- Chimera-users - RBVI Mailing Lists

How to read a volume in python script
by Huiya Zhou 22 Aug '19

22 Aug '19

Hello, I am trying to use UCSF Chimera to analysis cry-EM density maps. I would like to read a density map (for example: a .mrc file) in python script and get the array (or a three dimensional matrix) of all voxels of this density map. How could I realize this? By the way, I tried to learn some basic chimera functions which can be used in python on this website: https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html> However, it seems this website can’t be opened and it shows me a blank page. Best, Huiya

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copy/combine molecular models
by Rui Chen 22 Aug '19

22 Aug '19

Hello, I am working on a homodimer. I modelled loops of each chain one by one. I chose the best loops for each chain. Now I want to save them as a pub file. Please see the following screenshot. How to decide the new model's ID? I know the coordinate system is the reference coordinate, how do I decide which chain to use as the reference chain? Should I choose rename them uniquely? Looking forward to hearing from you. Thank you. [image: Screen Shot 2019-08-22 at 12.01.28 AM.png] Best regards, Rui

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how to guess ligand's net charge?
by Thomas Evangelidis 21 Aug '19

21 Aug '19

Greetings, How does Chimera guess the net charge of a ligand when prompted to select the charge type (AM1-bcc or Gasteiger)? I am doing high throughput protein-ligand MD simulations and would like to know which open source library Chimera uses for this task. Thanks in advance. Thomas -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: tevang3(a)gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/

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color by zone in chimeraX
by Pranav Shah 20 Aug '19

20 Aug '19

Hi Elaine and Co., I am trying to color a virus map with the relevant pdb file, the series of commands I am running are as follows, open virus.mrc open virus.pdb color /A plum target c color /B lightgreen target c color /C dodger blue target c color zone #1 near #2 dist 3 However, the resultant surface is rendered in splotches of red and blue, which leads me to think the it is coloring the surface using atom type. Could you tell me how I can get Chimera X to color the surface using the colors of the chains only? FYI, color by zone works flawlessly in chimera. Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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scipy problem
by William 19 Aug '19

19 Aug '19

Hello, I tried to install scipy in chimera python following the steps below: When I tried the third step, it raised midaserror. The error is as follows： Is there anything wrong with my path? Thanks.

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Match showmatrix true motion in original coordinates
by Ahmad Khalifa 13 Aug '19

13 Aug '19

Hi, Running match showmatrix true, gives two matrices. What's the difference between the two? I already saved the file after fitting it so it should have only one set of coordinates, its original coordinates?! Regards Motion of #76 in #2 coordinate system Matrix rotation and translation 0.99998889 -0.00169318 0.00440013 -1.57825672 0.00165962 0.99996960 0.00761849 -4.96792547 -0.00441290 -0.00761111 0.99996130 169.74075587 Axis -0.85023004 0.49200930 0.18717833 Axis point 0.00000000 21533.64775327 2718.66675667 Rotation angle (degrees) 0.51315730 Shift along axis 30.66940614 Motion of #76 original coordinates in #2 coordinate system Matrix rotation and translation 0.78916125 0.61416829 0.00467203 -143.02960322 -0.61417583 0.78916918 0.00023085 242.10381668 -0.00354524 -0.00305162 0.99998906 98.04867640 Axis -0.00267220 0.00668954 -0.99997405 Axis point 281.92931592 330.08522286 0.00000000 Rotation angle (degrees) 37.89294229 Shift along axis -96.04436567

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Chimera bug report submission
by Tanara Arenhart 12 Aug '19

12 Aug '19

The following bug report has been submitted: Platform: Windows64 (WGL) Microsoft Windows Unknown 10.0 (Build 17134) x64 Chimera Version: 1.13.1_b41965 Description Hi! I'm trying to dock my protein with a ligand, but everytime appears this message: "receptor and ligand cannot be the same model". I don't know why, because i'm doing the same things I always do. What could be happening? Thank you! Open models #0 3dbs.pdb #1 smiles:CC1CCC2C3(CCC(... #2 AutoDock Vina Search Volume Reply log: Failed to translate SMILES to 3D structure via NCI web service (SMILES: receptor and ligand cannot be the same model) Failed to translate SMILES to 3D structure via Indiana University web service (SMILES: receptor and ligand cannot be the same model) Web services failed to translate SMILES string to 3D structure. Translated SMILES to 3D structure via NCI web service (SMILES: CC1CCC2C3(CCC(C(C3CCC2(C14CC5=C(O4)C(=CC(=O)C5=O)C)C)(C)C)O)C) No incomplete side chains Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: 0 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Assigning partial charges to residue STP (net charge +0) with gasteiger method Running ANTECHAMBER command: C:/Program Files/Chimera 1.13.1/bin/amber16/bin\antechamber -i c:\users\nara_\appdata\local\temp\tmpi9opye\ante.in.mol2 -fi mol2 -o c:\users\nara_\appdata\local\temp\tmpi9opye\ante.out.mol2 -fo mol2 -c gas -nc 0 -j 5 -s 2 -dr n (STP) (STP) Welcome to antechamber 17.3: molecular input file processor. (STP) (STP) Info: Finished reading file (c:\users\nara_\appdata\local\temp\tmpi9opye\ante.in.mol2). (STP) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (STP) (STP) (STP) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (STP) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d "C:/Program Files/Chimera 1.13.1/bin/amber16/dat/antechamber/ATOMTYPE_GAS.DEF" (STP) Charges for residue STP determined Total charge for #0: 0.000 #0, chain A: phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit γ isoform Traceback (most recent call last): File "C:\Program Files\Chimera 1.13.1\share\chimera\preferences\base.py", line 447, in save WindowsError: [Error 32] O arquivo j� est� sendo usado por outro processo Cannot replace previous preferences file: C:\Users\nara_\AppData\Roaming\.chimera\preferences: WindowsError: [Error 32] O arquivo j� est� sendo usado por outro processo File "C:\Program Files\Chimera 1.13.1\share\chimera\preferences\base.py", line 447, in save See reply log for Python traceback. Residues with incomplete side chains: MET 143.A GLU 322.A Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' MET 143.A: phi none, psi -122.2 trans Chi angles for MET 143.A: GLU 322.A: phi -130.9, psi 172.4 trans Chi angles for GLU 322.A: Applying GLU rotamer (chi angles: -62.4 -179.4 -3.8) to GLU 322.A Applying MET rotamer (chi angles: -65.8 -61.8 -69.4) to MET 143.A Terminii for 3dbs.pdb (#0) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: MET 143.A Chain-initial residues that are not actual N terminii: GLU 267.A, CYS 357.A, LEU 460.A, PHE 497.A, HIS 525.A, ARG 544.A, GLU 981.A Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: ALA 253.A, GLU 322.A, CYS 435.A, GLY 489.A, ASN 522.A, ALA 528.A, HIS 967.A, VAL 1091.A 718 hydrogen bonds Adding 'H' to GLU 267.A Adding 'H' to CYS 357.A Adding 'H' to LEU 460.A Adding 'H' to PHE 497.A Adding 'H' to HIS 525.A Adding 'H' to ARG 544.A Adding 'H' to GLU 981.A Removing spurious proton from 'C' of VAL 1091.A Hydrogens added Charge model: AMBER ff14SB Total charge for #0: -8.000 receptor and ligand cannot be the same model receptor and ligand cannot be the same model OpenGL Vendor: Intel OpenGL Renderer: Intel(R) HD Graphics OpenGL Version: 4.4.0 - Build 20.19.15.4835 Manufacturer: Dell Inc. Model: Inspiron 5452 TotalPhysicalMemory: 4203823104 ―――――――――――――――――――― Multisampling: False Shadows: False Shadow texture size: 2048 Silhouettes: False Depth cue: True Subdivision quality: 1.50 Single-layer transparency: True Transparent background: False Shaders supported: True Using shader: True Window size: 1366 663 Camera mode: mono Orthographic projection: False Center of rotation: front center Near/far clipping: False Key light: True Fill light: True Back light: False Ambient light: 0.20 Specular sharpness: 30.00 Specular reflectivity: 1.00 ―――――――――――――――――――― AntialiasLines: native AntialiasPoints: native BlendEquation: native BlendFuncSeparate: native BrokenAttribLocation: native, disabled ChoosePixelFormat: extension ColorTable: not supported CompileAndExecute: native CompiledVertexArray: extension CubeMap: native CullVertex: not supported DrawElementsInstanced: native, disabled DrawRangeElements: native FBConfig: not supported FBOShadows: native FastMultisampling: native, disabled FramebufferMultisample: native FramebufferObject: native LimitVertexAttribDivisor: native, disabled Multisample: native Multitexture: native PackedDepthStencil: native PalettedTexture: not supported PointParameters: native SeamlessCubeMap: native SeparateSpecularColor: native Shading: native Shadows: native StereoMultisample: native StereoRubberBanding: native Texture3D: native TextureColorTable: not supported TextureEdgeClamp: native TrustColorLogicBlend: native TrustNormals: native VertexArray: native VertexAttrib: native VertexAttribDivisor: native VertexBufferObject: native, disabled WindowPos: not supported

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A question about the Volume Viewer
by Grosman, Claudio F 09 Aug '19

09 Aug '19

Hello everyone, I have (what I think is) a very simple question: what is the particular value of "level" (that is, the threshold) that appears automatically when one opens a 3D density map? After playing around with the threshold, I always feel like the initial value is the best one, but I wonder what exactly this value is. In the online documentation of Chimera, this issue is addressed. The text reads that the initial value of this threshold is such that 1% of the voxels have density values above it. Is this really the case? Only voxels with intensities above the threshold are displayed. Am I seeing only 1% of the voxels, then? I am afraid, I am confused. Thank you very much, in advance. Claudio

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Selecting one ID 0 when two ID 0s are present
by Ryan Harlich 09 Aug '19

09 Aug '19

Hi Chimera, I have a problem where there are two ID 0. One is the normal density map the other is a solid (or what seems to be a movie of the protein). I want to select the density map. In the GUI interface I would open volume viewer and select radio button surface for category Style. Then a little below select All instead of One. I was wondering how to do this with command line? What I am trying to do is get a chain of the pdb structure and zone the density map. However the files are really big so I am trying to do it via ssh on another computer so I will be doing it with the –nogui flag. So if I can do everything via command line that would be great. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Double chain IDs
by Albert WEIXLBAUMER 08 Aug '19

08 Aug '19

Dear Chimera developers, My apologies if this question has been asked before but I was not able to find an answer so far. I am dealing with PDB files that contain too many individual chains and as such need two-character chain IDs. Ideally I do not want to split the PDB-files (to be able and work with single-character chain IDs). In addition, the PDB-file also contains more than 100,000 atoms and thus uses alphanumeric atom numbers. It seems Chimera is not aware of the two-character chain IDs because selecting a certain chain in the GUI shows only single character chain IDs and it leads to the selection of the two distinct chains (e.g. chain AA and chain BA are both treated as chain A). Is there a workaround? I’ve also noticed that saving such a PDB-file in Chimera changes all ATOM records to HETATM - I don’t know if this is related to the double-character chain IDs or alphanumeric atom numbers but this causes problems downstream because it’s very difficult to change this back to ATOM records without also affecting true HETATM entries. Thank you for your help! Best regards, Albert -- Albert Weixlbaumer Centre for Integrative Biology Department of Integrated Structural Biology Institute of Genetics and Molecular and Cellular Biology IGBMC - UMR 7104 - U 1258 1, rue Laurent Fries BP 10142 67404 ILLKIRCH CEDEX FRANCE Phone: +33 3 6948 5103 Email: Albert.Weixlbaumer(a)igbmc.fr<mailto:Albert.Weixlbaumer@igbmc.fr> OpenPGP KeyID: 0x7F644168

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