- Chimera-users - RBVI Mailing Lists

Error reading multiple models
by Francesco Pietra 25 Sep '20

25 Sep '20

In my hands CHIMERA can't read multiple models as in .trj.xyz provided by ORCA software in QM calculations Error reading 5-sulf-min_trj.xyz: Coordinate line of XYZ file '/home/francesco/work_AGAs/VITTORIO/5-sulf-min_PBE0_OPT_FREQ_SMD/ 5-sulf-min_trj.xyz' is not element,x,y,z: '36' That is no problem for Jmol, however I would be interested in opening the models with also CHIMERA (which can open these models as a single-model-file. thanks for advice francesco pietra

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Open .mrcs stack in chimera
by Ahmad Khalifa 24 Sep '20

24 Sep '20

Can I open a .mrcs stack in chimera? What file type should I pass to Chimera in order to do that?

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Re: [Chimera-users] Stereo Red Cyan
by Greg Couch 24 Sep '20

24 Sep '20

Yes, the red and gray is normal, but you're seeing the combined channels. You need the glasses to separate the channels. Try viewing the image with the glasses that come with a 3D comic book. -- Greg On 9/21/2020 11:43 PM, Michael Elbaum wrote: > Red-cyan, sorry. No, I didn't look for stereo at all, just to > reproduce the condition posted that one channel appears in red and the > other in gray. Is that normal? > Michael > ------------------------------------------------------------------------ > *From:* Greg Couch <gregc(a)cgl.ucsf.edu> > *Sent:* Tuesday, September 22, 2020 4:57:50 AM > *To:* Michael Elbaum <michael.elbaum(a)weizmann.ac.il> > *Subject:* Re: [Chimera-users] Stereo Red Cyan > > Are you wearing red-cyan glasses to see the stereo? It doesn't work > without them. > > > -- Greg > > > On 9/21/2020 1:08 PM, Michael Elbaum wrote: >> >> I'm confirming the problem with a different dataset (optical >> deconvolution in tif format). Red-green shows red and gray, >> green-magenta shows green and gray. This is with version 1.14 on linux. >> >> regards, >> Michael >> >> >> >> ------------------------------------------------------------------------ >> *From:* Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf >> of Angus McDonald <amcdonald(a)boisestate.edu> >> *Sent:* Monday, September 21, 2020 9:46:24 PM >> *To:* chimera-users(a)cgl.ucsf.edu BB >> *Subject:* [Chimera-users] Stereo Red Cyan >> I am looking at some cryo em data. When I try to view a a 3D stack of >> em dat with the Red-Cyan stereo setting I seem to only get Red and >> grayscale. The data is in 32-bit floating point and is in MRC2014 >> header format. I cannot figure out what I am doing wrong. Is anything >> obvious? >> >> Thanks for your time. >> >> >> >> -- >> Angus McDonald >> amcdonald(a)boisestate.edu <mailto:amcdonald@boisestate.edu> >> >> _______________________________________________ >> Chimera-users mailing list:Chimera-users@cgl.ucsf.edu >> Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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electrostatic interactions
by Ruchika 23 Sep '20

23 Sep '20

Hi Elaine I do see "Find out clashes and contacts" feature in Chimera. I am wondering if there is any feature which can check on electrostatic interactions as well. Please let me know. Thanks !! Regards Ruchika

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Fitting structure in rescaled map
by Ahmad Khalifa 23 Sep '20

23 Sep '20

Hello, How to fit an atomic model after downscaling my map (map shrinks)? Are atomic models built to scale?! Regards.

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Writing a SINGLE pose (with ligand and protein) to a PDB file
by Edmund Marinelli 22 Sep '20

22 Sep '20

Hello: I used ViewDock to open a pdbqt file generated by use of AutoDock Vina. The ligand was shown in the graphics window. Then I opened the protein pdb file that was used in the docking experiment. The ViewDock dialog lists the poses obtained and I can select each and view the resulting pose in the graphics window fine. I opened the Model Pane. I selected from the list of models the first pose (#0.1) and the protein (#1) in the list. I assumed that saving these two into a file would give a file that contained only the protein and the ligand bound as in the best pose . I want to save the best pose as a pdb file wherein the protein and ligand are present. I gave a filename Test.pdb . Chimera returned the following error message: "You must provide a filename that contains either $name or $number , which will be changed to the model name or model number (respectively) in the final saved file name." I do not understand what this means. I tried using the pose number and also the protein name but it gave the same error. I don't understand what is meant by $name and $number - what do they refer to ? What do I need to do to save a single pose containing protein and the ligand to a unique file not containing other poses? The screenshot below is what I see: Note that in the models list I selected the best pose #0.1 and also the protein, which is at the bottom of the list, hence it is not visible in the picture. What is the filename syntax that I need to use to save a pose with protein to a single PDB file? Stated more plainly: Can you give a viable example of what I need to enter as a filename that will allow saving of the file? Or am I going about this all wrong? Sorry for the verbose email. [image: image.png]

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Stereo Red Cyan
by Angus McDonald 21 Sep '20

21 Sep '20

I am looking at some cryo em data. When I try to view a a 3D stack of em dat with the Red-Cyan stereo setting I seem to only get Red and grayscale. The data is in 32-bit floating point and is in MRC2014 header format. I cannot figure out what I am doing wrong. Is anything obvious? Thanks for your time. -- Angus McDonald amcdonald(a)boisestate.edu

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Using iBabel to convert Chimera's pdb to pdbqt
by Jatin Kashyap 19 Sep '20

19 Sep '20

Dear UCSF Chimera Community, I am trying to minimize a complex[1] and saving it in a pdbqt format. I minimize it in Chimera and saved in pdb[2], followed by using iBabel (GUI of open babel for Mac) to convert pdb into pdbqt. Here are two things: first, if I convert without using any flag then output gives me pdbqt file with BRANCH information which is not supported by Vina. To solve it I am using -XR flag in iBabel to trim the BRANCH information so that resulting pdbqt file can be read by Vina. But in that case iBabel is giving me weird looking structure and upon inspection of pdbqt file[3] I realized the complex was split into different models. I had successfully followed the same workflow for other minimization code i.e. YASARA. Can anybody please help me to fix it. I am attaching files below with corresponding citations. Thank you. [1] [2] [3] —— Jatin Kashyap Ph.D. Student Dr. Dibakar Datta Group Department of Mechanical and Industrial Engineering New Jersey Institute of Technology (NJIT) University Heights Newark, NJ 07102-1982 Phone- (201)889-5783 Email- jk435(a)njit.edu

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Setting a pathway/trajectory for a molecule
by Rani Wiswedel 18 Sep '20

18 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) 17 Sep '20

17 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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Zone in pixel or Angstrom?
by Dieter Blaas 14 Sep '20

14 Sep '20

Hi, is the zone around selected atoms cut out with "Volume Viewer > Features > Zone" measured in Angstroms or pixels? Thank you, regards, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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issue with heme minimization
by Rio Aquarius 14 Sep '20

14 Sep '20

Hi, I have an issue with heme minimization, Fe atom leaves a heme plane. I saw at least one user had the same issue and got help to solve it ( https://www.cgl.ucsf.edu/pipermail/chimera-users/2019-July/015972.html) I could try the protocol described there, but I don't have the heme.defattr file. I hope you can help me with it too. I have attached a pdb file with this issue.

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Re: [Chimera-users] Is it possible to make a dimer from a monomer protein in chimera?
by Elaine Meng 14 Sep '20

14 Sep '20

On Sep 14, 2020, at 12:07 PM, Tarazkar, Maryam <Maryam.Tarazkar(a)ucsf.edu> wrote: > > Hi Elaine, > I am wondering can you refer me to a tutorial in Chimera where it explains how to make a dimer protein from a monomer? > Thank you, > Maryam Hi Maryam, Yes, of course you can do it, but there is no specific tutorial: how to do it really depends what information is in the input file, what you know about the structure, etc. If it is an entry in the PDB database you could just try fetching the biounit directly and seeing if it is a dimer. E.g. menu File... Fetch by ID, use the "PDB (biounit)" choice. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/fetch.html> Some files have symmetry information in their files so that you can build the multimer with the "sym" command, e.g. open 1fav sym #0 #0 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> If it is not yet a deposited structure, but you already have a related structure that is a dimer, you can just open two copies of your protein and match it onto the two monomers of that other structure, e.g. with the Matchmaker tool. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> 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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PDB saving
by Henry Shook 14 Sep '20

14 Sep '20

Chimera Developers, I am working on a research project modeling and experimenting on biomolecules and I have just started using Chimera but whenever I am trying to save a PDB, it says that my permission is denied. Is there a way that this can be fixed? I am currently using a school computer and there are certain restrictions may be put in place so that might be the problem as well. Here is a video of what happens if it may help you: Thanks! Henry Shook -- ***** Please note: The Sender of this email is a Student of Pine Lake Preparatory and is not an employee or agent of Pine Lake Preparatory ***** -- ***************************************************************************** CONFIDENTIALITY NOTICE: This electronic mail message, including any attachment(s), contains information which may be confidential pursuant to the Family Educational Rights & Privacy Act (FERPA), 20 U.S.C. 1232g, and/or N.C.G.S. 115C-319, and/or proprietary non-public information. If you are not the intended recipient or the authorized assistant to the intended recipient, please notify the sender by replying to this message and deleting the e-mail from your system. Use, dissemination, distribution and/or reproduction of this message and/or its attachment(s), if any, by unauthorized recipients is not authorized and may be unlawful. *****************************************************************************

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Question regarding saving protein-ligand and docking in Chimera
by Tarazkar, Maryam 11 Sep '20

11 Sep '20

Dear Sir or Madam, I did molecular docking to find the protein-ligand interactions using Chimera. Now I am trying to save the results of docking ( I took the screenshot here) in a text file and save the structure of protein-ligand in pdb file so I do the analysis using Pymol. When I click on file--> save pdb a page appears where I have to select which models to be saved. ( I took the screenshot of the page here) but when I select ligand, protein and docked options all tigetehr, the program gives me error in saving the files. I appreciate if you help me and let me know how I can resolve it and save the protein-ligand structure in best binding site in pdb so I do further analysis on this. Best Maryam [cid:42d36ba9-f8f9-4ae7-9884-45480afe5dc2] [cid:6467c35e-bbaa-44c4-9a56-8b329bc8f3c1]

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installation issues
by Breves, Alexandra 10 Sep '20

10 Sep '20

Hello, I am having an issue installing chimera on my windows 10 (64-bit) computer. It is saying that I do not have 64x but I do. Can someone please assist me? Thank you, Alexandra Breves

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Saving relaxed system in pdbqt format for Vina
by Jatin Kashyap 09 Sep '20

09 Sep '20

Dear Chimera Community Members, I am new to this code, and tried to navigate through this wonderful piece of code by myself. However, I am not able to find a way to save the relaxed system(relaxation performed in UCSF Chimera) in pdbqt format. Can anybody please help me to understand how I can do it, OR am I doing something completely wrong? Thank you for your time, and efforts. —— Jatin Kashyap Department of Mechanical and Industrial Engineering New Jersey Institute of Technology (NJIT) University Heights Newark, NJ 07102-1982 Phone- (201)889-5783 Email- jk435(a)njit.edu

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