- Chimera-users - RBVI Mailing Lists

Ligand Receptor docking
by Shriwas, Pratik 20 Nov '18

20 Nov '18

Hi, I am trying to use UCSF chimera to study ligand-docking interactions. My protein is GLUT1 (4pyp - PDB) and a small molecule called DRB18 .I have used NIH pubchem browser to generate a smiles string for this compound and used the smiles string to generate a 3D structure in chimera. I have found that the compound interacts with protein in central cavity and interacts via hydrogen bonds (depending on parameters). I want to know whether my data is publishable. If docking studies performed using chimera are acceptable. People use softwares like Schrodinger/medusa among others. If you wish to see my work, I can send it in as well via email. Thank you. Regards, Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University.

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how to make/delete hydrogen bond and delete chains
by Paris Tzou 19 Nov '18

19 Nov '18

Hi, I have a protein-dna complex structure with protomer as A as protein and B as DNA. It is impossible in hbond function to "generate" hbonds between two chains (A and B). One have to parse protein and DNA into two files and load into Chimera as two models. Another question is that, once generated, hbonds cannot be "erased" in the chimera view. And "delete chain ID" cannot really delete one chain from protein-DNA complex. What I am doing is 5MCT, p53-DNA complex. Thanks a lot for your help. Paris

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generating/saving mask files using segmentation
by Uhnsoo Cho 19 Nov '18

19 Nov '18

Hi, I am a beginner and still in the learning phase of chimera. Here is my question. I generated the mask from relion (mask creation) and open the mask in chimera. Using segmentation, I successfully split the mask into three segments and saved them individually. Then, I found that each mask file changes its box size (smaller than the original mask) and failed to run the multi-body refinement in relion. Using relion_image_handler (--new_box), I changed the box size but now the origin is shifted and all three masks are overlapping each other by losing their relative position. Is there a way to save the segmented mask maps by maintaining its original box size and relative position? Thanks. Best, Uhnsoo

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Using headless chimera to create images
by Chemmama, Ilan 19 Nov '18

19 Nov '18

Dear developers, I am trying to create a bunch of images using Chimera. I wrote a script that create the scene using the following steps: mc_frame=str(INPUT_FRAME_NUMBER) rmffile=str("PATH_TO_RMF") runCommand('open '+rmffile) runCommand('set bgcolor white') runCommand('windowsize 1028 1028') runCommand('~set depthCue') runCommand('set projection orthographic') runCommand('wait 2') runCommand('scale 0.75') runCommand('copy file ./Image_'+mc_frame+'.png PNG supersample 3 dpi 300') runCommand('close all') runCommand('stop now’) While the scrips works in the headless version using PDB files, I have not been successful when using RMF files. The images when using the RMF files are just the background color (red when set to red, blue when set to blue) without the structure. I tried also to add the display .2 option as in: runCommand(‘display #0.2’) which corresponds to the RMF beads scene in the model panel. I should add that using the GUI version of chimera, the script works fine and all the images are properly created. Do you have any hints/clues on what could be done to make it work? (I am running the script the full version of chimera but the headless should be more efficient). Thanks, Ilan

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Difference map
by Yangqi Gu 18 Nov '18

18 Nov '18

Dear Chimera users, I am trying to examine two cryo-EM maps and want to know if there is a subtle change between these two. I want to calculate the difference map, is it doable in Chimera? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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Can the order of map histograms on Volume Viewer be sorted?
by Jun Ha Song 16 Nov '18

16 Nov '18

Dear RBVI, Sometimes I accidentally open more than 4 maps into UCSF Chimera session without changing the number of histogram that can be shown to some value higher than the default value of first 3 maps. UCSF Chimera places new histogram on the spot where the 1st map used to be, and the histogram order shown on Volume Viewer goes from - 1st map - 2nd map - 3rd map to - 4th map - 2nd map - 3rd map from top to bottom. I know that I can bring back the histogram of 1st map by clicking on Data drop-down menu, but it doesn't bring back the 1st map to the top slot. Is there any way to manually re-sort the order of the histogram so that it would be in the order of their loading (or in the order of their model ID)? Best, Junha Song.

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How can I export the list of hydrogen bonding and clash/contact?
by Paris Tzou 15 Nov '18

15 Nov '18

Hi, I have a structure of protein-DNA complex. How can I export the list of hydrogen bonding and clash/contact, please? Thanks a lot, Paris

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Re: [Chimera-users] Fwd: Re: How to correct this error: ~/usr/chimera-1.12/lib/libgomp.so.1: version `GOMP_4.0' not found (required by /usr/lib/libopenbabel.so.4)
by Francois Berenger 14 Nov '18

14 Nov '18

On 11/15/18 9:51 AM, Francois Berenger wrote: > > > -------- Original Message -------- > Subject: Re: [Chimera-users] How to correct this error: > ~/usr/chimera-1.12/lib/libgomp.so.1: version `GOMP_4.0' not found > (required by /usr/lib/libopenbabel.so.4) > Date: 14/11/2018 18:42 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: Francois Berenger <mlists(a)ligand.eu>, chimera > <chimera-users(a)cgl.ucsf.edu> > > That looks like a problem between libopenbabel and Chimera. The bug is > that libopenbabel.so was compiled with a newer compiler than what > Chimera was compiled with. You can try renaming > chimera-1.12/lib/libgomp.so.1 (eg., to libgomp.so.1.save) to see if it > fixes the problem. Yes, this workaround works: mv ~/usr/chimera-1.13/lib/libgomp.so.1.bck ~/usr/chimera-1.13/lib/libgomp.so.1.bck And I also needed to issue that one: mv ~/usr/chimera-1.13/lib/libz.so.1 ~/usr/chimera-1.13/lib/libz.so.1.bck > While I consider this a bug with the Python > openbabel package, it should be bundling and using a libopenbabel.so > that is compatible with the Python "manylinux1" ABI (based on CentOS 5), > we will investigate incorporating a workaround. Thanks a lot. Francois. > -- Greg > > > On 11/13/2018 5:53 PM, Francois Berenger wrote: >> Hello, >> >> On a Ubuntu 18.04.1 LTS, I get this error message when I start chimera. >> >> Is there a known fix? >> >> Am I running a too old version of chimera or should I run >> a version specially compiled for Ubuntu computers? >> >> Here is the full error message: >> --- >> # chimera >> Error while importing plipgui from >> /home/berenger/.local/lib/python2.7/site-packages: >> Traceback (most recent call last): >> File >> "/home/berenger/usr/chimera-1.12/share/chimera/extension/base.py", >> line 349, in _importExtension >> __import__(module) >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plipgui/ChimeraExtension.py", >> line 8, in <module> >> from plipgui.core import cmd_plip, cmd_unplip >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plipgui/core.py", >> line 50, in <module> >> from plip.modules.preparation import PDBComplex >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/preparation.py", >> line 13, in <module> >> from .detection import * >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/detection.py", >> line 12, in <module> >> from .supplemental import * >> File >> "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/supplemental.py", >> line 26, in <module> >> import pybel >> File "/home/berenger/.local/lib/python2.7/site-packages/pybel.py", >> line 53, in <module> >> import openbabel as ob >> File >> "/home/berenger/.local/lib/python2.7/site-packages/openbabel.py", line >> 21, in <module> >> _openbabel = swig_import_helper() >> File >> "/home/berenger/.local/lib/python2.7/site-packages/openbabel.py", line >> 20, in swig_import_helper >> return importlib.import_module('_openbabel') >> File >> "/home/berenger/usr/chimera-1.12/lib/python2.7/importlib/__init__.py", >> line 37, in import_module >> __import__(name) >> ImportError: /home/berenger/usr/chimera-1.12/lib/libgomp.so.1: version >> `GOMP_4.0' not found (required by /usr/lib/libopenbabel.so.4) >> --- >> >> Thanks a lot, >> F. >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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(1) Autodock Vina executable on windows (2) selection of submodels
by Visvaldas K. 14 Nov '18

14 Nov '18

Dear colleagues, I'd like to report a couple of issues which have cropped up. (1) On Windows, running Autodock Vina in Chimea using local executable fails due to spaces in file path (gives error something like "File "C:\Program" not found). The thing is, the university computer admins do not allow change paths or copy system files around. It should be possible to escape spaces in file names, wouldn't it? (2) The selection of submodels does not work if it is used as a part of the list. For example, "sel #1.1" selects just the submodel 1 (let's say I have a set of 20 molecules in sdf file), which is fine, while "sel #1.1,#0" selects ALL submodels in #1 in addition to #0, and that does not seem to be right. Best regards, Visvaldas

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Secondary structure recognition issue in homology model
by Monika Tokmina-Lukaszewska 13 Nov '18

13 Nov '18

Dear Chimera Team, In my homology model (see attachment) it looks like there has been some issue with secondary structure recognition in one of the domains (highlighted in cyan). In .py file I added one of the protein templates (yellow) based on which the C-terminal domain was constructed. I am not sure what has happened to a final model, since template for that domain looks good. I was wondering if there is an option in Chimera which could fix that issue? Thank you for your time, Sincerely, Monika Lukaszewska -- Monika Lukaszewska, Ph.D. Senior Research Scientist Chemistry & Biochemistry Department Montana State University Bozeman MT, 59717 lab: (406) 994 5418 tokminalukas(a)montana.edu <tokminalukas(a)chemistry.montana.edu>

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Chimera installation
by Gonzalez Fernandez, Cristina 13 Nov '18

13 Nov '18

Hi all, I am new in the molecular docking field and I would like to start using Chimera. I would like to install it in Linux but use a GUI as in Windows. Is it possible? Thank you in advance! Cristina

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Save measured distances
by Dhananjay 13 Nov '18

13 Nov '18

Dear all, I am calculating distance between CA atoms as follows: sel #0:13@CA, #0:129@CA color red selection distance #0:13@CA #0:129@CA I want to save the measured distance between residue 13@CA and 129@CA in a file. I can do it using GUI. How can I do this within the command line ? Any help would be appreciated !! Thank you -- Joshi

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Editing mol2
by Francesco Pietra 13 Nov '18

13 Nov '18

Hi all: Is it possible editing .mol2 files with chimera? thanks francesco pietrta

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Drawing vectors depicting the movement of one conformer to another
by Beth Stroupe 12 Nov '18

12 Nov '18

Hi, I would like to make a figure depicting the movement of an RNA molecule from one conformation to another. It is not a simple rigid body rotation or translation but a rolling motion where some parts of the molecule move more than others. I would like to show vectors to show the rotation that are colored coded by the distance of the move. Is there a straightforward way to do this in Chimera? Thank you, Beth

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how to create using Chimera?
by Paris Tzou 10 Nov '18

10 Nov '18

Dear Sir, I am studying PDB id: 5MCT (p53-dna) complex. There is a "BIOMT TRANSFORMATIONS" required to generate the biological unit. Would you please guide me how to do this? Thanks a lot, Paris

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Re: [Chimera-users] 1up opt
by Elaine Meng 09 Nov '18

09 Nov '18

Hi Zhengzheng The format of your PDB file is not standard because all the H atoms are all at the end instead of with their their residues. Also they are all in a different chain (chain A) than the other atoms (chain B). Whatever program wrote this file wrote it incorrectly. You can easily see all atoms, e.g. commands: ~ribbon display (or use Actions menu to do the same things) but if you use Chimera features requiring chemical knowledge (findhbond etc.) it will not work correctly if the H and the other atoms are not recognized as being in the same residue. I tried editing so that all atoms were chain B, but it did not fix the problem, which is apparently instead caused by placing all the H atoms at the end instead of with their individual residues. You could fix it be removing and re-adding hydrogens in Chimera, but then the H atom positions wouldn’t be exactly the same. Commands: delete H addh It is recommended to send questions to chimera-users(a)cgl.ucsf.edu (CC’ed here) in case I’m not available to answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 7, 2018, at 8:02 AM, zheng l <zhengsfriend(a)hotmail.com> wrote: > > Dear Dr. Meng > > I used Chimera software for analyzing many protein crystal structures and then modified them and it has so faithfully doing job for me. However, this structure that I attached below is very difficult to modify. > > The problem is that the hydrogens in structure are hidden. Usually when I need to, for example, replaces a carbon to a nitrogen in a Phe the nitrogen will attached with a hydrogen if I set to have 3 bond for the nitrogen. But this structure is not showing hydrogens at all > > Would you please help me find a way of show all hydrogens need for modifying the protein structure? > > Thank you! > > Best regards! > >> Zhengzheng > > <1tup chain b opt 2.pdb>

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(no subject)
by rekha pydala 08 Nov '18

08 Nov '18

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FW: Chimera [viewer] for iOS in the future?
by Williams, Joanne 05 Nov '18

05 Nov '18

From: Bryan Crawford <bryanc(a)unb.ca> Date: Wednesday, October 31, 2018 at 3:53 PM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: Chimera [viewer] for iOS in the future? Hello, I use Chimera occasionally in my research, and extensively for teaching (biochemistry, cell biology, developmental biology). It is now the only remaining piece of software I use that requires me to bring a laptop computer to class. For everything else (PDFs, animations, Keynote presentations, etc.) I can use my iPad which connects by AirPlay to the projector, and screencast everything using Doceri. Furthermore, the touch-screen interface of the iPad seems ideally suited for many of the analyses and/or molecular renderings people use Chimera for. So I’m wondering if there are any plans to produce either a full or partial version (perhaps with only viewing capabilities) of Chimera that runs on iOS? If there is, I would be very happy to help with beta testing. If not, can I ask if you can recommend any software that runs on iOS that I might consider? Cheers -- Dr. B.D.Crawford Professor Matrix Dynamics Lab Department of Biology University of New Brunswick Fredericton, NB, Canada

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Automating H bond distance retrieval
by Samuel FreemanFox 01 Nov '18

01 Nov '18

Hi, I was wondering about the possibility of writing a setup.com file which is capable of opening a receptor.pdb and ligand.pdb file, locating the H-bonds between these two structures and then reporting back the lengths of the bonds? Currently I am able to open both files, execute addh, addcharge, and hbonds with my setup.com file. However I am unsure of how to proceed from there. Many thanks and I look forward to your response. Samuel Freeman-Fox ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Porton Biopharma Ltd, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. *******************************************

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Batch Processing of Molecular Attributes
by Benjamin Feinsilver 01 Nov '18

01 Nov '18

Hello, Is it possible to pass a CSV file to Chimera containing a list of SMILEs, then output their molecular attributes in a new CSV file? For example, volume, surface area, the number of surface points with positive electrostatic potential, and the energy of the molecule's current 3D conformation. If so, would you please let me know how I would accomplish this? Thanks, Ben

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Chimera use
by Hui Min 31 Oct '18

31 Oct '18

Hi there, Sorry to disturb you. I have a question of how to use the Chimera software. If I've already got a .pdb file and use SMART to predict the domains, how can I mark the 3D structure with user defined color？ Thank you in advance for your help -- *Hui Min* Postdoctoral Scholar Research, Department of Internal Medicine, College of Medicine, University of South Florida, Tampa, FL 33612 minh8(a)health.usf.edu

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How can I load a list of residues of protein?
by Paris Tzou 30 Oct '18

30 Oct '18

Dear all, I want to load a file containing a lit of residues of protein which is already shown in Chimera. I don't want to manually select the residues under investigation through "Favorite -- Sequence". Is there a way of doing this ? I know I can do it using command line like:select #0:15-17.C,263-265, 300-310.A. Instead, I can have a text file with content like: 15,C 16,C 17,C 263,A 264,A 265,A Thank you very much. Paris Tzou

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Split map from command line
by armoelle 29 Oct '18

29 Oct '18

Dear Chimera Team, I am trying to call the split map command directly from a script but somehow I don’t seem to be able to get it to run - maybe you can help me? I am calling scolorzone (which works perfectly) and then ( as suggested in the mailing list) use the accelerator command ac sm to split the map. However, generally nothing happens - sometimes though (I don’t know what triggers it - and I am not doing anything different) it runs perfectly fine. I am a bit puzzled as the same is the case no matter if I run form command line or I use the keyboard shortcuts gui. Many thanks for your help! cheers Arne ________________________________ Dr. Arne Moeller Independent Research Group Leader Department of Structural Biology Max-Planck-Institute of Biophysics Affiliated Researcher DANDRITE, Aarhus University, DK www.moeller-lab.com www.biophys.mpg.de/en/moeller.html Arne.Moeller(a)biophys.mpg.de 0049 69 63033057 Max-von-Laue-Strasse 3 D-60438 Frankfurt am Main Office L.1.015

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CUDA on Mac OSX 10.14 Mojave
by David Bhella 26 Oct '18

26 Oct '18

Dear All I just learned (after updating) that nVidia CUDA support is not in place for the latest Mac OS X release. I have a 2010 Mac Pro with a Quadro 4000 card in - which is still fine as a desktop. Chimera throws an error now - complaining about the graphics settings being incorrect: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions." Presumably because the graphics driver is not working correctly. Has anyone succeeded in resolving this? Or do I need to roll back to 10.13? A quick scan of the Mac/nVidia Forums suggests that CUDA support may not be forthcoming anytime soon, but I thought I would check if anyone has resolved this before going through the hassle of downgrading. Thanks, D Dr David Bhella Director - Scottish Centre for Macromolecular Imaging MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella

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Dynamic Protein
by Alex Nazlidis 25 Oct '18

25 Oct '18

Dear Elaine, is there any way in chimera to produce a clip similiar to this ( https://www.youtube.com/watch?v=zm-3kovWpNQ at 5:44)? You know animating the dynamic nature of a protein and its folding process. Thank you very much in advance, Alex

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