September 2020 - Chimera-users - RBVI Mailing Lists

Setting a pathway/trajectory for a molecule
by Rani Wiswedel 19 Sep '20

19 Sep '20

Good day, I am an honours student attempting to set up my first molecular dynamics simulation, and am having some trouble trying to understand how to set a pathway for a substrate through a pore in Chimera. I am very unsure of how to do this, and was wondering if you could provide some help. I tried following the Trajectory and Ensemble Analysis tutorial, but essentially cannot get past the first step of downloading leap.top etc. I am also not sure if this is the correct tutorial to follow for what I am looking to do? Any advice would be greatly appreciated, I am in way over my depth. Thank you Kind regards, Rani Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.

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Re: [Chimera-users] alpha carbon atom as sphere
by Elaine Meng 18 Sep '20

18 Sep '20

On Sep 18, 2020, at 1:58 PM, Ruchika <Ruchika(a)ucsf.edu> wrote: > Hi Elaine > I am trying to select just alpha carbon on the atom and show it as a sphere, but I am having hard time doing that. When I select the atom, and go to actions and sphere, I must show the side chain and then going to sphere, shows the whole side chain as a sphere instead of just alpha carbon as sphere. Could you please help me with this issue ? > Thanks a lot !! > Regards > Ruchika Hi Ruchika, Assuming you are using Chimera, we recommend sending such questions to chimera-users(a)cgl.ucsf.edu (CC'd here) or else they may fall through the cracks. It doesn't make sense to me that you would need to show the sidechain. I can only guess that maybe you're showing ribbon and that is causing the confusion. If you are showing ribbon, you cannot see or select the alpha-carbon with the mouse, because ribbon normally hides the backbone atoms. If you select the ribbon it selects the whole residue. If you want to show backbone atoms at the same time as ribbon, use command "ribbackbone" or alternatively, just hide the ribbon, and then show whatever atoms you want. Select only the CA and then change it to sphere. Explanation of "ribbackbone" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html> Example commands: open 1gcn ribbackbone show :5@CA repr sphere :5@CA I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Backbone RMSD
by Zhang, Bixia 18 Sep '20

18 Sep '20

Hi, I am trying to get the backbone RMSD between two structures. However I tried selecting backbone and use matchmaker, it gives me same value with the whole protein. So there must be something wrong. Could you please teach me a command that can do this? Thank you so much for helping! Best, Bixia

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Re: [Chimera-users] Molecular Dynamics
by Jean-Didier Pierre Marechal 18 Sep '20

18 Sep '20

Dear Edmund, Elaine is completely right about everything. This interface was first developed for our lab for our own needs (training, short MD and Teaching) then we work with the Chimera’s team to make it look the way it looks today (a lot better than the initial shot). It can do a lot of things but in its actual state it remains a simple tool for first insights on the system and not necessarily convenient for all systems (especially if you look for large systems with long MDs). Typical time scale of MDs in today standards are difficult to performe with this interface. The main application we make of it is on small molecules and for teaching purposes it is fantastic. You could eventually look look for short MDs on a complex protein-ligand but I would reckon to go for standard MD drivers. We did not continue on this project because ChimeraX, that already integrates openMM, was about to be relased. Hope this help, JeanDI ***************************** Prof. Dr. Jean-Didier Maréchal (JeanDi) Associate Professor Insilichem Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es personal webpage: http://gent.uab.cat/jdidier insilichem webpage: http://www.insilichem.com

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Molecular Dynamics
by Edmund Marinelli 18 Sep '20

18 Sep '20

Hello: Very new to Chimera and to modeling in general. 1.) Does the Molecular Dynamics Tool allow simulation of a protein ligand complex? 2.) Does a protein ligand docking pose generated by Autodock, for example, qualify as a 'model' that can be read by the MD Tool and be employed in a MD run? Is there a comprehensive tutorial or manual discussing in detail the setting of MD run within Chimera? Any help would be appreciated. Thanks. Edmund R Marinelli, PhD

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measurement of arc-length (geodesic distance) between atoms on a protein surface?
by Wiener, Michael C (mcw2s) 18 Sep '20

18 Sep '20

New subscriber here, with a question about whether Chimera currently can measure arc-length (geodesic distance) between atoms on a protein surface (or, for example, generate a Calpha-Calpha distance matrix of this). I am (very) interested in measuring/obtaining distances between pairs of Calpha carbons (or pairs of other atoms, I suppose) of different amino acids that are on the surface of a protein. While the difference between arc-length (geodesic) distance and cartesian/Euclidean distance will be negligible if, for example, the two solvent-exposed Calpha atoms are on the same solvent-exposed face of an alpha-helix, the difference could be significant for residues on opposite “sides” of the protein. I did see that there are ways in Chimera to get distances between an atom and a molecular surface, or to place markers on the surface & obtain the lengths between these for a distance, but I am VERY interested in whether one can simply select two atoms and get the arc-length (geodesic) distance or generate an arc-length (geodesic distance) matrix of all surface-exposed Calpha pairs. Several computational methods have been developed for this sort of thing, via graph theoretical or other approximation method, and have been published (Hall et al., Biophysical Chemistry 190-191 [2014] 50-55). However, I have not yet (?) found this to be in any graphics/analysis program. I’m thinking that this could perhaps be useful to someone besides me? Any assistance would be greatly appreciated. My lab and I are (much) more on the user side than the developer side, so are not currently well-positioned to code it in-lab. Regards, -MW (btw, if anyone in the “Chimera Group” wants to know more about why I am interested in this, don’t hesitate to send me an email. This type of distance calculation is related to some experimental technology/assay development that we are doing.) ----- Michael C. Wiener. Ph.D., Professor Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville, VA 22908-0886 434-243-2731 (office); 434-243-2730 (lab)

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generate helical symmetry mates around an axis
by sadeem ahmad 17 Sep '20

17 Sep '20

Hi all, I am trying to generate a helical trimer from the monomer pdb around a central double-stranded RNA. The rise and twist are 46 A and 74.0 deg respectively. I opened my monomer pdb in chimera *(Screenshot-0)* and used the following command to generate an axis around the central RNA double helix: *define axis #0:.X,.Y* where X and Y are the chain IDs for the 2 RNA strands This command helped me generate an axis named *a1* along the RNA duplex *(Screenshot-1)*. Now I want to generate a helical trimer along the RNA duplex with rise=46A and twist=74deg. For this I used the command: *sym #0 group H,46,74,3 axis a1* However, it is not placing the symmetric copies around axis a1 but around a distant axis *(Screenshot-2)*. I am not sure how to generate the helical trimer along the a1 axis. Any help in this regard would be appreciated. Thanks. -Sadeem -- :-)

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Re: [Chimera-users] Chimera-users Digest, Vol 209, Issue 27
by Jatin Kashyap 17 Sep '20

17 Sep '20

Eric, Following are steps I followed: load the structure> del H > run Dock Prep(Add Hydrogen - ticked, Write Mol2 - unticked) > del :10.P@h :8.T@h > minimize (while deselecting the add hydrogen option) I got a warning that I am not sure about. I am pasting the log below[1], can you please confirm that I followed the correct steps and warning can be ignored in the log. [1] Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Residues with incomplete side chains: LYS 98.A ASP 100.A ASP 218.A ASP 824.A GLU 50.C Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' LYS 98.A: phi -78.3, psi 128.2 trans Chi angles for LYS 98.A: ASP 100.A: phi -70.1, psi -6.8 trans Chi angles for ASP 100.A: ASP 218.A: phi -127.8, psi 120.9 trans Chi angles for ASP 218.A: ASP 824.A: phi -92.0, psi 1.6 trans Chi angles for ASP 824.A: GLU 50.C: phi -60.9, psi -45.8 trans Chi angles for GLU 50.C: Applying LYS rotamer (chi angles: -62.5 -75.3 99.0 -88.6) to LYS 98.A Applying ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A Applying GLU rotamer (chi angles: -170.8 -83.2 -29.7) to GLU 50.C Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain A; guessing terminii instead No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain C; guessing terminii instead No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain P; guessing terminii instead No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain T; guessing terminii instead Chain-initial residues that are actual N terminii: VAL 31.A, LYS 2.C, G 10.P, U 8.T Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: U 20.P, C 21.T Chain-final residues that are not actual C terminii: THR 929.A, GLY 64.C 856 hydrogen bonds Removing spurious proton from 'C' of THR 929.A Removing spurious proton from 'C' of GLY 64.C Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: G H (G 10.P H) U H (U 8.T H) Total charge for #0: -30.384 The following residues had non-integral charges: U 20.P -0.6919 C 21.T -0.6919 Correct charges are unknown for 2 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No incomplete side chains Charge model: AMBER ff14SB Total charge for #0: -30.384 The following residues had non-integral charges: U 20.P -0.6919 C 21.T -0.6919 1 model(s) had non-integral total charge Details in reply log Using main parameter file parm10.dat modified by heme-iron.frcmod, frcmod.ff14SB, frcmod.ionsjc_tip3p Initial energy: -45283.236153 kJ/mol Step 12 Potential energy: -58447.379716, Gradient norm: 758.031360 Updated 15035 atoms. RMSD: 0.037342 Finished 10 of 100 steepest descent minimization steps Step 12 Potential energy: -64213.179928, Gradient norm: 362.328469 Updated 15035 atoms. RMSD: 0.018132 Finished 20 of 100 steepest descent minimization steps Step 12 Potential energy: -65930.345155, Gradient norm: 417.614654 Updated 15035 atoms. RMSD: 0.012606 Finished 30 of 100 steepest descent minimization steps Step 12 Potential energy: -67901.748990, Gradient norm: 190.328174 Updated 15035 atoms. RMSD: 0.010435 Finished 40 of 100 steepest descent minimization steps Step 12 Potential energy: -68928.640793, Gradient norm: 79.670023 Updated 15035 atoms. RMSD: 0.007430 Finished 50 of 100 steepest descent minimization steps Step 12 Potential energy: -70504.551913, Gradient norm: 192.974949 Updated 15035 atoms. RMSD: 0.016225 Finished 60 of 100 steepest descent minimization steps Step 12 Potential energy: -71243.383589, Gradient norm: 95.907393 Updated 15035 atoms. RMSD: 0.006255 Finished 70 of 100 steepest descent minimization steps Step 12 Potential energy: -71661.708391, Gradient norm: 193.911209 Updated 15035 atoms. RMSD: 0.006283 Finished 80 of 100 steepest descent minimization steps Step 12 Potential energy: -72255.311758, Gradient norm: 199.037193 Updated 15035 atoms. RMSD: 0.007288 Finished 90 of 100 steepest descent minimization steps Step 12 Potential energy: -72873.927407, Gradient norm: 84.768251 Updated 15035 atoms. RMSD: 0.005517 Finished 100 of 100 steepest descent minimization steps Step 12 Potential energy: -79350.452189, Gradient norm: 206.369396 Updated 15035 atoms. RMSD: 0.114423 Finished 10 of 10 conjugate gradient minimization steps —— Jatin Kashyap > On Sep 16, 2020, at 6:41 PM, chimera-users-request(a)cgl.ucsf.edu wrote: > > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Error "No MMTK name for atom "H" in standard residue ?G"" > (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 16 Sep 2020 15:41:33 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: Jatin Kashyap <jk435(a)njit.edu> > Cc: Chimera User Help <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Error "No MMTK name for atom "H" in > standard residue ?G"" > Message-ID: <9B74E727-F918-4A68-9E48-83F05E6B329E(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="utf-8" > > Ah I see. Because you also have missing side chains you have to do things a little differently. Namely run Dock Prep (Tools?Structure Editing?Dock Prep) first, keeping "Add hydrogens" on but "Write Mol2" off; then use the delete command to delete the two unwanted protons; then run Minimize. > > --Eric > >> On Sep 16, 2020, at 2:54 PM, Jatin Kashyap <jk435(a)njit.edu> wrote: >> >> I am sorry for the confusion. Actually I did that step by GUI options (Tools>Structure Editing>AddH). But I did it again by issuing ?addh? from command line along with other steps. >> But still I am getting the same error. >> >> ?? >> Jatin Kashyap >> >> >>> On Sep 16, 2020, at 5:49 PM, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >>> >>> It's "addh" not "add H". >>> >>> --Eric >>> >>>> On Sep 16, 2020, at 2:44 PM, Jatin Kashyap <jk435(a)njit.edu <mailto:jk435@njit.edu>> wrote: >>>> >>>> Hi Eric, >>>> >>>> Just for the clarification I am double checking it here, first I loaded the structure > del H > add H > del :10.P@h :8.T@h > minimize (while deselecting the add hydrogen option). >>>> >>>> But it is throwing the error [1]. >>>> >>>> >>>> [1] >>>> Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments. >>>> Automatically computing assignments using 'ksdssp' and parameter values: >>>> energy cutoff -0.5 >>>> minimum helix length 3 >>>> minimum strand length 3 >>>> Use command 'help ksdssp' for more information. >>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain A; guessing terminii instead >>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain C; guessing terminii instead >>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain P; guessing terminii instead >>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain T; guessing terminii instead >>>> Chain-initial residues that are actual N terminii: VAL 31.A, LYS 2.C, G 10.P, U 8.T >>>> Chain-initial residues that are not actual N terminii: >>>> Chain-final residues that are actual C terminii: U 20.P, C 21.T >>>> Chain-final residues that are not actual C terminii: THR 929.A, GLY 64.C >>>> 852 hydrogen bonds >>>> Removing spurious proton from 'C' of THR 929.A >>>> Removing spurious proton from 'C' of GLY 64.C >>>> Hydrogens added >>>> Residues with incomplete side chains: >>>> LYS 98.A >>>> ASP 100.A >>>> ASP 218.A >>>> ASP 824.A >>>> GLU 50.C >>>> Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' >>>> LYS 98.A: phi -78.3, psi 128.2 trans >>>> Chi angles for LYS 98.A: >>>> ASP 100.A: phi -70.1, psi -6.8 trans >>>> Chi angles for ASP 100.A: >>>> ASP 218.A: phi -127.8, psi 120.9 trans >>>> Chi angles for ASP 218.A: >>>> ASP 824.A: phi -92.0, psi 1.6 trans >>>> Chi angles for ASP 824.A: >>>> GLU 50.C: phi -60.9, psi -45.8 trans >>>> Chi angles for GLU 50.C: >>>> Applying ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A >>>> Applying LYS rotamer (chi angles: -178.9 71.3 178.8 68.6) to LYS 98.A >>>> Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A >>>> Applying GLU rotamer (chi angles: -170.8 -83.2 25.9) to GLU 50.C >>>> Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A >>>> Charge model: AMBER ff14SB >>>> Total charge for #0: -32.172 >>>> The following residues had non-integral charges: >>>> LYS 98.A -0.6068 >>>> ASP 100.A -1.0636 >>>> ASP 218.A -1.0636 >>>> ASP 824.A -1.0636 >>>> GLU 50.C -0.9909 >>>> U 20.P -0.6919 >>>> C 21.T -0.6919 >>>> 1 model(s) had non-integral total charge >>>> Details in reply log >>>> >>>> Residue #0:98.A (LYS/lysine) is missing atoms H_gamma_3, H_epsilon_2, H_zeta_3, H_delta_2, H_epsilon_3, H_alpha, H_beta_3, H_gamma_2, H_delta_3, H_beta_2, H_zeta_1 and H_zeta_2 >>>> >>>> >>>> ?? >>>> Jatin Kashyap >>>> >>>> >>>>> On Sep 16, 2020, at 5:32 PM, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >>>>> >>>>> Hi Jatin, >>>>> I you don't delete those phosphates, then Chimera will add spurious protons to them, which is what is causing the problem. In order to get this to work, you will have to run Add Hydrogens "by hand" before your minimization, delete the spurious protons, and then run your minimization -- being careful to skip adding hydrogens as part of the minimization process. >>>>> The command (Favorites?Command Line) to delete the unwanted protons in your case is "del :10.P@h :8.T@h". >>>>> >>>>> --Eric >>>>> >>>>> Eric Pettersen >>>>> UCSF Computer Graphics Lab >>>>> >>>>> >>>>>> On Sep 16, 2020, at 2:10 PM, Jatin Kashyap <jk435(a)njit.edu <mailto:jk435@njit.edu>> wrote: >>>>>> >>>>>> Dear Chimera Community Members, >>>>>> >>>>>> I am facing an error while minimizing a protein that have 5? terminal phosphates attached to it. >>>>>> Chimera is showing the warning that AMBER is unable to parametrize the phosphates and if you do not delete it, 0 charges will be assigned to it. >>>>>> I selected the option not to delete it but then it throws error[1] on the following step. I am pasting my log below [2]. >>>>>> >>>>>> Thank you for helping me to understand this. >>>>>> >>>>>> [1] >>>>>> No MMTK name for atom "H" in standard residue ?G" >>>>>> >>>>>> [2] >>>>>> Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments. >>>>>> Automatically computing assignments using 'ksdssp' and parameter values: >>>>>> energy cutoff -0.5 >>>>>> minimum helix length 3 >>>>>> minimum strand length 3 >>>>>> Use command 'help ksdssp' for more information. >>>>>> Residues with incomplete side chains: >>>>>> LYS 98.A >>>>>> ASP 100.A >>>>>> ASP 218.A >>>>>> ASP 824.A >>>>>> GLU 50.C >>>>>> Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' >>>>>> LYS 98.A: phi -78.3, psi 128.2 trans >>>>>> Chi angles for LYS 98.A: >>>>>> ASP 100.A: phi -70.1, psi -6.8 trans >>>>>> Chi angles for ASP 100.A: >>>>>> ASP 218.A: phi -127.8, psi 120.9 trans >>>>>> Chi angles for ASP 218.A: >>>>>> ASP 824.A: phi -92.0, psi 1.6 trans >>>>>> Chi angles for ASP 824.A: >>>>>> GLU 50.C: phi -60.9, psi -45.8 trans >>>>>> Chi angles for GLU 50.C: >>>>>> Applying LYS rotamer (chi angles: -62.5 -75.3 99.0 -88.6) to LYS 98.A >>>>>> Applying ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A >>>>>> Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A >>>>>> Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A >>>>>> Applying GLU rotamer (chi angles: -170.8 -83.2 -29.7) to GLU 50.C >>>>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain A; guessing terminii instead >>>>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain C; guessing terminii instead >>>>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain P; guessing terminii instead >>>>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain T; guessing terminii instead >>>>>> Chain-initial residues that are actual N terminii: VAL 31.A, LYS 2.C, G 10.P, U 8.T >>>>>> Chain-initial residues that are not actual N terminii: >>>>>> Chain-final residues that are actual C terminii: U 20.P, C 21.T >>>>>> Chain-final residues that are not actual C terminii: THR 929.A, GLY 64.C >>>>>> 856 hydrogen bonds >>>>>> Removing spurious proton from 'C' of THR 929.A >>>>>> Removing spurious proton from 'C' of GLY 64.C >>>>>> Hydrogens added >>>>>> Charge model: AMBER ff14SB >>>>>> Non-standard atom names: >>>>>> G H (G 10.P H) >>>>>> U H (U 8.T H) >>>>>> Total charge for #0: -30.384 >>>>>> The following residues had non-integral charges: >>>>>> U 20.P -0.6919 >>>>>> C 21.T -0.6919 >>>>>> Correct charges are unknown for 2 non-standard atom names in otherwise standard residues >>>>>> >>>>>> Charges of 0.0 were assigned to the unknown atoms >>>>>> >>>>>> 1 model(s) had non-integral total charge >>>>>> Details in reply log >>>>>> >>>>>> No MMTK name for atom "H" in standard residue "G" >>>>>> >>>>>> >>>>>> ?? >>>>>> Jatin Kashyap >>>>>> New Jersey Institute of Technology >>>>>> >>>>>> _______________________________________________ >>>>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>> >> > >

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Error "No MMTK name for atom "H" in standard residue “G""
by Jatin Kashyap 16 Sep '20

16 Sep '20

Dear Chimera Community Members, I am facing an error while minimizing a protein that have 5’ terminal phosphates attached to it. Chimera is showing the warning that AMBER is unable to parametrize the phosphates and if you do not delete it, 0 charges will be assigned to it. I selected the option not to delete it but then it throws error[1] on the following step. I am pasting my log below [2]. Thank you for helping me to understand this. [1] No MMTK name for atom "H" in standard residue “G" [2] Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Residues with incomplete side chains: LYS 98.A ASP 100.A ASP 218.A ASP 824.A GLU 50.C Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' LYS 98.A: phi -78.3, psi 128.2 trans Chi angles for LYS 98.A: ASP 100.A: phi -70.1, psi -6.8 trans Chi angles for ASP 100.A: ASP 218.A: phi -127.8, psi 120.9 trans Chi angles for ASP 218.A: ASP 824.A: phi -92.0, psi 1.6 trans Chi angles for ASP 824.A: GLU 50.C: phi -60.9, psi -45.8 trans Chi angles for GLU 50.C: Applying LYS rotamer (chi angles: -62.5 -75.3 99.0 -88.6) to LYS 98.A Applying ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A Applying GLU rotamer (chi angles: -170.8 -83.2 -29.7) to GLU 50.C No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain A; guessing terminii instead No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain C; guessing terminii instead No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain P; guessing terminii instead No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain T; guessing terminii instead Chain-initial residues that are actual N terminii: VAL 31.A, LYS 2.C, G 10.P, U 8.T Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: U 20.P, C 21.T Chain-final residues that are not actual C terminii: THR 929.A, GLY 64.C 856 hydrogen bonds Removing spurious proton from 'C' of THR 929.A Removing spurious proton from 'C' of GLY 64.C Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: G H (G 10.P H) U H (U 8.T H) Total charge for #0: -30.384 The following residues had non-integral charges: U 20.P -0.6919 C 21.T -0.6919 Correct charges are unknown for 2 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No MMTK name for atom "H" in standard residue "G" —— Jatin Kashyap New Jersey Institute of Technology

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Re: [Chimera-users] Euler angles and rotations
by Elaine Meng 16 Sep '20

16 Sep '20

Hi Stephen, In Chimera, you can write the current transformations of models to a file with "matrixget" and apply transformations from those matrices by reading the file with "matrixset." <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html> It doesn't have anything to do with Euler angles, though. Not sure if it suffices for what you want to do. To send a question for all staff to see, it is best to use the mailing list CC'd here. For ChimeraX, there is similar stuff in the "view matrix" command and saved "positions" files. However, the positions file doesn't include camera position, so in my opinion is not quite as useful for regenerating the view as matrixget(set) in Chimera. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> <http://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 16, 2020, at 12:04 PM, Chin-Bow, Stephen <stephen.chin-bow(a)yale.edu> wrote: > > Hello Elaine, > > I have a math question which hopefully you or the CGL staff can answer quickly. > > I am using the original Chimera (although I recently upgraded my GPU and I am curious to try ChimerX ). > > I am curious about Euler angles and rotations. I would like to learn more about them, but I suspect it has been too many years since I thought about matrices. > > I want another person to first download a published PDB from the RCSB before rotating it using a command line script. > > The final perspective I have was achieved after ten rotations. > > Is there a way I can apply Euler angles and matrix multiplication to summarize the final position using the fewest number of rotations? > > Yes, I can simply share a session file, but my future goal is more general. I want to encourage the other person to learn to use scripts, because the command line opens up the power of Chimera. > > Thanks a lot for the remedial math help! > > Stephen

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