- Chimera-users - RBVI Mailing Lists

Saving marker file on command line
by Rene Frank 08 Sep '20

08 Sep '20

Hi, I would like to save a .cmm marker file on the command line by specifying the model number. Please can you help me with what is the command to do this. Thank you, Rene

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how to set initial threshold when opening a mrc
by Shuo 04 Sep '20

04 Sep '20

Hi, When I open an .mrc map, Chimera will show the map with an initial threshold. But the initial threshold is not so good, so I changed it to high value with the scale bar in Volume Viewer. I want to save the map, so that when I open the map again, the initial threshold will be the high value, not the lower one. How could I do this? Best, Shuo

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Re: [Chimera-users] Chimera autodock vina for ligand docking on RNA
by Reeki Emrizal 03 Sep '20

03 Sep '20

Hi Elaine, Sorry about the subject. Just realised I forgot to add one after I hit send. I’ve tried autodock vina (not through chimera) and it works. However, I would like to automate both the receptor and ligand preparation steps and docking process and it seems to me that chimera is capable of it. Is there a help page that contains the command to turn off those options (Ignore chains of non-standard residues and Ignore all non-standard residues). The help page you provide doesn’t seem to provide a command that I can used in a docking script. Thanks for your help On Thursday, September 3, 2020, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Reeki, > I changed the subject line to something useful. > > The "Autodock Vina" tool in Chimera is just an interface that calls > Autodock Vina as a separate program. You should check the "receptor > options" in this tool: there are two options to ignore residues that are > not standard amino acids. I assume you should change those options to > "false". The options are explained in the Help page, which you can see by > clicking the Help button, or view the copy on our website here: > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> > > However, even if you change these options to false and the docking > calculation finishes, I do not know whether Autodock Vina is expected to > give good results for docking to RNA. Also, the tool in Chimera does not > allow very much sampling with Autodock Vina; for more thorough sampling of > space, you may want to use Autodock Vina directly (not from Chimera). > > The Chimera developers are not the developers of the Autodock Vina > program, so I am not an expert on this topic. Maybe you would find more > information about whether Autodock Vina is meant to work for RNA receptors > at the Autodock Vina website: > <http://vina.scripps.edu/> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Sep 2, 2020, at 5:02 PM, Reeki Emrizal <reeki(a)mfrlab.org> wrote: > > > > Dear Chimera team, > > > > I'm attempting to dock small molecule ligand on a RNA molecule using > chimera autodock vina. However, the docking process ended prematurely after > the receptor.pdb (the RNA molecule) file is made. Please find attached a > screenshot of the reply log. I'm suspecting the error comes from the > receptor.pdb file made by chimera. Please find attached the screenshots of > receptor.pdb files for a RNA molecule and a protein molecule. The > receptor.pdb for protein has the column for residue names parsed correctly > (e.g. "THR") but not for the receptor.pdb for RNA (e.g. "G" which I > believed should be " G"). > > > > My questions are: (1) Is chimera allows docking of small molecule ligand > on RNA molecule and (2) Is the a parameter that I've overlooked to allow > this? > > > > Kind Regards > > <receptor.pdb protein.png><reply log.png><receptor.pdb rna.png> >

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flipping model in chimera
by Dmitry Semchonok 03 Sep '20

03 Sep '20

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(no subject)
by Reeki Emrizal 02 Sep '20

02 Sep '20

Dear Chimera team, I'm attempting to dock small molecule ligand on a RNA molecule using chimera autodock vina. However, the docking process ended prematurely after the receptor.pdb (the RNA molecule) file is made. Please find attached a screenshot of the reply log. I'm suspecting the error comes from the receptor.pdb file made by chimera. Please find attached the screenshots of receptor.pdb files for a RNA molecule and a protein molecule. The receptor.pdb for protein has the column for residue names parsed correctly (e.g. "THR") but not for the receptor.pdb for RNA (e.g. "G" which I believed should be " G"). My questions are: (1) Is chimera allows docking of small molecule ligand on RNA molecule and (2) Is the a parameter that I've overlooked to allow this? Kind Regards

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Why is molmap changing the grid spacing and origin of simulated map
by Ouadou, Anes (MU-Student) 01 Sep '20

01 Sep '20

Hello, I am using molmap to simulate cryo-em density maps from protein pdb file. I follow the two steps outlined in Chimera tutorial (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html#onGrid) I first create an empty map with specific size, grid spacing, and origin. vop new #1 size 116,96,152 gridspacing 1 origin -99.0,-39.0,-58.0 Then simulate the pdb file on the empty map using the option the grid spacing molmap #0 3 onGrid #1 the resulting simulated map has grid spacing changed from 1A to 2A and the origin coordinates are also changed to half the values I provided. This does not happen with all cases. The following commands work perfectly and generate a simulated map with grid spacing of 1A vop new #1 size 78,88,121 gridspacing 1 origin -32.73,-28.64,-63.42 molmap #0 3 onGrid #1 I can re-sample the map to obtain 1A grid spacing, but it adds extra work (I doing this to 100s of examples) and seems to affect the resolution of the simulated map. Could you please adive me to why is this phenomenon is happening and how to solve it. best regards Anes Ouadou CS PhD Student University of Missouri-Columbia aomqc(a)mail.missouri.edu Mobile: (573 )-289-9073

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on mrc map splitting without losing resolution
by Smith Lee 01 Sep '20

01 Sep '20

Dear All, Suppose my protein complex pdb contains A,B,C and D subunits, and its mrc map is available. With Chimera, can we and how to get the mrc map for this protein complex with the part for subunit D cut out, without losing the resolution of the protein complex with subunit A, B and C? Smith

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Chimera, Modeller, and socket modules
by Casey Becker 31 Aug '20

31 Aug '20

Hello, I'm attempting to do some loop refinements using Modeller in Chimera while making use of Modeller's parallel job feature to use multiple CPUs. When I run the scripts directly through python's IDLE interface, it works. However, when I attempt to run a custom script including parallel jobs directly through the Chimera interface, I receive an error stating that I'm missing a socket module. I've contacted the Modeller help email and they referred me to you after suggesting I replace the mod9.24.exe with python.exe in the "Modeller executable," but that didn't work. In fact, it froze my Chimera. I've attached copies of my scripts and the error I get. Any assistance appreciated. Thank you.

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User-defined graphics in chimera: NMR tensor plotting
by Albert Smith-Penzel 31 Aug '20

31 Aug '20

Hello, I have a question about improving user defined graphics in Chimera. For background (maybe not necessary for answering): I’m working with nuclear magnetic resonance and MD simulation, and so I want to plot dynamically averaged spin-spin (H–C) dipole tensors, obtained from MD, on top of the corresponding H–C bonds. I’ve been relatively successful, but while one has a very high-resolution picture of the molecule itself, the tensors themselves are visibly triangulated. How I get this plot: Each tensor is expressed first in spherical coordinate (theta, phi, r). In python, I run Delauney from scipy.spatial on theta and phi to get a list of vertices that can be used for triangulation of the tensor. Then, for each tensor, I convert theta, phi, and r into cartesian coordinates, shift the center so that the tensor sits on top of the correct bond. Finally, I create a .bild file where I write out each triangle using the coordinates and vertices. Tensors have negative and positive values (red and blue in the plot), and so I only take triangles for which r for all vertices is positive, and then in a second step, take only triangles where all vertices are negative. This all gets written to the .bild file, and then opened in chimera on top of the molecule (see picture). The question: The result is certainly acceptable, however, there is clearly a quality difference in the molecule rendering vs. the tensor rendering (obviously, because the tensors are just made of triangles that I’ve created in python). Is there a better way to bring the surface data describing the tensors into chimera that would then allow usage of some sort of smoothing within chimera for a nicer image? (And possibly with a relatively simple data format….) Thanks for your help! Cheers, Albert Smith

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Error installing
by David Butler 28 Aug '20

28 Aug '20

Hi I get the error attached when trying to install the stable version of the software. My OS is Catalina 10.15.6 Thanks Dave David Butler, PhD. VP, Head of Therapeutics Development at Flagship Labs 63 600/700 One Kendall Square, Cambridge, MA 02139 781-866-1936 Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you should delete this message. You are hereby notified that any disclosure, copying, distribution or taking action in relation to the contents of this information is strictly prohibited and may be unlawful.

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On installation of Chimera linux version
by Smith Lee 27 Aug '20

27 Aug '20

Dear All, Fromhttps://www.cgl.ucsf.edu/chimera/download.html I have downloaded thechimera-1.14-linux_x86_64.bin, and have tried to install it exactly based onthe accompanied exact "Instructions”. After the installation completed, Igot to the bin folder, and try to launch chimera with ./chimera. However her俄 it says the installed/UCSF-chimera64-1.14/lib/python2.7/lib-tk/Tkinter.py was not configured for mypython. Will you please let me know howto configure TK for my python, which was a downloaded component of the chimerapackage? Best wishes, Smith

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Docking problem in my Protein ligand
by MUHAMMAD FURQAN AKBER 27 Aug '20

27 Aug '20

Hi hope you are fine? I cant find out the final result by protein ligand docking by chimera. This shows the error with pdb receptor. What can i do ?

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This Chimera plugin "sounds" interesting
by Eric Pettersen 27 Aug '20

27 Aug '20

Sonification for Structural Biology and Structure-based Drug Design - Paul Vickers <https://paulvickers.github.io/chison/>

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How to fit an atomic model into a topographic height volume
by Lee, Yun-Tzai (NIH/NCI) [F] 24 Aug '20

24 Aug '20

Dear Chimera developers, I am a research fellow who works at Frederick Biophysics Laboratory and working on an image processing project. I used Chimera to generate a topographic height volume data from a single plane image. You can find the attached file and use a command following to generate the topographic surface. % topography #0 height -40 smoothingIteration 5 But there is no option for me to fit the atomic model into the surface height volume by using Fit in Map tools. Can someone help me figure out what’s the issue? Is that possible to fit an atomic model into a height volume created by a single plane image or just simply need multiple planes? Thanks in advance. Best, Yun-Tzai

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INQUIRY
by Samiha I Amer 21 Aug '20

21 Aug '20

Hello Please how do I prevent chimera from renumbering my protein residue sequence in cases where I am working with a pdb structure that does not cover all the residues? For example, the attached pdb protein file (5trf.pdb) was downloaded from the pdb database with the first 9 residues missing. The first residue in the pdb structure is the 10th residue and this was numbered accordingly but whenever I upload such structures on Chimera, the numbering of the residues tend to scatter because chimera automatically numbers the first residue in the structure as 1, just as it appeared in the attached mol2 file. Please how do I avoid/correct such Thank you.

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Cannot dock molecule to targeted region?
by 孙业平 20 Aug '20

20 Aug '20

Dear all, I am trying to fit an antibody molecule to the cryo-EM density map for an antigen-antibody complex. The related files can be found at the following link https://drive.google.com/drive/folders/16ELIDsUxiNwRGp9ely2SRn-zjAdHCudH?us…. I first segmented the map ("emd_22158.map") and get the segment map ("emd_22158.seg") in chimera. Then I selected the regions corresponding to the antibody and use the "Fit to segments" tool of chimera to fit the antibody molecule. The "image1.png" shows the inital antibody postion and the expected docking postion in the segmented complex density (indicated by the red arrow). However, the antibody molecule cannot be fitted into the selected target region after this operation, but moved to the position shown in "image2.png (only the target regions are shown). I have tried to ungoup and regroup the target region to make its overall shape more simial to the antibody, and place the antibody into the region and ajust its orienation, but whatever I tried, the results are the same: the antibody will move to the position shown in "image2.png" after performing the "Fit to segments" action. I wonder whether it is impossible to dock the antibody to the expected position with chimera or there is anything wrong with my operation. Could you help me with this issue? I will appreciate any help from you. Best regards, Yeping Sun

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Fw: Open MTZ file
by Williams, Joanne 20 Aug '20

20 Aug '20

Hello! Can you help with the inquiry below? thanks, Jo ________________________________ From: Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> Sent: Thursday, February 22, 2018 5:01 AM To: chimera(a)cgl.ucsf.edu Subject: Open MTZ file Is it possible to open an .mtz file in Chimera? ~~~~~~~~~~~~~~~~~~~~~~~~~~ Sharyn A. Endow, PhD Professor of Cell Biology, DUMC Professor of NBD, Duke-NUS PO Box 3709 450 Sands Bldg/Research Drive Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Minimized Structures vs. Unminimized
by Jordan Harriman 17 Aug '20

17 Aug '20

Hi there, I have a protein I'm modifying, for a total of 28 unique mutations. My question is if it's possible to tell the energetic difference between a minimized structure vs. an unminimized structure. Following that, if it's possible to rank minimized structures in terms of greatest stability. Is there some quantifiable output I can use to compare structures? Best, Jordan

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Dock-preparation
by JAVAD KARIMBAYLI 17 Aug '20

17 Aug '20

Hi! I have got a problem and searched all previous posts for solutions but failed to find one. Therefore, I would be very much thankful to have your guidance. I have generated my protein model in I-Tasser and now I would like to do dock-prep. (Attached model-PDB file) However, when I run it: *Tools .. Strct edit .. Dockprep **All selected ** Add hydrogens (also consider H-bonds)* *Incomplete side chains:replace(Dunbrack 2010 rotamer library)* *Protonation states fro: his (residue-name-based)* *standart residues: AMBER ff14SB* *other residues: AM1-BCC* *Output:* No incomplete side chains No SEQRES records for model1 (1).pdb (#0) chain A; guessing terminii instead Chain-initial residues that are actual N terminii: MET 1.A 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: LEU 522.A 470 hydrogen bonds Removing spurious proton from 'C' of LEU 522.A Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: ILE HD3 (ILE 18.A HD3, ILE 31.A HD3, ILE 42.A HD3 + 26 others) ILE HD1 (ILE 18.A HD1, ILE 31.A HD1, ILE 42.A HD1 + 26 others) ILE HD2 (ILE 18.A HD2, ILE 31.A HD2, ILE 42.A HD2 + 26 others) Total charge for #0: 9.382 The following residues had non-integral charges: ILE 18.A -0.0558 ILE 31.A -0.0558 ILE 42.A -0.0558 ILE 77.A -0.0558 ILE 96.A -0.0558 ILE 132.A -0.0558 ILE 136.A -0.0558 ILE 151.A -0.0558 ILE 153.A -0.0558 ILE 163.A -0.0558 ILE 184.A -0.0558 ILE 193.A -0.0558 ILE 223.A -0.0558 ILE 236.A -0.0558 ILE 250.A -0.0558 ILE 256.A -0.0558 ILE 284.A -0.0558 ILE 297.A -0.0558 ILE 321.A -0.0558 ILE 370.A -0.0558 ILE 378.A -0.0558 ILE 401.A -0.0558 ILE 416.A -0.0558 ILE 436.A -0.0558 ILE 447.A -0.0558 ILE 450.A -0.0558 ILE 480.A -0.0558 ILE 489.A -0.0558 ILE 495.A -0.0558 Correct charges are unknown for 3 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms So, please kindly help me to solve the issue. Yours Sincerely Javad Karimbayli

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Modeling of mutlichain protein complex
by amit gaur 16 Aug '20

16 Aug '20

Hi, I am trying to model a multichain protein complex using modeller extension in chimera. But, I do.nt know how to do that? Can some one help me with this ? Thanks -- *Dr. Amit Gaur* *Post Doctoral ResearcherPI: Dr. Ji-Fang ZhangThomas Jefferson University* *1020, Locust Street, Suite 418* *Philadelphia, PA 19107*

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The command like volume zone in X
by Zheng, Fengwei 14 Aug '20

14 Aug '20

Dear Developer, I am wodering if there is a command of Chimera can achieve the same function like "volume zone" in ChimeraX? I tried the command "vol zone #2 near #0:.a range 2", but the chimera always said "unknow keyword #2"~ Another thing is that I wonder if there is a command of ChimeraX can achieve the same function like "turn z 2 360 precess 20" in Chimera (to achieve the Wobble motion / "wiggle-rock" motion, like nutation in pymol)~ The I tried 1.14, 1.15 and the latest daily built versions of Chimera. The ChimeraX version I used is 1.0, Many thanks! Best, Fengwei

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Coordinate bond problem
by Xelha ap 13 Aug '20

13 Aug '20

Hi! I have had problems minimizing the structure of a molecule that contais cordination bonds. Chimera does not recognizes the bond. The structure is a BODIPY, and its characteristics is the coordination bond between Boron atom and one nitrogen. Can you help me to minimize mi structure? is there in chimera any option to select coordination bonds? When i tried to minimize it, i selected that the boron atom is tetrahedral and subtituents but, with the following conditions to select dis not work for me. I get "Failure running ANTECHAMBER for residue UNKCheck reply log for details". I have been changed the next selections and I get the same answer. Can you help me please? M. en C. Xelha Araujo Padilla Estudiante de Doctorado del Programa de Biomedicina y Biotecnología Molecular Lab. de Citopatologia Ambiental, Depto. de Morfología, Escuela Nacional de Ciencias Biológicas-IPN, Zacatenco. Ciudad de México Tel. +52(55) 57296300 Ext. 52399.

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Problem opening Chimera "vop zFlip" mrc map in CADD MOE
by Paul Miller 13 Aug '20

13 Aug '20

Hi I opened an MRC file in UCSF Chimera 1.13.1 and used the "vop zflip" command and then saved the flipped map. The original map opened in CADD MOE, but the flipped map would not open. Is this a known issue? Just wondering if there's a solution. Cheers, Paul Paul Miller, PhD University Lecturer in Pharmacology Department of Pharmacology University of Cambridge Tennis Court Road Cambridge CB2 1PD +44 1223 761267 https://www.phar.cam.ac.uk/research/miller

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Using python to run rotamer
by mailman-bounces＠cgl.ucsf.edu 12 Aug '20

12 Aug '20

From: benjamintam <benjamintam(a)um.edu.mo <mailto:benjamintam@um.edu.mo>> Subject: Using python to run rotamer Date: August 5, 2020 at 12:49:55 AM PDT To: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu>> Dear all, I am trying to simplify tedious and repetitive work through using Chimera. My work has to substitute a list of residue on a protein. For each row of the list, after the substitution, I need to save it as a separate file. Since I am a beginner of python coding, I would like to ask the following question before I attempt to code: -From what I said, is it possible to do it in Chimera? -Do I just call the Rotamer program out by using “useRotamers()”? If it is using that, how do I provide the residue number and residue type into the program? Thanks for your time and help. Best regards, Ben

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Blast protein analysis
by Bernadette Ataku 12 Aug '20

12 Aug '20

Hi, I have been using Chimera for some time and lately I can't seem to blast my protein sequence. "BLAST Database error: No alias or index file found for protein database [/databases/mol/blast/db_current/pdbaa] in search path [/wynton-local/usr.local/opal25-tomcat7/webapps/ROOT/appBlastProtein2Service1597130953690-1008200060::]" This statement is generated when I try to blast my protein sequences. What could be the problem? and how can I fix it. Kind regards, Bernadette Kutima

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