- Chimera-users - RBVI Mailing Lists

Dual transparency in chimerax
by Yehuda Halfon 21 Nov '18

21 Nov '18

Hi all, I want to make a picture with one protein in transparency 90 and one of its subunits in transparency 40. On thier on this works fine. But when I try them together the 40 is gone inside the whole protein. Is there a way to do it in chimerax? Yehuda Halfon

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Enquiry docking
by Thuluz 20 Nov '18

20 Nov '18

Dear Chimera users and technical assistance, I would like to ask you about molecular docking issue. We are performing a number of blind dockings, always by posing the grid box at the centre of a given molecule, the box had always the same size. Our question is why sometimes we get docking results very close to the centre and sometimes further away from it? is it only random or depends on physic-chemical properties? thanks in advance for any help on this matter, my best regards -- *Dr. Thuluz Meza Menchaca*

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Helix axis and correction
by Gulsevin, Alican 20 Nov '18

20 Nov '18

Hello everyone, I have a question about the "helical correction" option for calculating helix axes. I've been trying to find the exact calculation Chimera uses to correct the helix axis, but I couldn't find anything specific in the archives and I also couldn't figure it from the source code. Where can I find a detailed description of how the helix axes and the corresponding corrections are calculated? Thanks for your help, Alican Gulsevin, PhD Postdoctoral Researcher Vanderbilt University Department of Chemistry Center for Structural Biology - Meiler Laboratory 465 21st Ave South Nashville, TN,37221 Office: MRBIII, Room: 5150C Phone: (615)-936-6594

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Movie Recorder Frame Options not available
by Angela Gehrckens 20 Nov '18

20 Nov '18

Dear Sir or Madam, I am trying to record a movie in Chimera 1.13.1, but I consistently get the following error without a proper error message: "An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: ". I think there might be a problem with the frame directory, but I can neither change the frame options (they are hidden) nor do I find any information on how to get the permission to change the fram options. I'd be very happy to receive help from you concerning this matter. Kind regards, Angela Gehrckens --- Diese E-Mail wurde von Avast Antivirus-Software auf Viren geprüft. https://www.avast.com/antivirus

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Some UCSF Chimera marker (.cmm) bonds written as pseudobonds in pdb
by Jun Ha Song 20 Nov '18

20 Nov '18

Dear RBVI, I have UCSF Chimera marker set made by Volume Traver, and I used "Write PDB" in the model panel to transfer the .cmm file as .pdb file. However, when I opened newly created .pdb file, only about 4.3% of bonds were being shown as bonds, and the rest were being shown as pseudobonds. Is there any reason for this phenomenon? Best, Junha.

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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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