- Chimera-users - RBVI Mailing Lists

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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Making PDBs with over 10,000 atoms
by Ryan Harlich 07 Aug '19

07 Aug '19

Hi Chimera, I am trying to make a PDB with over 10,000 atoms. Currently we have this marked as a limitation to our project. I am researching to see if there is a way around this. Our current idea is to make the next 10,000 atoms another chain. Although when I apply this to a sample I get a break point between chain A and chain B. I do want them connected and to be different chains. So: 9,998.A 9,999.A 0.B 1.B connect. In addition, I would need helices and sheets to span over these two chains. So helix or sheet would start at 9,998.A and end at 1.B. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Superimpose protein chains
by Peter Snyder 07 Aug '19

07 Aug '19

How can I superimpose two (or three) chains from a single structure (ie two homologous subunits that form a multimeric protein)? Thank you Pete

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Is "volume #0 voxelSize 1" a isosurface display changes
by Ryan Harlich 06 Aug '19

06 Aug '19

Hi Chimera, Is "volume #0 voxelSize 1" a isosurface display changes? So if I volume save this would it save this change? Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Morphing, ligands, and secondary structure
by Yan Kung 06 Aug '19

06 Aug '19

Hi Chimera, I’m a new-ish user, and I’ve found that morphing structures is usually very straightforward and easy to use. But I’m now running into an issue with morphing and ligands (and secondary structure). I’d like to make a single morph composed of states A-B-C-B-A (so 4 movements between 5 states). These movements are: (1) A-B: domain opens, (2) B-C: a ligand flies out, (3) C-B: the same ligand flies back in, and (4) B-A: domain closes. First problem: the ligand does not appear in the resulting morph, a problem suggested by the documentation, which I have tried (and failed) to solve using the tips I found in archived posts from this mailing list. Also, because the ligand has to fly in and out, I can’t simply superimpose the ligand from any of the individual states over the morph. So I tried a workaround: make each movement a separate morph. This works for movements 2 and 3 (where the ligand flies out and in). But the ligand still does not appear in movements 1 and 4 (where the ligand remains in place and the domain moves). I’m not sure why the ligand’s appearance would depend on whether it flies in/out, or whether a domain moves… But it seems to. Moreover, a second problem emerges that has to do with secondary structure and is difficult to explain. (Essentially: a few protein regions are on the border between helices and loops such that they appear as helices in some states but as loops in others, and vice versa. If possible, I’d like the secondary structure to remain constant across all states, or else it’s distracting. Even still, I’ve tried to embrace this and use ksdssp to show the helices/loop switching back and forth, but this is distracting as they flicker between helices and loops, each region at its own separate frame. Specifying ksdssp only in certain frames to minimize the flickering doesn’t work either, as different regions switch back and forth at different times.) The only solution I can think of that would maintain the same secondary structure throughout is to just make a single morph of all movements (and not use ksdssp). But this puts me back where I started! Any ideas? (Separately, I realize that I could make a simpler morph of just A-B-C, then record it as “roundtrip”, i.e. forward and backwards, to achieve the same thing as A-B-C-B-A. But this doesn’t solve the problems above.) Thanks very much, Yan -- Yan Kung Assistant Professor Department of Chemistry Bryn Mawr College http://www.brynmawr.edu/people/yan-kung Follow: @KungLab<https://twitter.com/KungLab>

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Nvidia 3D Vision on a large display
by Tom Goddard 02 Aug '19

02 Aug '19

Krish Raman asked what kind of large displays might work with Nvidia 3D Vision stereo glasses with Chimera. Hi Krish, I believe any display capable of a high refresh rate, at least 120 Hz (even 100Hz would do) will be able to show stereo with Nvidia 3D vision. Conventional 60 Hz displays could only show stereo at 30 Hz in each eye (since the display first shows the left eye, then shows the right eye in sequence), and 30 Hz is too slow causing flicker. Video gaming displays are usually advertised as 144 Hz and I believe any of those would work. It is hard to find big displays at 144 Hz, but here is an example, 49 inch ultra wide Samsung CHG90 https://www.amazon.com/Samsung-49-Inch-Curved-Monitor-LC49HG90DMNXZA/dp/B07… <https://www.amazon.com/Samsung-49-Inch-Curved-Monitor-LC49HG90DMNXZA/dp/B07…> If one person is using this sitting at a desk it is very wide and would probably give very nice immersive stereo because of the width. It is not ideal for your use with an audience standing further back because of its extreme 32:0 aspect ratio. You could look for a video gaming TV, such as these https://www.tomsguide.com/us/best-4k-gaming-tv,review-4837.html <https://www.tomsguide.com/us/best-4k-gaming-tv,review-4837.html> Keep in mind your Nvidia 3DVision system may not work with any of these. I would strongly recommend testing at a store with your 3DVision before buying. Stereo is an an extremely obscure niche product and there is no telling if it will work without testing. Another option is to use a high refresh rate projector. That is what we use at my lab -- (ours is a $50,000 Christie, so I don't recommend it). Also I am sure you are aware that Nvidia discontinued support for 3D Vision and it will not work with any Nvidia drivers released after April 2019. So the 3D Vision system is going to be dead soon. Tom

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crash on using Preset Publication 2
by Dieter Blaas 02 Aug '19

02 Aug '19

Hi, I have been using the Publication Preset 2 for making figures of a number of pdb structures without problems. However, I now have a pdb that shows up well in Chimera and does not have any obvious problems. However, when trying rendering it with the Preset Publication 2 (and only with this one) Chimera crashes with the error message below: *** stack smashing detected +++: /home/blaas/.local/UCSF-Chimera64-1.10.2/bin/python2.7 terminated Since I have prepared the other figures with this setting I'd like using it as well for the next figure but how? Thanks a lot, best regards, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. 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, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Chimera Viewdock Bug
by Sacco, Michael 02 Aug '19

02 Aug '19

Hello all, I would like to report a bug. When using Chimera in dual monitor mode on windows OS and loading the viewdock module, Chimera becomes unresponsive. However, when the second monitor is unplugged, it functions normally. I have confirmed this on multiple computers. After force closing Chimera a pop-up appears with the message "Chimera exited abnormally; the exit code was: 1.". Thanks everyone! Michael

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OBJ files are exported too small and won't open on other programs.
by Josh Moon 01 Aug '19

01 Aug '19

Hello! I am a relatively new and inexperienced user of Chimera. I am having a difficult time working with obj files. The Scenes I'm exporting as obj's end up having a very small file size (67 bytes in one case) and are being processed very quickly. The resulting file won't open successfully on any program that should understand an obj. Stl's are fine. Conversely, when I try to open an obj file into Chimera, it asks me to manually "Designate the File Type" as though it doesn't know what to do with it. Can someone please suggest what features I'm missing so that I can successfully export an OBJ? I'm also interested in how best to handle color information. Thank you! Josh ----------------------------------------- Josh Moon, Ph.D. (he/him/his) Educational Technology Specialist Kalamazoo College (269) 337-7415

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inquire about molecular docking
by Mohamed Hegazy 31 Jul '19

31 Jul '19

Hey , My name is Mohamed Hegazy, beginner in molecular docking , recently I performed a molecular docking procedure using chimera and I found that the initial structure of the ligand differs from the minimized one , and the binding score for a ligand would change during my different runs. The binding score you obtain from my docking cannot be a constant number. Sent from Mail for Windows 10 Mohamed Said Hegazy --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

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AreaSAS Issue
by Rucco,Dominic J 31 Jul '19

31 Jul '19

Hello, I'll start by saying your software has helped me visualize protein structure for quite some time and overall has been easy to use! I do have a question however: I was recently using the "render by attribute" feature to display areaSAS measurements but have run into an issue. I can no longer select this attribute from the dropdown menu. I noticed this when I attempted to render it on the protein mCherry (PDB 2H5Q). Even when I have gone back to other PDB entries I know have worked for areaSAS rendering, it doesn't appear as an option anymore. The only time I can get it to appear is when I load a session that already has the rendering performed on the protein. Any help would be appreciated, thank you, Dominic Dominic Rucco | Ph.D. Candidate George and Josephine Butler Polymer Research Laboratory Center for Macromolecular Science and Engineering Department of Chemistry University of Florida Leigh Hall 314 | PO Box 117200 | Gainesville, FL 32611-7200 drucco(a)ufl.edu<mailto:drucco@ufl.edu> | www.savin.chem.ufl.edu<http://savin.chem.ufl.edu/>

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--nogui gets permission denied when fetching pdb id
by Ryan Harlich 30 Jul '19

30 Jul '19

Hi Chimera, I am trying to run a script with the –nogui option and run command “open 1a1x” and I get permission denied. It works with the GUI so I am not sure why it is not working with –nogui. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Minimization with sulfur atom
by sara20＠mail.ustc.edu.cn 30 Jul '19

30 Jul '19

Dear users I have complex structure with ligand having sulfur atom in it. I am trying to minimize it but it fails giving the following error: (LIG) /home/usr/.local/UCSF-Chimera64-1.12/bin/amber16/bin/antechamber: Fatal Error! (LIG) Cannot properly run "/home/usr/.local/UCSF-Chimera64-1.12/bin/amber16/bin/sqm -O -i sqm.in -o sqm.out". I assume it's because of sulfur atom in ligand because I tried running it with out sulfur and it worked fine. I checked MMKT Atom database for sulfur file and it's already there: name = 'sulphur' symbol = 'S' mass = [(31.97207070, 95.02), (32.97145843, 0.75), (33.96786665, 4.21), (35.9670806, 0.02)] color = 'yellow' vdW_radius = 0.18 b_coherent = 2.847*fm b_incoherent = 0.188*fm b_coherent_deut = 2.847*fm b_incoherent_deut = 0.188*fm Any help would be highly appreciated. Thanks Sara

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Applying session parameters to another pdb file.
by David Sáez 29 Jul '19

29 Jul '19

Dear Chimera experts, I have saved a session of Chimera showing the perfect angle and size for the molecules of interest. Now I would like to apply the same parameters to visualize another (but similar, only differnet coordinates) pdb file. Is there a way to do that? Thanks in advance. David

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Editing sequences within Chimera
by Joshua Plank 26 Jul '19

26 Jul '19

Hi, I am wondering if it is possible to edit the amino acid sequence somehow? I have a .pdb file of the protein I'm interested in, but would like to change two of the amino acids to something else. Is this possible? thanks, Josh -- *Joshua Plank* *PhD Student* *Department of Electrical and Computer Engineering* *University of California, Riverside* *email: jplan002(a)ucr.edu <jplan002(a)ucr.edu>* *phone: 505-977-9919*

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Measuring the distance between residues and a surface
by Stanley, Julian A 25 Jul '19

25 Jul '19

Hello! I'm fairly new to Chimera, so if you're able to point me towards any resources that can help me answer questions like this one independently in the future, please do! Here's the question: I would like to measure the distance between the ends arginine and lysine residues and a surface, using Chimera's python modules. Typically, I would load my .pdb file, generate a surface, and then use the "measure distance" command and parse the output from the Reply Log. This approach works fine, except since "measure distance" prints to the reply log, I need to run my script in GUI mode. If possible, I'd prefer to run everything from the command line only. I thought that I might be able to do this with the distance() command, but I can't figure out how to pass a surface to that command. Does anyone have any tips/advice? In summary, what I usually do: ``` from chimera import runCommand as rc # load the file rc("open " + pdbFile) # Generate a surface rc("select protein") rc("split") rc("surface allComponents false") rc("~select") # Measure distance between arg and lys and the surface rc("select #0") rc("~select #0:@") rc("measure distance :arg@cd|:lys@ce selection multiple true show true") ``` And then I parse out the distances from the Reply Log. What I would prefer to do: It would be better to have the output to go to STDOUT when I run the script. I imagine that I'd use something like the `distance()` command, of the premade scripts (like here: http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/atomdist.py) but they are designed to measure the distance between atoms or residues, not between residues and a surface. Thanks for your help! Sincerely, Julian

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Modeller Restraints
by Danilo Boškovic 24 Jul '19

24 Jul '19

Dear all, how do i add restraints specific to my templates that i use for comparative modelling in chimera? Specifically what are the names assigned to those templates? Do i need the names to specify the template residues that i want to restrain? Are the names same as in the tab when i choose the templates for the run? Thanks, D. B.

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Re: [Chimera-users] Cannot resample to voxel size of 1
by Tom Goddard 23 Jul '19

23 Jul '19

It sounds like you just want to resample a map at a new grid spacing. Chimera does not have such a feature. The vop resample command is intended make the grids of two different maps match each other. Tom > On Jul 22, 2019, at 1:54 PM, Ryan Harlich <ryanharlich(a)hotmail.com> wrote: > > Hi Tom, > > I need the voxel size to be 1, so subdivideSurface and subdivisionLevel options won’t work. Also, vop new won’t work because I need it to have the same bounding box as the input surface. > > Best, > Ryan Harlich > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Monday, July 22, 2019 1:49:38 PM > To: Ryan Harlich <ryanharlich(a)hotmail.com> > Cc: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Cannot resample to voxel size of 1 > > Hi Ryan, > > Resampling only works on the grid of another map as you can see from the documentation so "vop new" allows you to make that map. If you just want to make the mesh of a surface depiction of a map finer then look at the volume command subdivideSurface and subdivisionLevel options. > > https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.…> > > Tom > > >> On Jul 22, 2019, at 12:03 PM, Ryan Harlich <ryanharlich(a)hotmail.com <mailto:ryanharlich@hotmail.com>> wrote: >> >> Hi Elaine, >> >> I think you missed the point. I am trying to take an existing surface and resample it to a grid Spacing of 1. I am not sure I see the point of making a new map. >> >> Best, >> Ryan Harlich >> >> Sent from Mail <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgo.micros…> for Windows 10 >> >> From: Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> >> Sent: Monday, July 22, 2019 11:59:06 AM >> To: Ryan Harlich <ryanharlich(a)hotmail.com <mailto:ryanharlich@hotmail.com>> >> Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> >> Subject: Re: [Chimera-users] Cannot resample to voxel size of 1 >> >> Hi Ryan, >> You can make a new map of whatever grid spacing you want without any atoms using “vop new”: >> <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u… <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…>> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> > On Jul 22, 2019, at 11:33 AM, Ryan Harlich <ryanharlich(a)hotmail.com <mailto:ryanharlich@hotmail.com>> wrote: >> > >> > Hi Chimera Bug Team, >> > >> > I am unable to resample surface to a grid spacing of 1 to be 1 voxel. >> > >> > Currently I do this: >> > 'molmap #2 6 gridSpacing 1\n' >> > 'vop resample #3 onGrid #2.1\n' >> > >> > But this requires me to have a pdb structure. I would like to do this without a pdb structure. >> > >> > Another alternative is I could automatically without GUI interface make a 3 atom pdb structure with python script that is the size of the surface’s boundary box. Although there is no way to get surface’s boundary box x,y,z. >> > >> > Any help would be much appreciated. Option 1 would be a much better approach. >> > >> > Best, >> > Ryan Harlich >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.…>

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Cannot resample to voxel size of 1
by Ryan Harlich 22 Jul '19

22 Jul '19

Hi Chimera Bug Team, I am unable to resample surface to a grid spacing of 1 to be 1 voxel. Currently I do this: 'molmap #2 6 gridSpacing 1\n' 'vop resample #3 onGrid #2.1\n' But this requires me to have a pdb structure. I would like to do this without a pdb structure. Another alternative is I could automatically without GUI interface make a 3 atom pdb structure with python script that is the size of the surface’s boundary box. Although there is no way to get surface’s boundary box x,y,z. Any help would be much appreciated. Option 1 would be a much better approach. Best, Ryan Harlich Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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same volume data values over the entire volume
by Dieter Blaas 22 Jul '19

22 Jul '19

Hi, Trying to color a volume according to "volume data" I get the same numerical values for all colors and a speckled appearance. When using "volume data gradient norm" I get the expected colors, i.e. strong local changes of the volume data are red and spots where there is essentially no change are in blue. How is this possible? If I understand correctly, "volume data gradient norm" colors according to the first derivative of "volume data" or is this wrong? Do I need something like a normalization? Thanks a lot for explanations, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. 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, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Fitting the structure into the map after changing origin
by Ahmad Khalifa 22 Jul '19

22 Jul '19

Is there a shortcut way of transforming the model to fit the map after I change, center or reset the origin? Best regards.

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RMSD Chimera
by Ishita Gupta 22 Jul '19

22 Jul '19

Hi, I have a few questions in mind regarding rmsd calculation in chimera: 1. Does the matchmaker tool calculate c alpha? 2. Do we consider RMSD of pruned atoms or the total atoms while reporting? 3. If we use structural comparison match align tool then rmsd is based on multiple sequence alignment? And it also gives C alpha? 4. If we calculate rmsd from multi align viewer by clicking on the structure and then match. What these rmsd values denote? Please elaborate on these points. Thanks Ishita

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Measurement similarity protein structure
by Nail Besli 19 Jul '19

19 Jul '19

Hi I superimposed two proteins in chimera with winch algorithms( blossom62) and p250. The result is the same. Why is the result same for both two proteins, although I tried two different algorithm settings? I am using the chimera's MatchMaker tool. The only thing different is the sequence alignment score. I attached the result file. kind regards

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what laptop configuration should I get for using Chimera and ChimeraX with very large volumes?
by Ilona Nudelman 19 Jul '19

19 Jul '19

Hi, I'm looking for an upgrade to my PC laptop (Windows) and wanted to ask if anyone has any advice on the configuration needed to run Chimera and ChimeraX with very large volumes and lots of heavy pdb's docked in. I am looking for a mobile workstation type laptop but I don't want to spend too much money - maybe 2,500-3,500$. Within these confines what memory, GPU, processor etc. would you recommend? Thanks! Ilona

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how to obtain information regarding complexes
by Quadir, Farhan (MU-Student) 18 Jul '19

18 Jul '19

Hello, I am relatively new to chimera. I am stuck with a problem of how to perform the following from a pdb file which contains multiple chains: 1. I would like to find regions which are 5.0 Angstroms or less between selected chains. 2. After obtaining that I would like to get from (1) a list of the residues and their positions in the chain that are interacting with each other inter-chainwise. Regards, Farhan Quadir PhD Student and Graduate Research Assistant Bioinformatics, Data Mining and Machine Learning (DBM) Lab 304 Engineering Building 1 Electrical Engineering and Computer Science (EECS) Department University of Missouri, Columbia, MO 65201, USA Email: fqg7h(a)mail.missouri.edu Phone (Cell): 573-846-4047

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Finding dimensions of density map
by Ryan Harlich 16 Jul '19

16 Jul '19

Hi Chimera, I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process? Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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energy minimization
by sara20＠mail.ustc.edu.cn 16 Jul '19

16 Jul '19

Dear I am trying to minimize a structure with HEME cofactor. I added heme frcmod and prep files from Amber parameter database in parm and prep folders respectively.I minimized the structure at different steps of steepest descent from 100 to 1000.But in all the structures FE of heme is not well aligned with HEME structure (it is pointed out of structure).I tried with both all atom and united atom frcmod and prep files but the results are same.Please find attached the minimized structure. Kindly tell me where am I wrong. Any help would be appreciated. Thank you Regards Sara

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visualizing distance restraints using Chimera
by Matthew Fountain 16 Jul '19

16 Jul '19

Is there any way to import a list of distance restraints and have Chimera display them based on the restraint violation. -- Matthew Fountain Professor and Chair Fredonia State University of New York Chemistry and Biochemistry Department

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Export morph confirmation scene to 3D Studio Max
by Edel Fenix 16 Jul '19

16 Jul '19

Hi, I just discovered Chimera and love the morph confirmation function! Amazing! I would like to export a full morph confirmation scene with surface render from Chimera with all frames in a format that I can import in 3D Studio Max as a complete animation. I can import individual OBJ but not what I am looking for with higher number of frames. I've tried all formats Chimera can natively export as but I can not open any of them in 3D Studio Max. Has anyone done this? Didn't find a relevant prior post when I searched. Is there a way to export formats multiple times to achieve this? Deeply appreciate any help in finding a solution. Best regards, Edel

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command lines to replace "joint models"
by wangdj7＠mail.ustc.edu.cn 15 Jul '19

15 Jul '19

Dear Chimera developers, I'm so sorry to interrupt you. I have to run Chimera in Linux,but there is no command line of "joint modeles".I need to get 2 modified amino acids or peptides together and not creating crashes.In windows,"joint models" is my best choice,it's very convient and perfect.But in Linux,I tried some command line,such as "combine","bond",but it can't automatically repositioning the models and the structure was not right. So,could you please tell me how to use command lines to replace "joint models" function? Thanks in advance Best Regards Daojiong Wang

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Parse error Chimera
by Dorfner, Maja 15 Jul '19

15 Jul '19

To whom it may concern, Using Swissmodel, I have constructed a model based on an original PDB file. NAP is part of this model. The docking works when the option of either "Ignore chains of non-standart residues" or "Ignore all non-standart residues" is chosen as false. The Problem is that in the PDBQT file of the receptor shows that NAP was not considered during the docking, making the Substrate float either within the NAP or to far from it. The docking worked fine with the original PDB file but not with the newly modeled one. Could the problem be that the NAP is a separate chain? I have already tried to erase the H before using AutoDock Vina. Here is the Reply log: Running AutoDock Vina for PmWT.pdb failed; see Reply Log for more information Application stderr ----- Parse error on line 3578 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. ----- Application stdout ----- ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, Journal of Computational Chemistry 31 (2010) # # 455-461 # # # # DOI 10.1002/jcc.21334 # # # # Please see http://vina.scripps.edu for more information. # ################################################################# Detected 4 CPUs Reading input ... ----- Thank you for your patience. Sincerely, Maja Dorfner

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Surface render error in MD movie for morph conformation
by Edel Fenix 15 Jul '19

15 Jul '19

Everything works at the basic level and has produced very useful data and animations. I am most grateful for these tools and your help. The BIG problem I have is that for some frames no surface is rendered at all. Other parts "magically" disappear and reappear during the transformation. *What I would want to do:* 1. There are missing structures/regions in need of repairs in the PDB files I work with (see attached screenshot example). The files are for the same protein but different regions missing in different models and they differ some, ideally they shouldn't. I am using Chimera and Modeller to repair these with loops/refinement. Ideally I would want to match/alter the proteins so the gaps connect correctly and their amino acid structure is the same for all models. I feel like this may be the/one cause for the surface errors when rendering? I've tried using modeller both locally and the web service so I have verified installation, integration and function. Must I generate multiple drafts and manually review and select the one best corresponding or is there a way to get it performed for all models loaded of the same protein? Further, if I want them to have the same genetic makeup, can I somehow use one as reference to alter the others? 2. Align the protein snapshots from the configurational change using matchmaker (works great!). 3. Use morph conformation to generate an animation of the configurational change with surface rendered. Works sort of, with errors for some frames where no surface is rendered at all or regions magically appearing/disappearing. 4. Solve the surface error I get, see attached error message :( If I use split copying from the example page, the model looks nothing like it should look like and more like boiling gruel. I am not experienced with Chimera but I feel like if I ensure the files have no gaps and are structurally identical with the same amino acid makeup it may work as is? *The problems with existing suggested solutions:* The link below present 4 possible solutions linked from the error message. Solution 1 looks nothing like what I want when rendered in my test. Solution 2 does not solve the issue of disappearing structures magically appearing again. I am not sure of the cause but could be because the models have different structure/missing parts. If repaired and matched across all protein models in the animation might work? If so, might not even give an error message? Looks viable but does not solve the problem. Solution 3 is not viable as I am looking to render the surface in details, not "overall" look for large structures. Solution 4 is not applicable as I do not want CPK. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html Any help would be greatly appreciated, Edel [image: Screenshot 2019-07-15 at 12.05.12.png] [image: Screenshot 2019-07-15 at 14.30.00.png] )

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Integer Values instead of Floats in Render by Attribute
by Daniil Prigozhin 11 Jul '19

11 Jul '19

Hello, I am using the latest nightly build and in the Render/Select by attribute window the values in the Value box (defining the color scheme) are reported as integers and accept only integer input, when in fact the Attribute that I defined is a float, and shows up as a float. This does not happen with "native" attributes, only with the newly defined one. Is it a problem with the defattr function not determining/passing the data type correctly? I am pasting the top of the attribute deffinition file below. Many thanks, - Daniil attribute: shannonEntropy match mode: 1-to-1 recipient: residues #0:1.L 0.865 #0:2.L 0.743

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Issue regarding Chimera-Vina
by Prabuddha Bhattacharya 11 Jul '19

11 Jul '19

Dear Sir, I am a beginner in the field of molecular docking. However, I started doing it using Chimera Vina. UCSF Chimera 1.13rc provides the interface while AutoDock Vina does the docking part. For a couple of cases I have found that inspite of keeping all the parameters same, the best obtained dock scores are coming different for each individual job-run. Is it so because it is a stocastic method? With such different dock scores, what should I do? I will be extremely grateful of you can kindly address this issue. Thanking you in advance, Best regards -- *Prabuddha Bhattacharya *

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Structure overlay
by Chakraborty, Joydeep 11 Jul '19

11 Jul '19

Dear all, I am trying to overlay two structures. 1. Wild type enzyme and 2. A mutant, with a single point mutation on the wild type. However, somehow when I am opening the structures, both are overlapping automatically and showing as one structure. I need to have two separate strands overlay, so I can show the change in the active site pocket. I was hoping if anyone could shed some light on this issue. Thanks, Joydeep.

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Volumes comparison
by Dmitry A. Semchonok 09 Jul '19

09 Jul '19

Dear colleagues, How to compare 2 volumes in Chimera by cross-correlation? Thank you. Sincerely, Dmitry

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Associate Scientist/Scientist Position in Protein Engineering
by Andrew Waight 07 Jul '19

07 Jul '19

Dear Chimera Users We are seeking a fresh phD graduate or postdoc with a structural, biophysics or computational background to join our group. This is an excellent opportunity for anyone looking to break into the extremely desirable field of antibody engineering for immuno-oncology. The position entails the design, cloning, purification and in vitro testing of multispecific antibody type molecules. The training involves in silico design (including MD analysis) molecular biology, HEK and CHO expression, Antibody purification and biophysical analysis including SEC, MALS, DLS, RP, Mass Spec, Kinetic analysis (Octet) Binning, Humanization, and *in vitro* validation including FACs analysis, immune cell activation and cancer cell line killing assays. Although experience is not necessary, we expect interview candidates to have researched the above topics thoroughly and to express and explicit interest in the field of protein engineering for immuno-oncology. If interested, please see the link below and feel free to contact me personally with any questions. So sorry to the rest of Chimera-users for the spam. https://www.linkedin.com/jobs/view/1358848339/

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Question regarding RR Distance Maps
by Meysam T. Chorsi 03 Jul '19

03 Jul '19

Hello, I need to use Chimera to determine the distance map, but for some reason the output matrix is not symmetric. I used other software as well, they all giving a symmetric matrix which makes sense to me. Could you please let me know how can I fix this? Thank you Sincerely, Meysam -- *Meysam T. Chorsi* *University of Connecticut * *191 Auditorium Road, Storrs, CT 06269, USA*

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Cylinder coloring extension
by Thomas Marcellino 03 Jul '19

03 Jul '19

Dear Chimera Team, I am aiming to color a stucture according to the B factor and represent it as a cylinder (pipes and planks) is there any possibility to apply different colors within the same cylinder or assign the coloring scheme to the cylinder representation in the same way as doing it with surface ? Looking forward to an answer, Thank you for your time reading my suggestion. Thomas M

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Creating a smooth disk
by Henrique C. S. Junior 02 Jul '19

02 Jul '19

Dear list, I'd like to create a disk that didn't show lines in the surface depending on the orientation angle (see the image attached). Right now I can clearly see that the circle is formed by several triangles, so I'd like to smooth things up. I can actually get rid of the triangles by disabling the silhouette of the plane, but I'd like to keep it to show where the plane ends. Thanks in advance -- *Henrique C. S. Junior*

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Volume save after volume changes
by Ryan Harlich 01 Jul '19

01 Jul '19

Hi Chimera, I am having problems saving changes of volume. Here is my script: 1. open C:\Users\ Desktop\density.map 2. volume #0 level 1.0 3. sel #0 4. volume sel save C:\Users\ Desktop\density2.mrc This does not save the change at line 2. How can I go about to save the change? Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Saving .pdb file in location of .mrc file
by Ryan Harlich 27 Jun '19

27 Jun '19

Hi Chimera, I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1. So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1. An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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