- Chimera-users - RBVI Mailing Lists

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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