- Chimera-users - RBVI Mailing Lists

Distance measurement file
by Marco Sette 08 May '17

08 May '17

Dear all, I have to measure the same interatomic distances in different molecules: it is possible to create a file like distance ... distance ... distance ... and use as input, just to avoid typing the same command many times? Thanks for your help, Marco

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hbonds and distances movie script questions
by mfellner＠msu.edu 05 May '17

05 May '17

Good day I am making a movie by writing a chimera command script and I searched through existing chimera topics but I could not find a solution for these issues: Is there a command to display hbonds, I have made a script now to select residues and find the hbonds, even color + line width them and then I get rid of them later by ~hbonds. What I would prefer is to have them premade (so I dont need to select residues during the movie) but not displayed, later I then displayed and undisplayed them with a scipt command. Also I could not get the lineType command to work inside the hbond script (lineWidth worked fine), I had to use the setattribute command in a second script line, so for a splitsecond I have a different linetype displayed. The second question is about distance labelling. I can set the options in the gui and then distances are displaed by a script with the distance in Angstrom shown. Is there a way to undisplay the distance label later but keep the dashed line, so change the gui option with a script? Also I assume this is not possible, is there a script to change where the label will show up next to the line? I have not looked into displaying and undisplaying 2D labels with scripts, maybe that is a possibility? Lastly which is not that important, is there any way to trim the corners easily? I think I am recording a lot of white space to the left and right throughout the movie, if I resize the window the molecule gets focused, so its no longer exactly where I had it related to the corners and I think I would have to adjust the script. Thank you so much, I hope I made my questions clear, chimera is an awesome program, movie is 21 minutes at the moment. Best wishes Matthias Fellner Michigan State University

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Sub-region selection
by Soumya Govinda Remesh 05 May '17

05 May '17

Hello, I am analyzing some tomography data. I am working with multiple maps - one which defines several cells and another that defines their inner organelles. I want to be able to select and save the map for individual cells and their corresponding map for the organelles. In addition to using the sub-region selection in Volume-viewer is there another way to select the cells? Thanks Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh(a)lbl.gov

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Contact Maps (RRdistance Maps) questions:
by Nicole Persky 03 May '17

03 May '17

Hi All, I've just found the RRdistance Map function on Chimera and would like to compare between structures. I would like to: 1- make contact map of protein 1 to protein 1 with a cutoff of about 6 angstroms 2- make a contact map of protein 2 to protein 2 with a cutoff of about 6 angstroms 3- compare these two contact maps using the colors available for the whole contact map. I can only seem to compare the ENTIRE contact map of protein 1 to the ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6 angstroms. Alternatively, if anyone knows of a way to export residue lists of contacts from the contact map site I could just compare them that way. ALSO: Anyone know of a way to map defined attributes onto a contact map? Thanks so much! Sincerely, Nicky

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Working with Electron density map
by MOHD HOMAIDUR RAHMAN 03 May '17

03 May '17

Dear Chimera user's I am trying to super impose molecular dynamics calculated density on cryo EM density and then slice densities to visualize each in different colors. I fitted density successfully now during slicing their X Y Z co-ordinate is not matching. The similar analysis were publish in Marzinek et al., 2016, Structure 24, 1–11 August 2, 2016 http://dx.doi.org/10.1016/j.str.2016.05.014 Please see figure 3 for more details and image attached here. Thank Regards Rahman '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' *M*d* H*omaidur* R**ahman *( Research Scholar ) Lab No. 510, Computational Biophysics Lab. Department of Biotechnology Indian Institute of Technology-Madras Chennai-600 036, India *Mobile No = +91- 7845991785 <078459%2091785>* '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''

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Issue with docking in chimera and autodock vina
by Miss Charles 02 May '17

02 May '17

Dear Chimera Team, I have been trying to dock the small molecules pino-stilbene and trans-stilbene to chainA of the estrogen receptor on chimera using autdick vina. Suddenly, with almost no changes to my protocols I have been getting error message 13 permission of pino-stilbene denied or error message 134 permission of trans-stilbene denied. What am I supposed to do to avoid getting that error message? Thank you so much for your time and your help. Sincerely, Alexis Charles

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assistance
by Arthur Szabo 01 May '17

01 May '17

I asked this question several months ago, but rarely have applied the answer. I have a structure that has a long stretch that is disordered. In the structure it appears as a dashed line. If I highlight this section of the total sequence and then apply a color (red) the whole structure is then colored red. So how can I make the dashes slightly larger, and secondly color that stretch of dashes with a particular color without coloring the rest of the molecule? Thank you Arthur G. Szabo

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Re: [Chimera-users] [chimerax-users] animations
by Elaine Meng 01 May '17

01 May '17

> On Mar 6, 2017, at 6:21 AM, Giorgio Luciano <giorgio.luciano(a)gmail.com> wrote: > > Hello ! In the effort to create a more integrated pipeline with vastly used 3d software (I use mainly C4D and modo) is there a way to export animation from chimera in a format that other software can interpret. To make an example. If I wiggle a molecule in chimera, can I export the animation in a format that does not lot this info ? And eventually are there plan to create this feature in chimeraX ? > Giorgio Hi Giorgio, Chimera supports several export formats, see “File… Export Scene” in the menu or the “export” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> However, these are for individual conformations, not for a whole animation, so you’d have to export at each step. Although ChimeraX is in early development, currently the “save” command formats include STL and X3D. The command “save formats” lists all the formats that can be saved. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> These may be subject to the same limitations mentioned in the Chimera manual links above. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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independent rotation of multiple models
by Stefano Luciano Ciurli 01 May '17

01 May '17

Hello, if I have more than one structure in the same session, is there a way to rotate all models together along their respective axes (for example their intrinsic y-axis) without having to do so after selecting each individual model from the model panel? Regards and thanks, Stefano Ciurli

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coloumbic coloring when surface can't be calculated?
by Oliver Clarke 29 Apr '17

29 Apr '17

Hi, I have a structure (well, lots of structures) for which surface calculation fails in Chimera. I can rescue surface calculation using the ‘grid’ option (e.g. surf #0 grid 1), but then I can’t figure out how to apply coulombic coloring to that surface. I could use APBS, but PDB2PQR seems to choke on especially large/complicated structures. Is there any way around this? Would it be possible to export the coloumbic potential as a .dx file and use that for electrostatic surface coloring? Cheers Oli

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Pipes and Planks
by chemocev marker 27 Apr '17

27 Apr '17

Hi Chimera users I am wondering if its possible to assign 2 different color to 2 different helix when use the pipes and planks option in depiction. best Jiri

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file opening problem
by Arthur Szabo 27 Apr '17

27 Apr '17

I had a major problem with my computer - too long a story - Needless to say a computer shop technician had to reinstall my operating system, Windows 7, install Microsoft Office 2016. Of course there were several other programs that had to be reinstalled. So recently I downloaded the latest version of Chimera and have been able to work with PDB files and do all the things that I am used to doing. However, I always save the sessions that I have worked on. They are saved to the desktop C:\users\user\desktop The session files are saved to the desktop. Now comes the problem. When I double click on the file I want [cid:image002.png@01D2A987.C67BFFE0] I get the following message [cid:image001.png@01D2A986.AAC7D360] If I right click on the file then in the menu window click on open with Another window opens with Chimera being the recommended program. Click on OK and the same window as above comes up. This happens even with a .py file that I worked on today. I am puzzled. Ideas will be appreciated. Arthur G. Szabo

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Hey I'm
by Lia Thompson 21 Apr '17

21 Apr '17

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cutting the structure
by Dmitry Semchonok 20 Apr '17

20 Apr '17

Dear colleagues, I did a fit using the predicted models. Now I would like to cut the those parts which don't ft in my EM map. How can I do that? (My EM model has C2 symmetry). Thank you! Sincerely, Dmitry

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[chimerax-users] Chimera bug report submission
by shumaila 19 Apr '17

19 Apr '17

Hi, I want to add oxygen molecule to iron atom in chimera . Kindly help me out how should I add O2 molecule? I tried by Addd bond option but the oxygen molecule is not attached at the desired place. Attached is the protein complex to which I want to attach O2 molecule.Kindly find the attachment. Thank You File attachment: pro time_15000ps.pdb _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

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Re: [Chimera-users] How to install package in chimera python?
by hy liao 19 Apr '17

19 Apr '17

Hi, this was posted here, but where exactly do I invoke the said chimera command? I open chimera with IDLE; a python shell opens with the following Python 2.7.10 (default, May 4 2016, 01:09:35) [GCC 4.6.2] on linux2Type "copyright", "credits" or "license()" for more information.==== No Subprocess ====>>> >>> import chimera>>> I tried what the posting said, but got an error>>> chimera --nogui --script get-pip.pyTraceback (most recent call last): File "<pyshell#3>", line 1, in <module> chimera --nogui --script get-pip.pyNameError: name 'nogui' is not defined Thanks,SL [Chimera-users] How to install package in chimera python? | | | [Chimera-users] How to install package in chimera python? | | |

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SAS exposure question
by Kyle Novakowski 17 Apr '17

17 Apr '17

Hi there, I'm hoping to get some clarification on how to calculate the SAS of a defined set of residues within a molecular structure. I currently have 3 molecular structures in a chimera file and was hoping to compare the SAS of a specific region within 2 mutant proteins relative to that same region of the wildtype protein. Thanks. Kyle -- *Kyle Novakowski, B.Sc.* *Ph.D. Candidate: Medical Science (Infection & Immunity) and Laboratory Manager* *Faculty of Health ScienceDepartment of Pathology and Molecular MedicineMcMaster UniversityE: novakoke(a)mcmaster.ca <novakoke(a)mcmaster.ca>P: 905-525-9140 ext. 21551 <905-525-9140%20ext.%2021551> (work/laboratory)*

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How to show local agreement between cryo-EM map and model
by #AHMED TOFAYEL# 17 Apr '17

17 Apr '17

Dear developers and users, Is it possible to generate/color a cryo-EM map to show local agreement between the map and the model generated using the same map? If I am not wrong, the following figure had accomplished the job but I don't understand how to generate a similar figure for my project: http://d2ni3bh4dzb2ig.cloudfront.net/content/embojnl/28/6/755/DC7/embed/inl… Best regards, Tofayel NTU Singapore

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How DMIN, DMAX, DMEAN is re-calculated if particular portion of MRC is chopped in Chimera
by SALIM SAZZED 13 Apr '17

13 Apr '17

Hello, I am a Ph.D. student of Computer Science department at Old Dominion University, USA. I am using Chimera for my research. Can you please tell me how Chimera calculates *DMIN, DMAX, DMEAN *value of MRC header after chopping a portion of original MRC/MAP*?* My understanding about that- *DMIN: T*he minimum density value of the voxels in the MRC/MAP Cube. *DMAX: T*he maximum density value of the voxels in the MRC/MAP Cube. *DMEAN: *The average density of voxels (add all the voxels density value and divide it by the number of voxels). It will be really helpful if you clarify. Thanks Salim Sazzed

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Gold atoms
by Dominique Matt 13 Apr '17

13 Apr '17

Dear Colleagues, I am an enthusiastic Chimera user. I recently got some structures of gold complexes and noticed that the when using the ball&stick or the sphere representation, gold atoms are too small, while palladium atoms are absolutely OK. What can I do to increase the size of the gold atoms ? Or could you correct this directly in the online program ? I thank you for your help Sincerely, Dominique MATT CNRS Research Director Laboratoire de Chimie Inorganique Moléculaire et Catalyse Institut de Chimie de Strasbourg UMR 7177 CNRS-Université de Strasbourg 4 rue Blaise Pascal, 67070 Strasbourg cedex, France Phone : + 33 3 68 85 17 19 E-mail : dmatt(a)unistra.fr web: http://lcimc.u-strasbg.fr

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saving the session
by Dmitry Semchonok 13 Apr '17

13 Apr '17

Dear colleagues, How to save the session and in the same time all pdb + volume maps in it (all at once)? Thank you Sincerely, Dmitry

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Re: [Chimera-users] Displaying side chains
by Mark J. van Raaij 13 Apr '17

13 Apr '17

As I understand it, Chimera by default displays those side-chains that are near ligands, and assumes that any non-water, non-protein molecule is a ligand. Mark J van RaaijCNB-CSICwwwuser.csic.es/~mjvanraaij -------- Original message --------From: Manish Manish <manishjnu8(a)gmail.com> Date: 13/04/2017 08:55 (GMT+01:00) To: Chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Displaying side chains I have opened PDB ID 1iep using "fetch structure by ID from PDB" through chimera GUI menu. I can see the side chain of few residues such as PHE 317.A and Valine 299.A are automatically displayed. Also by moving the mouse cursor, one can find the distance between different atom types such as between CA and CB. Whereas side chain of many residues such as Lysine 274.A and ASP.276 have not been displayed. My question is how the chimera decides this differential display? Whether chimera directly uses information from PDB files to differentially display the side chains and distance. Or chimera has its own algorithms to decide this. It will be a great help for me if one can point me toward the portions of PDB file or source code from Chimera which does this. I have also attached the image file. Sincerely Manish

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Displaying side chains
by Manish Manish 12 Apr '17

12 Apr '17

I have opened PDB ID 1iep using "fetch structure by ID from PDB" through chimera GUI menu. I can see the side chain of few residues such as PHE 317.A and Valine 299.A are automatically displayed. Also by moving the mouse cursor, one can find the distance between different atom types such as between CA and CB. Whereas side chain of many residues such as Lysine 274.A and ASP.276 have not been displayed. My question is how the chimera decides this differential display? Whether chimera directly uses information from PDB files to differentially display the side chains and distance. Or chimera has its own algorithms to decide this. It will be a great help for me if one can point me toward the portions of PDB file or source code from Chimera which does this. I have also attached the image file. Sincerely Manish

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How to open four volumes simultaneously in Chimera
by Barnali Waugh 12 Apr '17

12 Apr '17

Hi All, I am using Chimera volume viewer to open four volume simultaneously (*.mrc tomogram; 256 256 256 voxel). However, I can open any three volumes at a time. When I try to open the fourth one, it replaces one of the open volumes. I would be thankful for any suggestion. Regards, Barnali.

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given viewing angle
by hy liao 11 Apr '17

11 Apr '17

Hi, How can I specify the elevation and the azimuth angles to view my density map on chimera? In Matplotlib, one can specify the elevation and azimuth, so I was hoping chimera can do something similar that is based on INPUT ANGLES and not having to get involved with tedious transformation matrices and such. Thanks,SL

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