- Chimera-users - RBVI Mailing Lists

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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Radius of Gyration questions
by George Tzotzos 10 Apr '17

10 Apr '17

Taking a reference PDBID 3n7h, I’ve generated for an MD simulation topology and restart files. I’ve loaded on Chimera 3n7h and then the starting frame of the MD simulation. Used the MatchMaker and found perfect superposition of the protein backbone and two ligands (3n7h is #0 and the ligands #0:129.A and #0.132.B I run the radius of gyration script (see attached). I found that the radii of gyration for the ligands in the two models are completely different. #0 center of mass: 12.6543 10.4356 15.4086, radius of gyration: 21.182 #1 center of mass: 42.7381 42.5171 42.6163, radius of gyration: 37.390 I don’t follow why this is so. Any explanation would be most welcome. A second question regards the units of the radii of gyration. Are they Angstrom or nm? Thank you in advance George

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mysteries
by Arthur Szabo 10 Apr '17

10 Apr '17

After several different occurrences at different times of the same thing I finally decided to ask 1) What happened ?2) How can I reverse it? Now the hard part is to try to described what happened. I was working on a figure - it does not seem to depend on its complexity. I had a figure on the screen, ribbons colored, selected amino acids visualized. I did something with the mouse I believe, though it might have been that my finger touched something on the keypad - what happened was that the majority of the structure disappeared. Parts of it were there. I could rotate it and different parts of the structure would come into view and what had just been visible faded away. It was like on rotation portions of the structure would be moving in the plane of the view, but could move out of that plane I was also able to enlarge whatever portion of the image was on the screen. I know that this is difficult to answer because one really has to see the result of whatever I clicked or something else. It is not just a random event. Thanks for any tips. Arthur G Szabo

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question about Chimera
by Richard Collins 10 Apr '17

10 Apr '17

Hello I would like to highlight certain residues of interest in my molecule, preferably by colorizing them in Chimera. Is there a way to do this? Richard Collins Lab Research Project Coordinator Department of Cell Biology Peter Gilgan Centre for Research and Learning Room 199420, bench HH Hospital for Sick Children 686 Bay St. Toronto, ON CANADA M5G 0A4 T (ext): 416 813-8474 T (int): 308474 E: rcollins(a)sickkids.ca ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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FINDING SALT BRIDGE
by Qistina Hassan 08 Apr '17

08 Apr '17

Hi, 1. How to find salt bridges of 50 selected residues in a protein using Chimera? 2. How to measure distances of one residue to another residues to determine if the residues could form salt bridge or not? Thank you, Qistina

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Non-ASCII error
by ARMIN HODAEI 06 Apr '17

06 Apr '17

Dear Chimera users, My PDBhas some extra HOH water molecules in it. when I delete them manually from the pdb I could not open the PDB with Chimera, it gives the error Non-ASCII file. What can I do to fix it? Or is there any way to delete extra HOH atoms from the PDBfile inside the Chimera software? Cheers, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

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building modeller loops refinement
by ARMIN HODAEI 06 Apr '17

06 Apr '17

Dear Chimera Users, I want to use refining loop option to build missing residues for my target protein. First I get the FASTA file structure of protein then I load it into Chimera, after that in the Structure tab I select load structure, then I see the protein. After that Again in the "Structure" tab I select Modeller(loops/refinement). The rest is easy for creating the new structure PDB. But the problem is that I want whole protein to be treated in this refinement, but it only chose one chain, How can I do this for both chains at once? Sincrely, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

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(no subject)
by Kavya Shankar 05 Apr '17

05 Apr '17

Hi, I would like to know how the axis of symmetry is calculated in a dimer as in the precise algorithm that is used to do this. Thank you. Regards, Kavya Shankar

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Defining glycosidic bond of nucleotide objects
by Charles-Alexandre Mattelaer 04 Apr '17

04 Apr '17

Dear Chimera-users I'm currently doing modeling on hexitol nucleic acids and using Chimera to visualize the trajectories. Since the atoms in the hexitol-ring are numbered differently than in the standard ribose, Chimera has some difficulties displaying the correct ribbon (backbone) and slab (bases). I've been able to define my own ribbon style using the Ribbon Style Editor and creating a new ribbon style based on the standard 'nuleic acid' trace and replacing the existing backbone atoms with the corresponding atom names for the non-standard hexitol residues. The main problem is setting a slab object to replace the base atoms. The 'nucleotide objects' settings are based on a glycosidic bond on the C1' of ribose. In HNA the glycosidic bonds are found on C2' of hexitol. I believe this is causing the problem. Additionally, I can add that using the 'ladder'-like objects, a gap between the 'steps' and the backbone occurs. (I've tried setting the base as anchor but to no avail.) I was wondering if there would be a way to redefine the anchor atom of the nucleotide objects? (I searched in the manual but haven't found any ways to redefine the anchor itself.) This would greatly improve visibility of larger oligonucleotides and would help me a lot. Kind regards and thank you in advance Charles-Alexandre Mattelaer

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attributes
by John Mercer, Ph.D. 04 Apr '17

04 Apr '17

Hi, If you have a structure file so large that it needs loaded as two separate files, e. g. a ribosome, is it still the case that a designer attribute file for individual subunits across the whole structure would still be handled by the usual single file attribute mechanism or is something else necessary? Does ChimeraX have an attribute mechanism that is the same as Chimera? Best, -John Mercer Duke University

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another question
by Arthur Szabo 04 Apr '17

04 Apr '17

In the menu used to save images there are two boxes, one for the image width and the other for the image height In the part of the menu below I have set the pixel units for the image width to 5000, with the height being automatically set. These are not the default settings. How can I make them the default settings? In the version of Chimera that I recently downloaded the default settings were 1600 and 796, respectively. The default settings of the former chimera download (my computer had been corrupted so downloaded Chimera again). I can't find anywhere in this image saving menu to change the default settings. Thank you Arthur G. Szabo [cid:image001.png@01D2AD56.F614B2B0]

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[summovie]
by Edoardo D'Imprima 04 Apr '17

04 Apr '17

Hi Oli, one quick question: I noticed the interesting question you posted on the Unblur forum regarding the use of summovie. Did actually worked out the “corrected” version by Tim that should allow you to perform dose weighting and saving the aligned movies? Cheers, Edoardo --------------------------------------------------- Edoardo D'Imprima PhD Student Max Planck Institute of Biophysics Structural Biology Department Max-von-Laue Straße 3 60438 Frankfurt am Main Germany Tel: +49 (0) 69 6303 3015

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(no subject)
by Kavya Shankar 03 Apr '17

03 Apr '17

Hi, I learnt that a dimer axis of symmetry is got by using matchmaker and then the rotation is measured from it. I would like to know the algorithm that is used to calculate the axis of symmetry and how exactly it is done if possible. Thank you. Regards, Kavya Shankar

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active questions
by Arthur Szabo 03 Apr '17

03 Apr '17

I am working with a structure that is largely a protein, and there is a short oligonucleotide associated with it. In the tools menu the sequence of the protein is Chain A and the short oligonucleotide is Chain C. I have shown their respective sequences. I also know how to highlight components of each chain etc. However, there is a short dinucleotide with two thymine residues that are also part of the structure. I was able to select these residues and the two thymine residues in the oligonucleotide by using the SELECT menu: residues: dT. So in total four thymine residues are selected and with the ACTIONS menu I can visualize them. Going to Chain C I can hide the two thymine residues on the longer oligo. How can I select the other two thymine residues that make up the short dinucleotide? One of these thymines is covalently bound to a tyrosine residue through a phosphodiester bond. I can visualize the tyrosine monophosphate through Chain A, and one can see it connected to the relevant thymine residue. But I would like to color the two thymine residues. But I cannot select them or at least I do not know how to select them. I am not an expert at using the command line. Likely there is something there. Again your assistance is sincerely appreciated. Arthur G. Szabo

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Stereo
by Arthur Szabo 03 Apr '17

03 Apr '17

Is it possible to create a stereo view image from a single pdf image. I have colored different segments of the original pdf image. Thanks A G Szabo agszabo(a)outlook.com<mailto:agszabo@outlook.com>

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Residue information failed
by Kunrong Mei 03 Apr '17

03 Apr '17

Hi all, I have met a problem as I used the mouse pointer to show the residue information. Normally, Chimera automatically displays the residue information (residue name, model ID, chain ID, and residue number...) by default when the mouse pointer is placed at a special position. This is ultra helpful when analyzing structures. My problem is that, after I registered to Chimera today, this function lost and it doesn't show the residue information any more. Has anyone met this kind of problem before? Or does anyone know how to fix it? Thanks, Kunrong

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Re: [Chimera-users] Chimera comparing homodimer with flipped homodimer
by Elaine Meng 03 Apr '17

03 Apr '17

Hi Kavya, The “mm” command used to align the structures and “measure rotation” used to report the resulting rotation are fully described in the documentation, see <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> Regards, Elaine > On Apr 3, 2017, at 8:15 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > Hi Elaine, > > I want to know exactly how the axis of symmetry has been calculated for the dimer. What coordinates are used to perform the alignment of the chains? This will really help me out with my research. > > Thank you. > > Regards, > Kavya Shankar > > On Thu, Mar 30, 2017 at 11:25 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Kavya, > I didn’t have a good example handy yesterday, but here is a more specific example, in commands: > > open 5hvp > open 5hvp > mm #0:.a:.b #1:.b:.a pair ss > show :241.b > measure rotation #0 #1 > > This opens PDB 5HVP twice, matches it to itself except pairing A in one with B in the other and vice versa, shows only residue 241 in chain B so that you can see pairing is A-B, and measures axis of rotation between the two copies of 5HVP. The measurement is also reported in the Reply Log (open from Favorites menu): > > Position of 5hvp (#1) relative to 5hvp (#0) coordinates: > Matrix rotation and translation > -0.32555997 0.82635225 -0.45951350 0.78339640 > 0.82635225 0.01248149 -0.56301524 15.06413576 > -0.45951350 -0.56301524 -0.68692152 28.23994571 > Axis 0.58070648 0.71150597 -0.39565040 > Axis point -5.75571422 -0.00000000 18.30836454 > Rotation angle (degrees) 180.00000000 > Shift along axis 0.00000000 > > I also attach an image below. > 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 > > <flip-axis.png> > >> On Mar 29, 2017, at 10:10 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Kavya, >> I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with “measure rotation.” >> Elaine >> >>> On Mar 29, 2017, at 10:05 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: >>> >>> Hi, >>> >>> To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged. >>> >>> Thank you. >>> >>> Regards, >>> Kavya Shankar >>> >>> On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>>> On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: >>>> >>>> Hi, >>>> Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. >>>> Thank you. >>>> Regards, >>>> Kavya Shankar >>> >>> Hi Kavya, >>> Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> >>> >>> After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> >>> >>> 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 >>> >>> P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues >>> >>> >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> > >

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I figured it out
by Arthur Szabo 03 Apr '17

03 Apr '17

Thanks A G Szabo

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question
by Arthur Szabo 03 Apr '17

03 Apr '17

Previously I had stumbled on how to change the shading on ribbon structures. The default has shading, but with the default setting the colors of the ribbons are shaded and this shading changes when one rotates the structure. Kindly remind me how I can alter the shading of the ribbons. Presumably the settings are through the Tools section. Thank you Arthur G. Szabo

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UCSF Chimera installation - library ubuntu 16.04
by Vasileios Kargas 01 Apr '17

01 Apr '17

Dear Chimera developer, I am trying to install UCSF-Chimera and I have an issue with the libXext.so.6 library I 've installed the library package that contains this and I can locate it at: /usr/lib/x86_64-linux-gnu However I get this error: vk335@hunter:~$ ./chimera-1.11.2-linux.bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/home/vk335' inflating: chimera_install_L6RcLz/installer inflating: chimera_install_L6RcLz/chimera.bin Enter install location: ~/UCSF-Chimera-1.11.2 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /home/vk335/UCSF-Chimera-1.11.2' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org) Install desktop menu and icon? yes Traceback (most recent call last): File "/home/vk335/UCSF-Chimera-1.11.2/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/home/vk335/UCSF-Chimera-1.11.2/share/chimeraInit.py", line 603, in init import chimera File "/home/vk335/UCSF-Chimera-1.11.2/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: libXext.so.6: wrong ELF class: ELFCLASS64 ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_L6RcLz' Installation is done; press return. If I install it in the default Chimera directory without desktop icon it proceeds to the installation but I can not run chimera - taking the same error: ImportError: libXext.so.6: cannot open shared object file: No such file or directory Any suggestions how to solve it? Should this be linked to somewhere else in order the Chimera to find it? Thank you very much in advance. Best regards, Vas

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Residue information failed
by Kunrong Mei 31 Mar '17

31 Mar '17

Hi all, I have met a problem as I used the mouse pointer to show the residue information. Normally, Chimera automatically displays the residue information (residue name, model ID, chain ID, and residue number...) by default when the mouse pointer is placed at a special position. This is ultra helpful when analyzing structures. My problem is that, after I registered to Chimera today, this function lost and it doesn't show the residue information any more. Has anyone met this kind of problem before? Or does anyone know how to fix it? Thanks, Kunrong

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Add secondary structure or symbols to headers of multalign viewer (sequence）
by 陈柳青 31 Mar '17

31 Mar '17

Dear all ! Is it possible to add secondary structure or symbols to multalign viewer headers? I know can use "alignment header definition files" do this , but i don't know how to make the definition files, anyone can give me these files or tell me how to do it? thanks! Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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Re: [Chimera-users] Chimera comparing homodimer with flipped homodimer
by Elaine Meng 31 Mar '17

31 Mar '17

Hi Kavya, Your “mm” command matched A to A and B to B, so there was no rotation between the two copies. It was hard to see if you entered exactly the same “mm” command as in my example (needs to be exactly the same, with colon : dot . and no extra spaces), but it you did, maybe you are using an old version of Chimera that interpreted the command differently. I only started Chimera and entered those 5 exact commands to get the result I showed. Tested in Chimera version 1.11.2 and recent 1.12 daily build. Elaine > On Mar 31, 2017, at 6:55 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > I have attached the screenshots. I have opened the same pdb file. > > Thank you. > > Regards, > Kavya Shankar > > On Fri, Mar 31, 2017 at 9:37 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > Thank you so much. When I do this I get a rotation angle of 0 degrees. Am I doing something wrong? > > Thank you. > > Regards, > Kavya Shankar > > On Thu, Mar 30, 2017 at 11:25 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Kavya, > I didn’t have a good example handy yesterday, but here is a more specific example, in commands: > > open 5hvp > open 5hvp > mm #0:.a:.b #1:.b:.a pair ss > show :241.b > measure rotation #0 #1 > > This opens PDB 5HVP twice, matches it to itself except pairing A in one with B in the other and vice versa, shows only residue 241 in chain B so that you can see pairing is A-B, and measures axis of rotation between the two copies of 5HVP. The measurement is also reported in the Reply Log (open from Favorites menu): > > Position of 5hvp (#1) relative to 5hvp (#0) coordinates: > Matrix rotation and translation > -0.32555997 0.82635225 -0.45951350 0.78339640 > 0.82635225 0.01248149 -0.56301524 15.06413576 > -0.45951350 -0.56301524 -0.68692152 28.23994571 > Axis 0.58070648 0.71150597 -0.39565040 > Axis point -5.75571422 -0.00000000 18.30836454 > Rotation angle (degrees) 180.00000000 > Shift along axis 0.00000000 > > I also attach an image below. > 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 > > <flip-axis.png> > >> On Mar 29, 2017, at 10:10 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Kavya, >> I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with “measure rotation.” >> Elaine >> >>> On Mar 29, 2017, at 10:05 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: >>> >>> Hi, >>> >>> To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged. >>> >>> Thank you. >>> >>> Regards, >>> Kavya Shankar >>> >>> On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>>> On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: >>>> >>>> Hi, >>>> Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. >>>> Thank you. >>>> Regards, >>>> Kavya Shankar >>> >>> Hi Kavya, >>> Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> >>> >>> After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> >>> >>> 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 >>> >>> P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues >>> >>> >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> > > > > <step1.png><step3.png><step4.png><Step2.png>

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Get side-view model? Or, height of clipping planes?
by Abba E Leffler 30 Mar '17

30 Mar '17

Dear All: I'm making a figure showing a ligand bound deeply in a cryptic pocket of a protein. To show it best, I've oriented the complex so that I am looking down directly on to it. Then, I adjust the hither and yon clipping planes to bracket the ligand so you get a cross-section through the protein containing the ligand and binding site. Is there a way to get the heights of the clipping planes, and then draw planes representing them? Better yet, can the image in the side view planning somehow be saved to high resolution with the yellow clipping planes indicated, but perhaps without the red field of view lines? Basically, for the figure I need some way of showing the viewer where the clipping planes are on the protein. This is critical because viewers need to know in a broad sense where the ligand is located. Thank you for your help

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Collaboratory
by Theodor Emil Gescher 30 Mar '17

30 Mar '17

Dear Chimeramasters and mistresses, I'm having some serious difficulty starting a collaboratory session in UCSF Chimera on Mac. I have tried both an outdated version (build 40427) and the latest (build 41367). I can't find any mention within the program of collaboratory, and because of the Mac OS I don't think it's possible to start a hub from outside Chimera. Is there an additional extension that needs to be downloaded and installed seperately? Yours studiously, Theo

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Re: [Chimera-users] [chimera-dev] (no subject)
by Elaine Meng 30 Mar '17

30 Mar '17

Hi Kavya, I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with “measure rotation.” Elaine > On Mar 29, 2017, at 10:05 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > Hi, > > To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged. > > Thank you. > > Regards, > Kavya Shankar > > On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > > > Hi, > > Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. > > Thank you. > > Regards, > > Kavya Shankar > > Hi Kavya, > Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> > > After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> > > 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 > > P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Scripting commands for existing morph
by Cristina Paulino 29 Mar '17

29 Mar '17

Dear all, I would like to create a movie from an existing morph between two pdb coordinates. I was able to create a movie via the GUI as described in the manual. However I prefer to use scripts as it allows me to control every single step. I would like to be able to define exactly which frames should be shown when. For example, I would like to define in a script that it should wait at endpoint one (first structure) for x number of movie frames. Then interpolate (morph) to the other endpoint (second structure) for x number of movie frames and then wait again for a specified number of movie frames. Or even more complicated rotate the molecule or superimpose something else while it is interpolating/morphing between the pdb coordinates. Can anyone help me out? I couldn't find any good description for this. Many thanks in advance Cristina

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Re: [Chimera-users] [chimera-dev] (no subject)
by Elaine Meng 29 Mar '17

29 Mar '17

> On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > Hi, > Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. > Thank you. > Regards, > Kavya Shankar Hi Kavya, Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> 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 P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues

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ChimeraX Alpha release
by Eric Pettersen 28 Mar '17

28 Mar '17

Hi all, We have released an alpha version of ChimeraX. While it still lacks many features, it has enough useful new and fun features that you might want to take it out for a spin even if it doesn’t prove ready to be your day-to-day workhorse yet. Hope you like it! Home page: http://www.cgl.ucsf.edu/chimerax/ <http://www.cgl.ucsf.edu/chimerax/> Download page: http://www.cgl.ucsf.edu/chimerax/download.html <http://www.cgl.ucsf.edu/chimerax/download.html> —Eric Eric Pettersen UCSF Computer Graphics Lab

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来自"高振飞" <16110440015@fudan.edu.cn>的邮件
by 高振飞 28 Mar '17

28 Mar '17

Dear professor: I'm a student from Fudan University, I want use the software -- chimera. But I can't download it, can you send it to me by using E-mail? thank you very much. with my best regards yours sincerely Zhenfei Gao -- Zhenfei Gao(高振飞) Department of Macromolecular Science Fudan University 310 Yuejin Hall 220 Handan Rd. Shanghai, China 200433 M: +86-18516637266 QQ: 7693692

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Create an entire virus from Octant
by Li, Zongli 27 Mar '17

27 Mar '17

Hello, I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? Thanks, Zongli

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