- 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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MD analysis outputting to file
by Neha Gandhi 23 Mar '17

23 Mar '17

Dear Chimera support, I want to calculate the centroid of the sugar ring and the distance from the centroid to another atom of amino-acid. I know this can be done using the Structure analysis tools in Chimera. I want to use distance command in the MD ensemble analysis and output it to the analysis to the text file. How can I write output per frame to a text file in Chimera? Your insight is appreciated. -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate

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Ensemble models
by Mohamed Noor 20 Mar '17

20 Mar '17

Hello. I have an ensemble of models from phenix.ensemble_refinement. I notice that Chimera automatically loads the models and displays only a subset of atoms as "atoms/bonds". Can I save this as a preset while changing other settings manually so that I can go back to the automatic preset if I make a mistake somewhere? Secondly, is it possible for Chimera to calculate rmsf of each residue and output the values to a CSV file? I would like to replot them in Excel. Thanks. Mohamed

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Looking at docked data with the receptor shows as surface
by Jonathan Y Wang 20 Mar '17

20 Mar '17

To whom it may concern, Hi! I recently docked a ligand onto a receptor using the AutodockVina tool and when I opened the data the ligand seemed to be placed in the middle of the trimer. I showed the receptor as surface and it seems as if the ligand is too big to fit inside any of the holes surrounding the trimer, but somehow it has placed itself inside. I additionally opened it using PyMol to double check the file, but it also seems too small to fit inside any of the holes. My inquiry is this: Does AutodockVina take into account surface projections when performing docking? Thank you so much for your time, Jonathan Wang

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Getting names of selected atoms and renaming
by Vladyslav Dziuba 17 Mar '17

17 Mar '17

Dear Sir or Madam, I have some difficulties with using ORCA and UCSF Chimera together. Let me describe my problem first. I need to freeze some atoms (actually, a lot of atoms) in my calculations (geometry optimization), e.g. make their coordinates constant. To do that I need to specify numbers of atoms from xyz file, which is obtained from pdb-file. The problem is that for every atom in pdb-file OpenBabel generates a new number (for example H27 may become 100th atom in xyz file), so that specifying atoms that must be frozen becomes much more complicated. Given that, I'd like to ask to help me find answer on some questions: 1. How can I rename atoms? It would greatly help me identificate atoms that must be frozen. Can I rename only all selected atoms? 2.Can I modify names of selected atoms? 3. How can I get list of numbers of selected atoms? For instance I've chosen some aminoacids residues and I want to get names or numbers of all atoms chosen. Because if I one wants to get a list of atoms in xyz file, he needs names or numbers of atoms in pdb file, but the last ones are disordered. Manual atom picking and comparison in pdb- and xyz-files is very time-consuming. UCSF Chimera is a truly powerful program so I believe there must exist an elegant solution to my problem. Hope to receive a letter from you soon. Thanks in advance! Best regards, Vladislav Dziuba

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Re: [Chimera-users] Smoothing and binning volume data
by Tom Goddard 16 Mar '17

16 Mar '17

Set "step 1” above the histogram in the Volume Viewer window to display the full resolution of the data. If step is 2 that means only every other density map grid point is shown along each axis. The step gets set automatically to values greater than 1 when the map is large to avoid slowing down the graphics (rotating, zooming…). The initial step it chooses is controlled by the volume viewer menu Features / Data Display Options… , “Adjust step to show at most [N] Mvoxels”. Tom > On Mar 16, 2017, at 11:41 AM, Andrea Fera <andrea.fera(a)gmail.com> wrote: > > Hi Tom! > > Tank you for your information. > Let me try to explain better what I asked. > > What I seem to have revised is that the virtual sections of my maps have a much higher resolution than the rendered images by Chimera. > This should be because, evidently, I didn't understand yet how to control the default smoothing and/or binning in the volume viewer, of which I used until now the default value. > Can you tell me how to do, or what to vary? > > Thank you for the tip about using two colors in the rendering. Going to try immediately. > Thanks, > Andrea > > > > > > > > > > -- > Andrea Fera, PhD – [Senior Research Scientist] > Advanced Molecular Imaging ; DUNS 824-XXX-XXX > Unit for Cytoskeletal Dynamics , NICHD, National Institute of Health > Email: andrea.fera(a)gmail.com <mailto:andrea.fera@gmail.com> > > > On 16 March 2017 at 14:28, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Not sure what you are asking. You can do Gaussian filtering to smooth a map, or binning to average 2x2x2 voxels together producing a smaller smoother map using the Volume Filter tool. > > To color “solid” style map rendering different colors at different data values click the nodes on the yellow line on the volume viewer histogram and then click the color button below the histogram to change the colors. > > Tom > > >> On Mar 15, 2017, at 7:49 PM, Andrea Fera wrote: >> >> Dear Tom, >> >> How are you? >> I am using Chimera more and more recently, and I have come to the point where I need to be able to control the amount of smoothing and/or binning that it inserts passing from the virtual sections to the rendering. >> >> Could you please send me some information on where I could look for this information? >> >> Another, related, thing. Is there a way that I can color in red or brighter color the part of the rendering including voxels below (or above) a certain threshold value? >> >> I hope that I am not asking anything too strange. >> Especially the first thing would help me greatly. >> >> Thank you, >> Andrea >> >> -- >> Andrea Fera, PhD – [Senior Research Scientist] >> Advanced Molecular Imaging ; DUNS 824-XXX-XXX >> Unit for Cytoskeletal Dynamics , NICHD, National Institute of Health

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Smoothing and binning volume data
by Tom Goddard 16 Mar '17

16 Mar '17

Not sure what you are asking. You can do Gaussian filtering to smooth a map, or binning to average 2x2x2 voxels together producing a smaller smoother map using the Volume Filter tool. To color “solid” style map rendering different colors at different data values click the nodes on the yellow line on the volume viewer histogram and then click the color button below the histogram to change the colors. Tom > On Mar 15, 2017, at 7:49 PM, Andrea Fera wrote: > > Dear Tom, > > How are you? > I am using Chimera more and more recently, and I have come to the point where I need to be able to control the amount of smoothing and/or binning that it inserts passing from the virtual sections to the rendering. > > Could you please send me some information on where I could look for this information? > > Another, related, thing. Is there a way that I can color in red or brighter color the part of the rendering including voxels below (or above) a certain threshold value? > > I hope that I am not asking anything too strange. > Especially the first thing would help me greatly. > > Thank you, > Andrea > > -- > Andrea Fera, PhD – [Senior Research Scientist] > Advanced Molecular Imaging ; DUNS 824-XXX-XXX > Unit for Cytoskeletal Dynamics , NICHD, National Institute of Health >

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VPAT (Voluntary Product Accessibility Template)
by Ashdale, Martin 16 Mar '17

16 Mar '17

Good Morning, I am looking into using your product with my AP Biology classes and I need to get approval to download your software. The IT Department would like the VPAT (Voluntary Product Accessibility Template) so that I can submit it for approval. If you have it available could you please send it to me. I appreciate your time and look forward to teaching with your product. Thanks, Martin Ashdale Biology Teacher Harford Technical High School 200 Thomas Run Road Bel Air, MD 21015 (410) 638-3804

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Selecting certain atoms with exception
by Kelvin Lau 14 Mar '17

14 Mar '17

Dear Chimera users, I'm trying to do the following: -select all the atoms of a single residue (trp) -except for one (residue number 285) I am not sure how to use a negation command to leave out only 285. Any ideas? Cheers Kelvin -- Kelvin Lau Structural Plant Biology Laboratory Department of Botany and Plant Biology Science III University of Geneva 30 Quai E. Ansermet 1211 Geneva Switzerland Email: kelvin.lau(a)unige.ch Phone: +41 22 379 3026

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possible Chimera bug - saving bonds in MOL2 format
by Marek Maly 13 Mar '17

13 Mar '17

Hello, it seems that Chimera (1.11.2) has problem to save some bonds in MOL2 format. If you open attached file "source.mol2" , Chimera reads/show perfectly all the bonds including those where is "Ru" atom present, but when you save it in MOL2 format in Chimera (see attached file "Chimera_MOL2.mol2"), then all the "Ru-x" bonds are omitted and naturally if you open this "Chimera MOL2" file in Chimera no "Ru-x" bonds are shown. Interestingly, if the original MOL2 file "source.mol2" is opened in Chimera and then saved in PDB format ("Chimera_PDB.pdb"), all bonds are written and so if this PDB file is opened in Chimera all bonds are visualized. Would be nice if the perfect bond preservation which works in MOL2->PDB case worked also in MOL2->MOL2 case. Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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chimera 1.11.2 interlaced stereo
by Jean-Marie WURTZ 13 Mar '17

13 Mar '17

Hi, I am a long time user of chimera and had never such a problem. I would like to use the interlaced stereo with a zalman monitor but I get the following error : Unable to turn on stereo viewing (Unable to find hardware stereo support (couldn't choose pixel format Couldn't configure togl widget)). I must say that VMD stereo is working. But I understood also that both programs work differently with regard to steero. My configuration: Dell M4500 precision Windows 10 Quadro FX 1800M driver 342.01 What can I do to get it working? Thanks for your help. Best regards -- Jean-Marie Wurtz Professeur de Bioinformatique Tél : +33 (0)3 69 48 51 04 Fax : +33 (0)3 88 65 32 76 jm.wurtz(a)unistra.fr<mailto:jm.wurtz@unistra.fr> wurtz(a)igbmc.fr<mailto:wurtz@igbmc.fr> IGBMC-CEBGS Département de Biologie et de Génomique Structurales Equipe de Biologie Structurales de Cibles Epigénétiques Parc d'Innovation, 1 rue Laurent Fries BP 10142 F - 67404 ILLKIRCH CEDEX http://archive.igbmc.fr/recherche/Prog_ISB/Eq_JCava/index.html [UniversitÃ© de Strasbourg]<http://www.unistra.fr>

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Re: [Chimera-users] [chimerax-users] animations
by Elaine Meng 12 Mar '17

12 Mar '17

Hi Giorgio, You would still have to use the “export” command that exports one file at a time, but it can be run at every frame by combining it with the “perframe” command. For example, in Chimera the following (should be all one line even though the Mail app may break it up): perframe "export ~/temp/$1.x3d" zero 2; play wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 50; wait 50; ~perframe …where ~/temp is a directory that already exists, will make files 01.x3d …. 50.x3d in that directory. In ChimeraX, there is a “perframe” command and “save” to export X3D, but no “play wiggle” command. <http://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> 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 > On Mar 9, 2017, at 11:44 AM, Giorgio Luciano <giorgio.luciano(a)gmail.com> wrote: > > Thanks for the info and sorry for my late reply. I generally export using x3d what I was thinking about is, how can someone export the single model for an animation ? As an example if I make wiggle a molecule play (wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 200 ) may I export in batch the molecules for the single frame ? > Any help will be greatly appreciated :) >

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Re: [Chimera-users] question on MAV
by Elaine Meng 10 Mar '17

10 Mar '17

> On Mar 10, 2017, at 12:59 AM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Elaine, > I would appreciate it if you could let me know how to make specific residues bold in MAV. Not all of them but only specific residues. > Thank you so much for your help. > Jackie Vitali Hi Jackie, Sorry, MAV (Multalign Viewer) does not have the option to use different fonts for different residues… as you probably saw, the Preferences… Appearance options only change the font of all the residues. To highlight specific residues in MAV, you could draw a box around them to make a region, and then using the Region Browser, change region background color and/or outline color, <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> ...or you could create a custom header to put a symbol above the column. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Best, 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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replay morph created with vop morph?
by Oliver Clarke 09 Mar '17

09 Mar '17

Hi all, Is there any way to replay a morph created using vop morph? Or to change the representation of the map prior to playing? I have a sequential morph of multiple different conformations (which I can’t make with the morph map GUI tool), but I would like to change the display of the map before creating a movie (which vop morph does not seem to allow). Example command: vop morph #1,2,3,4,5 interpolateColors false constantVolume true Cheers Oli

2 3

Can you delete a residue attribute?
by Mungo Carstairs (Staff) 08 Mar '17

08 Mar '17

Hi, I would like to be able to set and remove residue attributes (using Chimera commands over the REST service). Setting is fine, but removing seems to be limited to changing the value to either an empty string or None. https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html Is there any way to actually remove attributes after they have been set on residues? Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

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running DockPrep and Vina from python
by Lee A.G. 06 Mar '17

06 Mar '17

Hello I have been trying to run DockPrep and Vina from a python script to generate a pdbqt file to be used in subsequent Vina docking studies (with a config file). What I have at present is the following (I have edited DockPrep\_init_.py to make nogui=True ; the receptor has been loaded as model #0, and the ligand as model #1) from DockPrep import prep model=Midas.open('4iaq.pdb') prep(model) modelname='4iaq.mol2' from WriteMol2 import writeMol2 writeMol2(model, modelname) #VinaRun OutFileName='C:/Autodock/5HT/4iaq/Test2/4iaq' rc("vina docking receptor #0 ligand #1 output " + OutFileName + " prep true wait true") The generated 4iaq.receptor.pdb file contains the protein as modified by DockPrep, without the charges etc, and with the original PDB residue numbering. The 4iaq.receptor.pdbqt file contains the unmodified protein with charges etc, and with the original PDB residue numbering. The 4iaq.mol2 file contains the modified protein, with charges etc, but with residue numbering modified to start at 1. What I hoped to produce was a 4iaq.receptor.pdbqt file containing the modified protein with charges etc, and with the original PDB residue numbering, and this is just about the only thing I don't have. Any help would be very gratefully received. Anthony

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Re: [Chimera-users] Moving icosahedron to model
by Tom Goddard 03 Mar '17

03 Mar '17

Hi David, I could not tell from the image if the surface was from a PDB or a density map. If it is from a PDB then the coordinate system is based on the crystal packing. That means the origin could be anywhere and the rotation can be arbitrary. So then getting an icosahedron outline aligned can be a real pain, although sometimes the crystal packing has a virus centered at 0,0,0 and a standard orientation like 2-fold symmetry axes along x,y,z (e.g. 2bbv). In the hard cases there are various tricks. For instance use the shape command to center the icosahedron on the atomic model (e.g. "shape icos radius 200 center #0 mesh true div 1") Tom > On Mar 3, 2017, at 11:12 AM, David Bhella wrote: > > Hi Tom > I think Kok Lian's structure is a surface from a PDB file created using multiscale models. I feel the origin and symmetry should be available from the PDB file in some way, but I too have struggled with getting icosahedral structures from PDB into a sensible orientation. > > Sent from my iPhone > >> On 3 Mar 2017, at 18:38, Tom Goddard wrote: >> >> Is your virus surface from a density map? If so it probably has the origin set in such a way that the center of the virus is not 0,0,0 while the center of your icosahedron outline is 0,0,0. To remedy that you would change the origin of the map in Volume Viewer, menu Features / Coordinates set origin index to for example 128 if the map size is 256 grid points. That is likely to put the map origin at the center of the virus particle. >> >> Tom >> >>> On Mar 3, 2017, at 1:18 AM, KL Ho wrote: >>> >>> Dear All, >>> I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you. >>> >>> Best wishes, >>> KokLian >>> <image1.png>_______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

1 0

Moving icosahedron to model
by KL Ho 03 Mar '17

03 Mar '17

Dear All, I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you. Best wishes, KokLian

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move icosahedron surface to a model
by Ho Kok Lian 03 Mar '17

03 Mar '17

Hi All, I am a beginner of chimera. Sorry for the simple question. May I know how to move the icosahedron surface (see attached figure) to the model according to its symmetry? Many thanks. Kok-Lian

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Segmentation fault when issuing chimera command
by Hui Shi 01 Mar '17

01 Mar '17

Hi there, Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here. I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed. But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version. I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work. Any suggestions on how to deal with problem? Thanks a lot in advance! Hui

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Re: [Chimera-users] Error opening larger proteins
by Eric Pettersen 01 Mar '17

01 Mar '17

Hi Catherine, It turns out that the singular value decomposition function that Chimera uses to get the eigenvectors and eigenvalues for the plane computation uses a lot of memory if you use a large number of atoms to define the plane (or axis for that matter). There is a non-default setting for that svd function that I just discovered that uses much less memory and seems to produce identical results, so I have switched Chimera to using that setting. The switched version will be available as the next daily build. Look for daily builds dated March 1 or newer. Also, you may be able to get your current version to work if you simply use less atoms to compute the plane. The selection you were using — “sel :.A,.B,.C,.D” — will not only select all the protein but also all the waters, ligands, and ions. Perhaps just “sel protein” would be more appropriate (depending on what you want the plane for) and might work in your current build. —Eric Eric Pettersen UCSF Computer Graphics Lab > On Mar 1, 2017, at 9:09 AM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > Hello, > > When I try to open large protein in Chimera, and try to define plane for the protein, It is throwing me an error saying "Memory Error". Can you please help me with this error? > > Note: Attached a snapshot of the error. > > Thanks, > Catherine > <Screenshot.png>

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MMTK/Chimera interface error
by ADIL AHIRI 27 Feb '17

27 Feb '17

hi everyone, I work on the modeling of the effect of phosphorylation on segment peptide. I had a problem when i use this interface MMTK/Chimera interface because when i use a doubly phosphorylated peptide i have this message: KeyError: 'No parameters for bond Atom 0.ARG_12__0_0_1_286__B.peptide.C (atom type C) - Atom 0.TPO_13__0_0_1_287__B.N (atom type n)' You will find attached a sample problem source file. Is there anyone who can help me solve this problem please. Codially

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coloring a surface based on proximity to a point
by Hamish Todd 27 Feb '17

27 Feb '17

Hey everyone. So I have a coloration for a set of surfaces that is very close to what I want. I want to make a change to it though: I want parts of the surfaces close to certain points to change their color. And I want the rest of the surface to be unchanged from the current coloring. Is this possible? Would be much obliged if any advice could be offered! Hamish Todd -- @hamish_todd

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starting pre-existing morph
by Elena Zehr 27 Feb '17

27 Feb '17

Hi, I have a chimera session with a morph between two structures. I wish to start playing the morph from the command line. What would be the argument for this? Many thanks, Elena

2 1

FW: Commercial Chimera
by Williams, Joanne 27 Feb '17

27 Feb '17

On 2/26/17, 10:29 PM, "Agnieszka Dobinska" <adobinska(a)okinawa-pt.com> wrote: >Dear Sir/Ma'am, > >I have a questions regarding commercial use of Chimera. > >Provided that we are commercial users of Chimera (subject to commercial >agreement), and we are creating files using Chimera, does our customers >need to >have the commercial Chimera to browse the files we have sent them, or >they can >use the free one. > >Best regards, >Agnieszka Dobinska > >~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~ >Agnieszka Dobinska >Sales & Marketing Manager >Okinawa Protein Tomography Ltd. >1919-1 Tancha, Onna Village, Kunigami, >Okinawa Prefecture 904-0411 Japan >Tel. +81-98-982-3359 　FAX +81-98-982-3361 >Skype: okpt.sales >http://www.okinawa-pt.com >~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~ > > >

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models disappear after using "split"
by Leschziner, Andres 24 Feb '17

24 Feb '17

Hi, I used “split” to break a model into its 19 component chains. The chains appear in the Model Panel and are marked as “Shown" but are gone from the display. Everything else I have in the session works normally but nothing I have tried so far makes the split models show up. Any help solving this would be much appreciated! -Andres ______________________________________ Andres Leschziner Professor Department of Cellular and Molecular Medicine and Section of Molecular Biology, Division of Biological Sciences University of California, San Diego Leichtag 483 9500 Gilman Dr. La Jolla, CA 92093-0694 aleschziner(a)ucsd.edu<mailto:aleschziner@ucsd.edu> 858-246-1252 ______________________________________

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density maps
by Antonio Coluccia 24 Feb '17

24 Feb '17

Dear all I have computed a molecular dynamic and i would like to have the density maps for some molecules of the system. I tried with isopropanol molecules and I obtain the map for each atom type: H; C3; O3, CH and another called density map_iso.mcr My concerns are about the last one map. What does it mean? Is it the map for the whole molecules, while the other maps are for each atom type? Is it possible to analyse the maps contemporary thus I am able to visualize just three per time? Any help will be really appreciated. Antonio Antonio Coluccia Ph.D. Department of Chemistry and Drugs Technology Rome 00185 Piazzale Aldo Moro 5 antonio.coluccia(a)uniroma1.it

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Two questions about a model
by Steven D. Aird 23 Feb '17

23 Feb '17

Dear Elaine, I have a couple of questions about the attached model set. These are catalytic residues and residues forming the hydrophobic channel in four phospholipases. The first question almost seems silly. I decided to experiment with the label command and labeled one residue in the lower right enzyme of the figure. I didn’t like the position or form of the label. I couldn’t get rid of the “.A” on the label and when I tried to delete the entire label, I couldn’t. Selecting the residue and then selecting LABEL>Off, doesn’t work. In all four plots there are fine lines that resemble the earlier ribspline problem, but they are not resolved by "ribspline cardinal.” Any idea as to what these are? As always, thank you for your tutelage. I am making steady progress. Sincerely yours, Steve Steven D. Aird Technical Editor Faculty Affairs Division Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp

2 1

Windows & dialogues outside the screen
by Hernando J Sosa 22 Feb '17

22 Feb '17

Dear UCSF-Chimera, I have noticed (perhaps since I upgraded, currently running v1.11.2) that when opening new windows/dialogues many times they pop-up outside the screen. This seems to happen more often when many windows are opened simultaneously. It is more of a nuisance than a real problem but it can get annoying having to continuously search for those elusive windows. So I wonder if there is a way to fix this behavior (e.g. to force newly opened windows to always appear on top and within the screen boundaries) . I am running Windows 64 UCSF-Chimera version 1.11.2 on a Windows 7 and Windows 10 machine (problem occurs in both computers) Thanks Hernando

2 1

Converting a part of a molecule in pdb to xyz format
by Vladyslav Dziuba 22 Feb '17

22 Feb '17

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Re: [Chimera-users] MatchMaker working beautifully, and Transform Coordinates definitely does move things....
by Elaine Meng 17 Feb '17

17 Feb '17

> On Feb 17, 2017, at 3:47 AM, Steven D. Aird <steven.d.aird(a)gmail.com> wrote: > > Dear Elaine, > I apologize for the deluge of Email, but within minutes of writing you, I figured out how to use MatchMaker to align two ribbon models of interest. Again, it’s simple and elegant. > > I also found the transform coordinates command, which I had missed earlier. That enables me to move one of the models relative to the other. But moving a model is tricky because it seems impossible to know what relationship the two models have with a Cartesian coordinate system. I had assumed that x, y, and z would be relative to the monitor surface, but that is not the case. > > Is there a more intuitive way to move molecules while maintaining the same relative orientation? > Thanks very much for your help. > Sincerely yours, > Steve Hi Steve, Thanks for the kind words! After you use Matchmaker (or matrixcopy or the mouse or some other method) to position structures relative to one another, you shouldn’t have to do anything special… now when you move “everything” they will still retain their relationships. I.e. you can rotate and translate everything with the mouse and structures will still be superimposed, docked, etc. as they were after you moved them separately. Personally I never use the Transform Coordinates tool and I don’t understand why you wanted to use it. You can translate and rotate relative to screen coordinates (X horizontal Y vertical Z normal to screen) using commands “move” and “turn” and these can apply to everything or only certain models (they have a “models” keyword option). You can also move only certain models with the mouse by activating/deactivating (freezing) them with the “A” checkboxes in the Model Panel, which can be opened from the Favorites menu. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> Also, for future reference, we really prefer questions to be sent to chimera-users (CC’d here) so that other people can benefit from the answers, and also give you better support if I don’t know the answer or am away. 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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Chimera refuses to attach short peptide to protein C-terminus
by Steven Douglas Aird 16 Feb '17

16 Feb '17

Dear Sirs: I am modeling novel proteins on homologous structures from other organisms using SWISS-MODEL. After the model is completed I import the PDB file into Chimera to form disulfides and to produce publication quality graphics. I thought all was going well until I discovered that SWISS-MODEL was actually truncating one or both termini of my target sequences by 1-5 residues. In one case, I created the missing C-terminal tripeptide using MacPyMol, but MacPyMol will not not add the tripeptide to the C-terminus, because it is designed only to create intramolecular bonds. So I imported the protein and the tripeptide into Chimera. I selected the C-terminal oxygen of the protein and the N-terminal nitrogen of the tripeptide and tried to create a peptide bond using Build Structure>Adjust Bonds>Add Bond. Chimera claims that only one atom is selected, but in fact, both are selected. I do not want to try to build a tripeptide one atom at a time. Is there any way to do ligate the tripeptide? Thanks very much! Steve Aird Steven D. Aird Technical Editor Faculty Affairs Division Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp<mailto:steven.aird@oist.jp>

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Visualisation of membrane proteins
by James Starlight 15 Feb '17

15 Feb '17

Dear Chimera users! I am on the preparation of interactive molecular visualisation, focusing on ligand-binding representation in GPCRs system. Working with the X-ray structures of the receptor bound with the ligand, I wonder to ask some suggestions: 1 - I need to move ligand from ligand binding pocket burried within receptor (as on default in the X-ray structure) towards the selected position outside of it - e.g in case where I would like to depict "vestibule" for the ligand enterance. As I understood for the realisation I should to select ligand within the current model and than to copy it to new model (layer) which then should be moved against the structure, shouldn't it? 2- Is it possible using some Chimera tool to indicate "approximate" membrane plane assuming that GPCRs structure is shown in latteral perspective? Thanks so much for the help! James

2 3

electrostatic surface
by chemocev marker 13 Feb '17

13 Feb '17

Hi I am calculating the electrostatic surface of the protein that has a peptide bound inside the catalytic camber. There are two ways to calculate, either i can split the molecule in indivual chain and calculate their surface indivdually and run the APBS server for the electrostatic potential, or i can do it use the surfcat command. Both of them works but the results are different. To me the results are more logical by splitting the molecule in indivual chain, but u am not sure if its right to do that specially when you want to measure the electrostatic potential. What is your opinion. best Jiri

2 1

Write out coordinates for Centre of mass
by Soumya Govinda Remesh 10 Feb '17

10 Feb '17

Hello, I wanted to know if I can write out the coordinates for the object placed at the 'centre of mass' of selected atoms from a domain. I used the following command to place a marker at the location of interest. - measure center sel mark true 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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Re: [Chimera-users] CHIMERA ERROR
by Eric Pettersen 10 Feb '17

10 Feb '17

> On Feb 8, 2017, at 9:07 AM, Stellamaris Sotomayor Burneo <stellamaris_sb(a)yahoo.com> wrote: > > > Dear Dr. Eric, > > My name is Stellamaris. I am an undergraduate student from Ecuador. There is almost no one working in molecular docking in my country so far. So, it is very difficult to find somebody to ask for help. I would like to kindly ask you a question about the problem I am having with Chimera and I would really appreciate your help. > > I am trying to convert a set of receptors (named receptor.pdb) to receptor.mol2. using chimera. However i am having problems with the charges of FAD, NAD, NDP, and FMN. Receptors that have problems in those groups are not being transformed. > > Is there a way to transform those files without having to change to charges? I have tried changing the charges and it seems to work. However, I am very afraid of changing the conditions of my simulations if I change the charges. > > I have gotten the following message: > NAD) Error: cannot run "/opt/UCSF/Chimera64-1.10.2/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit > Failure running ANTECHAMBER for residue NAD Hi Stellamaris, As you have discovered, the underlying tools that Chimera relies on to derive charges (AmberTools/antechamber/sqm) sometimes fail for entities with concentrated areas of negative charge. It is for this reason that Chimera already includes pre-calculated charges for ADP, ATP, GDP, and GTP. These charges were taken from the AMBER parameter database <http://research.bmh.manchester.ac.uk/bryce/amber>. Charges for the moieties you mentioned are also in that database, and I’ve gone ahead and added NAD and NDP to the ones that Chimera knows about without needing to do a calculation. Precalculated NAD/NDP charges will be available in daily builds dated Feb. 9 or later. Unfortunately, FMN and FAD are more problematic in that Chimera doesn’t protonate them in the standard way used in the database. It adds a proton (and positive charge) to the isoalloxazine ring system so that the central ring becomes aromatic. Obviously, the simplest way to deal with this if you don’t need FAD/FMN as a cofactor is to simply delete them. If you do need them then things get hairy. I guess what I would do is: 1) Delete FMN/FAD. 2) Run Dock Prep which will get you a Mol2 file of the remainder of the system with charges. 3) Close your system and reopen it. 4) Delete everything but the FMN/FAD. 5) Set the IDATM types of the FMN/FAD so that they correspond to the standard protonation pattern. 6) Add hydrogens. 7) Write another Mol2 file with just FMN/FAD. 8) Edit this second Mol2 file and transcribe the charges found in the corresponding Amber parameter database file to the atoms. 9) Combine your two Mol2 files. Step 6 is a little tricky in that the atom names in the “OFF” parameter files aren’t all the same as the PDB standard names, but there is connectivity information in the OFF file, so you can figure out which atom is which. You can do step 5 by running the “defattr” command with the file I have attached, which will set the types of FMN/FAD heavy atoms to the standard protonation pattern. Also, instead of step 8, you could work up another “defattr” file to assign charges to the FMN/FAD before you write out the Mol2 file. Probably easier. —Eric Eric Pettersen UCSF Computer Graphics Lab

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large structures and two letter chain IDs
by Petr Leiman 09 Feb '17

09 Feb '17

Dear Chimera Users and Developers, I am writing to ask if there is a way to animate multiple conformations of a structure containing 144 chains (~300,000 atoms)? Is it possible to read in such a structure into Chimera and preserve chain IDs? We have to use two-letter chain IDs, something that Chimera does not seem to like. Thank you, Petr -------------- Petr Leiman UTMB Galveston, TX77555

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Re: [Chimera-users] Fwd: chimera MAV
by Elaine Meng 09 Feb '17

09 Feb '17

Hi Jackie, Yes, see the sequence window menu: "Preferences… Appearance. " There are several options for spacing, font, and coloring, including “Space between wrapped blocks.” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Best, Elaine > On Feb 9, 2017, at 12:45 AM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Elaine, > > Thank you so much. Doing it by hand is the easiest. > Also, is there a way to increase the distance between wrapped blocks? > > Jackie Vitali > Cleveland State University > > On Wed, Feb 8, 2017 at 1:39 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > You can also: > > (1) hide/show the header lines (Conservation, Consensus, etc.) using the sequence window Headers menu > (2) change how Conservation is calculated (sequence window Preferences… Headers) > (3) add your own headers with quantities or symbols, e.g. put stars over the columns with superfamily-conserved residues > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > Elaine > > > On Feb 8, 2017, at 8:30 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > Hi Jackie, > > You can draw boxes (we call them “regions”) in the alignment wherever you want with click and drag, and then change their colors using the Region Browser. > > > > Multalign Viewer: > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> > > > > Regions, including how to create them manually: > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > > > Region Browser (click the square color wells to change colors): > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > > > I hope this helps, > > Elaine > > > > > >> On Feb 7, 2017, at 10:57 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > >> > >> Elaine, > >> > >> I would appreciate it very much if you could let me know how to highlight specific conserved residues in a sequence alignment between 2 proteins with chimera using the MAV? I highlight helices and beta sheets with colors, conservation between the 2 proteins is shown with the blocks on top. But there are 15-20 residues conserved in the superfamily of proteins and i would like to use blocks around them or highlight them in different color. In other words, 60 residues are conserved between the 2 proteins and 20 are special and need to be shown in a different way. > >> > >> I hope my question is clear. > >> > >> Thank you in advance. > >> > >> Jackie Vitali > >> Cleveland State University > >

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Re: [Chimera-users] Fwd: chimera MAV
by Elaine Meng 08 Feb '17

08 Feb '17

Hi Jackie, You can draw boxes (we call them “regions”) in the alignment wherever you want with click and drag, and then change their colors using the Region Browser. Multalign Viewer: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> Regions, including how to create them manually: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Region Browser (click the square color wells to change colors): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> 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 > On Feb 7, 2017, at 10:57 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Elaine, > > I would appreciate it very much if you could let me know how to highlight specific conserved residues in a sequence alignment between 2 proteins with chimera using the MAV? I highlight helices and beta sheets with colors, conservation between the 2 proteins is shown with the blocks on top. But there are 15-20 residues conserved in the superfamily of proteins and i would like to use blocks around them or highlight them in different color. In other words, 60 residues are conserved between the 2 proteins and 20 are special and need to be shown in a different way. > > I hope my question is clear. > > Thank you in advance. > > Jackie Vitali > Cleveland State University >

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Re: [Chimera-users] Upgrade to Sierra
by Elaine Meng 06 Feb '17

06 Feb '17

> -------- Forwarded Message -------- > Subject: Upgrade to Sierra > Date: Sun, 5 Feb 2017 17:58:53 +0100 > From: F.Xavier Gomis-Rüth <fxgr(a)ibmb.csic.es> > > Dear Elaine, > I recently had to upgrade to Sierra from Mountain Lion and now I find that ions are displayed as black spheres only > in Chimera v. 1.9. Any ideas on what I should change? > Kind regards, > Xavier > On Feb 5, 2017, at 9:11 AM, F.Xavier Gomis-Rüth <fxgr(a)ibmb.csic.es> wrote: > > Elaine, it's not only the ions, its all the atoms and bonds. > Ribbon appear fine though.... > Dear Xavier, I’m not an expert on this kind of thing, so I’m forwarding to the chimera-users list. (Sending to the list is always recommended… I will still answer it if I can, just as fast!) Although I don’t know if it’s related, maybe you should get a newer version of Chimera. Using Chimera versions 1.11.2 and 1.12 daily build on both a laptop and a desktop running Sierra, I do not have this problem. Best, 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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Re: [Chimera-users] Contour level animation ?
by Elaine Meng 04 Feb '17

04 Feb '17

> On Feb 3, 2017, at 4:21 PM, esserlo(a)helix.nih.gov wrote: > > Hi Elaine, > for a small demonstration, I want to make a movie in chimera where I animate > a change in contour level. I have an EM map with noisy features that improve > upon changing the level. I can do it by hand in the volume section but I > cannot figure out what parameter it is even if I wanted to set it on the > command line. > Setting it on the command line I suppose would be the first step but then my > question is: can this parameter be changed during an animation? > Thanks, > Lothar Hi Lothar, Yes, you can use the “volume” command “level” option to change the contour level. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> The “volume” command doesn’t itself have frames option, but you can combine it with the “perframe” command to perform a gradual change in a single line, as illustrated with this video mini-example: <http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.htm…> We generally encourage emailing questions to chimera-users (CC’d here) unless they involve private data, since others may like to know the answer. 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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Re: [Chimera-users] [chimera-dev] (no subject)
by Tom Goddard 02 Feb '17

02 Feb '17

Hi Kavya, How about just measuring the distance between the two monomer center of mass points of the homodimer and dividing that distance by 2 since the line between the two monomers will intersect the symmetry axis in the middle. For example for monomer chains A and B "measure center :.A ; measure center :.B ; distance #1,2”. Send this type of question to chimera-users instead of the chimera-dev list which is for developer programming questions. Tom > On Feb 2, 2017, at 1:39 PM, Kavya Shankar wrote: > > Hi, > > Is it possible to find the distance between a point and a line in chimera? I am trying to find the distance from the center of mass of the protein to the 2 fold axis of the homodimer. > > Thanks. > > Regards, > Kavya > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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3D movies for projects
by Kenward Vaughan 02 Feb '17

02 Feb '17

Hello, I'm developing a project for my class which feels like it's taking on Chimera (as in the creature) like proportions for the students. The thought is to have presentations of their visualization studies presented in a conference like setting at our school, open to all students. The question that has pounced into my thoughts is the possibility of using some settings within Chimera allowing them to record a movie (even as simple as a screen capture) which can then be played using an Oculus headset (or similar) with a phone. This would be a simple way to get the technology out into the street, so to speak. I do not yet have one of these myself so really don't know this first hand, but thought using wall-eye stereo made sense...?? Has anyone tried this, hopefully successfully? Kenward ps. Is there a way to use the phone as a monitor so one can manipulate the images via an external device, or use a Bluetooth hand controller? (I expect this is not possible given the graphics constraints of phones...) -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

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Help with coordinates please
by drew richardson 01 Feb '17

01 Feb '17

Hi, I am very new chimera and I am having to use it for a project at university. I have to create a picture from chimera and then list commands so anybody can recreate it just by typing in the commands in the command box. The problem I am having is: once I have rotated and zoomed manually using the mouse I don't know how to recreate that position and view by using typed commands. I can't even seem to find anywhere the coordinates of the new rotation. Could you please help me? How do I recreate the zoom and rotation using commands only, so that anyone wanting to recreate the view I have can do it just by typing in a list of commands after loading my original PDB file? Kind regards Drew Richardson ID: 27927431 (1st year biochemistry)

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Help!
by Kempfer, Jamie E. 31 Jan '17

31 Jan '17

i cannot get chimera to work on my windows computer!

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Re: [Chimera-users] on chimera unit cell function
by Elaine Meng 31 Jan '17

31 Jan '17

Hi Smith, The Unit Cell results for a structure with and without “pack” are equivalent because the symmetry describes a repeating pattern: each single copy could be shown in any of several places around the first copy. In other words, as I said before, there are multiple equally correct ways of presenting the same information. Although I cannot spend a lot of time looking at your specific data, I see the 3 structures are all the same space group with similar unit cell dimensions and angles, and the paper says “we could present nucleotide-induced conformational changes in the same crystal lattice by eliminating possible artificial structural differences because of different crystal packing.” Therefore I infer that the crystal packing is approximately the same in the 3 structures. It cannot be EXACTLY the same, however, since there are conformational changes between the structures. Since I didn’t write the Unit Cell code or look at the symmetry matrices in detail, I don’t know why the structures don’t give the same arrangement without “pack,” but I don’t think it is important, since the different possible arrangements for a single structure are equally correct. I hope this helps, Elaine P.S. please send questions to chimera-users rather than to me individually - thanks > Begin forwarded message: > > From: "Smith Liu" <smith_liu123(a)163.com> > Subject: Fw:Re: [Chimera-users] on chimera unit cell function > Date: January 31, 2017 at 7:01:54 AM PST > To: meng(a)cgl.ucsf.edu > > Dear Elaine, > > Related to our previous communication on "on chimera unit cell function" , here I have more to discuss with you. > > Attached 1 was the paper “Nucleotide-Dependent Conformational Changes and > Assembly of the AAA ATPase SKD1/VPS4B” published in Traffic 2008. PDB ID 2ZAM, 2ZAN, 2ZAO were 3 pdbs from this paper, and 2ZAM was the VPS4B without any nucleotide, 2ZAN was the VPS4B bound with ATP, 2ZAO as the VPS4B bound with ADP. > > As the paper wrote, “Because our attempts to crystallize SKD1 (VPS4B) in the presence > of ATP or ADP failed, we soaked the apo form crystals in solutions of ATP or ADP”, thus the 2ZAN and 2ZAO were got by soaking the crystal for 2ZAM with ATP and ADP separately. All 3 crystals were with space group P 65. > > The pdb for the 6 mates for each of 2ZAM, 2ZAN and 2ZAO are attached in attachment 2, 3, 4 separately (prepared without clicking ""Pack molecules in unit cell"). If viewed by Chimera, you will find the mates of 2ZAM arrange in the same way as the mates of 2ZAO, i.e., the 6 mates connect each other closely (side by side) and packed in a screw way. However for the 6 mates of 2ZAN, although still in screw way, the 6 mates arrange not closely but have a space between the adjacent mates. Correspondingly, the diameters of the z-axis projection of the 6 mates of 2ZAM and 2ZAO were much smaller than that of the 6 mates of 2ZAN. > > However, if we by Chimera we click the "Pack molecules in unit cell",we will find the 6 mates of 2ZAN displayed exactly (or very similarly) as the 6 mates of 2ZAM and 2ZAO (Am I right). > > Then my question would be, in the crystal for 2ZAN and 2ZAO, do the proteins arranged in exactly the same pattern? And why if we did not click ""Pack molecules in unit cell", the mates of 2ZAN and 2ZAO were displayed differently, and with clicking ""Pack molecules in unit cell",the mates of 2ZAN and 2ZAO were displayed similarly? > > If the protein arranged differently in the crystal for 2ZAN and 2ZAO, then in the crystal packing of 2ZAN, how can I identify the 6 protein which were from the 6 screwed mates in 2ZAM? > > I am looking forward to getting a reply from you. > Smith > -------- Forwarding messages -------- > From: "Elaine Meng" <meng(a)cgl.ucsf.edu> > Date: 2017-01-30 04:05:22 > To: "Smith Liu" <smith_liu123(a)163.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] on chimera unit cell function > Hi Smith, > The number of copies and their positions are all correct no matter whether you choose the “pack” option or not. If you cut out a part of the real crystal, there will be a real copy in the same place as the copy from Chimera. So imagine if you had specified an infinite (or large) number of unit cells in Chimera, a chunk from the middle of the result would look the same as some chunk of the real idealized crystal, regardless of whether you used “pack”. However, since you are probably specifying 1 x 1 x 1 or some small number of unit cells, yes choose the “pack” option to show the copies packed together, instead of with some spaces where a copy is shown inside a neighboring box rather than in the central outline box. > Best, > Elaine > > > On Jan 29, 2017, at 5:10 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > > > Dear Elaine, > > > > I am still confusing on the function of "Pack molecules in unit cell" in Chimera. If we cut out a cube (or a volume) of crystal based on which a pdb was got, do you think the molecules packed in the cube in the way without "Pack molecules in unit cell" clicked, or the molecules packed in the cube in the way with "Pack molecules in unit cell" clicked? > > > > I am looking forward to getting a reply from you. > > > > Smith > > > > > > At 2017-01-29 00:50:44, "Elaine Meng" <meng(a)cgl.ucsf.edu> wrote: > > >Hi Smith, > > >It is my understanding that you will get the same number of copies whether or not you choose the “pack” option, and that there are multiple equally correct ways in which the copies will be positioned according to the symmetry information. The “pack” option simply chooses, out of these many equally correct alternatives, a configuration that places the centers of all the copies inside one unit cell outline box instead of spreading them out among neighboring boxes. > > >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 > > > > > >> On Jan 28, 2017, at 1:47 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > >> > > >> Dear All, > > >> > > >> In Chimera, we do Tools →Higher-Order Structure→Unit Cell, then what will be the diffenrence if we clicked "Pack molecules in unit cell" in comparison with if we did not click "Pack molecules in unit cell"? Does it mean that what we observed (or what Chimera displayed) if we click "Pack molecules in unit cell" , was really part of what it displayed if we did not click "Pack molecules in unit cell" but we increased the "Number of Cells" significantly? > > >> > > >> I am looking forward to getting a reply from you. > > >> > > >> Smith >

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Save marker sets from command line or python
by Kyle Morris 30 Jan '17

30 Jan '17

Dear Chimera dev and community, I would like to save a marker set from the command line and ultimately do so in a script. Using the write command which I would use for PDB's, marker sets get saved in PDB format, of course. Is there a command to save the marker set as XML .cmm as it would from the volume tracer menu? I notice at the bottom of the following page this is a suggested development: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/… - supply Python code for reading and writing the XML files containing saved marker sets Is it there already and I can't find perhaps? Thanks for your help as ever! Best wishes, Kyle

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on chimera unit cell function
by Smith Liu 29 Jan '17

29 Jan '17

Dear All, In Chimera, we do Tools →Higher-Order Structure→Unit Cell, then what will be the diffenrence if we clicked "Pack molecules in unit cell" in comparison with if we did not click "Pack molecules in unit cell"? Does it mean that what we observed (or what Chimera displayed) if we click "Pack molecules in unit cell" , was really part of what it displayed if we did not click "Pack molecules in unit cell" but we increased the "Number of Cells" significantly? I am looking forward to getting a reply from you. Smith

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Metal Geometry Analysis - per frame
by Ilkow, Veronica 27 Jan '17

27 Jan '17

Dear All, Is there a way I could include the metal geometry analysis as a per frame script for a MD movie? Ideally I would like to have an output file which lists the best geometry and essentially prints out the co-ordination table for two atom selections per frame. I am trying to figure out how to use the python or chimera per-frame commands to specifically select an atom and then print an output file. Any hints and suggestions on how to do this will be greatly appreciated. Thank you in advance for your help. -Veronica

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Re: [Chimera-users] dipoles
by Tom Goddard 25 Jan '17

25 Jan '17

Hi Vatsala, To change the arrow thickness change the line of code in the dipole.py script bildString = ".arrow %g %g %g %g %g %g .1 .2 .9" The values at the end control the shape, the “.1” is the cylinder radius, the “.2” is the arrow tip cone radius, and the “.9” is the fraction of the arrow length taken by the cylinder. This is described in the Chimera BILD format documentation here https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> Tom > On Jan 25, 2017, at 10:02 AM, Sagar, Vatsala (NIH/NEI) [E] wrote: > > Hi Tom, > Do you know how to change the dipole vector thickness. I am using dipole.py program to calculate dipoles in Chimera, and it is giving me a very thin line. > Thanks a lot, I sincerely appreciate it, > Vatsala Sagar > > From: "Sagar, Vatsala (NIH/NEI) [F]" > Date: Friday, January 6, 2017 at 10:09 AM > To: Tom Goddard , "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" > Subject: Re: [Chimera-users] dipoles > > Hi Tom, > I am attaching the PQR files and raw PDB files of the crystal structure of human gamma D with two monomers rotated 90 degrees to one another. Please take a look at it and tell me what you think, > Thanks, > Vatsala > From: Tom Goddard > Date: Thursday, January 5, 2017 at 7:07 PM > To: "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" > Subject: Re: [Chimera-users] dipoles > > Hi Vatsala, > > I guess you are refering to the dipole.py script on the Chimera Python scripts web page: > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > > Yes it should give the same answer for a molecule and a copy of that molecule rotated by 90 degrees. Without have the structure and rotated PQR files I don’t know what is going wrong. > > Tom > > >> On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F] wrote: >> >> Hi, >> Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? >> Thanks, >> Vatsala Sagar >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

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on Multiscale Models
by Smith Liu 23 Jan '17

23 Jan '17

Dear Al, In the "Mutiscale Models" Windows , will you please tell me what does it mean for the item "Range"? I am looking forward to getting a reply from you. Smith

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