjust the model between refinements in coot using Real Space Refine (or even Regularize for that matter) the RNA explodes with atoms going every which way. This didn't happen before I had added in hydrogens (with Molprobity via Reduce). Also, when I Real Space Refine residues from the protein portion, the heavy atoms (C, O, N) behave normally while about half of the riding hydrogens go wandering off. Any particular reason why this might be happening? Hydrogen can be quite explosive. Have you tried helium? But seriously, if the program you used to hydrogenate uses a nomenclature that coot/refmac doesn't expect, this could happen. Also the zero occupancy might be the culprit. However you mentioned that without hydrogens it was hard to maintain proper geometry. This might be a cause for concern, or re- examination of the structure and its density.
