- Chimera-users - RBVI Mailing Lists

chimera options opening in tabs and not windows
by Pranav Shah 17 May '18

17 May '18

Dear Developers, I have somewhat of a strange problem with chimera where, different options of the program open into tabs in the same window as opposed to having their own windows. While this is mildly irritating especially when I am using the volume viewer to change the contour level of the map and not being able to visualise the changes in the map as they appear, what gets my goat is that the options/prgorams become unavailable to access when i pull the tab out into its own window. I know this isnt a chimera problem as i have the same issue with other python based programs such as imod and eman. Would you know where i can tweak the preferences so that the programs do not open in tabs but their own independent windows? I appreciate your assistance. Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Harvard Medical School 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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Calculating screw transformation between two protein subunits
by Nikita Chopra 17 May '18

17 May '18

Hi I have two protein subunits, which I have aligned along the z-axis. I am considering both the subunits as rigid bodies. Is there a way I could find the screw transformation (rotation along z-axis and displacement along xy plane) between them in chimera ? Thank you for your help.

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Volume viewer levels question
by Markus Heller 15 May '18

15 May '18

Hi all, I have an issue displaying a map file that I opened using the insightgrid.py script. When displaying the grid at the highest level I can get, the levels are still too low, but when I set the levels higher by typing something into the level field (e.g. 1.2e+03 instead of the 1e+03), the levels disappear altogether as shown in the second screenshot. As soon as I adjust the slider, the levels reset to 1e+03. What am I doing wrong? Thanks Markus [cid:image001.png@01D3EC35.74E6A210] [cid:image004.png@01D3EC35.9B86A230]

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insightgrid.py
by Markus Heller 14 May '18

14 May '18

Hi all, I'm looking for a copy of Tom's insightgrid.py script, referenced here: http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009651.html If somebody could let me know how to get hold of a copy, that'd be great! Thanks and Cheers Markus

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query about splitting volumes using local resolution criterion
by Banavali, Nilesh K (HEALTH) 14 May '18

14 May '18

ResMap, a program that calculates local resolutions for cryoEM maps, also provides a chimera script to visualize the local resolution. This script opens Volume #0 (cryoEM map), and colors its regions using the values from Volume #1 (ResMap-generated file) as follows: open #0 example_map.mrc open #1 example_map_resmap.mrc volume #1 hide scolor #0 volume #1 cmap 3.00,blue:5.00,cyan:7.00,green:9.00,yellow:11.00,orange:13.00,red I was wondering if there is a way to generate split maps based on the resolutions stored in Volume #1 instead of just coloring the original map. Alternatively, is there way to play with the transparency of the regions with specific resolutions stored in Volume #1. The goal is to separate low resolution regions from the higher resolution regions in the original map to be able to better understand/annotate the accuracy of atomic models that are generated based on the map. I tried to look for ways to do this using 'volume', 'scolor zone', and 'vop' options, but was unable to make any progress. Any help would be greatly appreciated. Thanks, Nilesh

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Regarding saving image in chimera nogui
by NAGARAJAN 14 May '18

14 May '18

Hi all, I have to use chimera --nogui and do the following 1. load a structure 2. make Surface representation 3. Color surface of selected residues with a selected color 4. save image Any idea how to do the 4 steps in chimera --nogui? Thank you

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tiling multiple chain structures
by Healey, Joe 11 May '18

11 May '18

Hi chimera team, Sorry for pestering you again so soon! Very quick question though. If I have a couple of structures on screen which are made up of multiple PDBs, is there any way to tile them, but as groups? e.g. if I have one complex A-B-C, and another X-Y-Z, that I group into Group1 and Group2, I'd like to tile group1 and group2 next to each other. The tile command, as far as I can tell, is only capable of tiling A B C X Y Z as seperate models though (unless I went through the process of saving them all as a single PDB first). Is there any way to do this without the hassle of saving and reloading? Many thanks! Joe Joe Healey M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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Re: [Chimera-users] saving new position of the model (map saving)
by Elaine Meng 10 May '18

10 May '18

Hi Dmitry, You need to specify two maps, the one you are sampling and the one whose grid you are sampling on, e.g. vop resample #0 onGrid #1 This means map #1 with the desired grid must already exist. As mentioned in that link, you could create it with “vop new” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new> You can show outline boxes indicating axis orientation with the data display options in Volume Viewer or “volume” command, and move models separately by specifying model to move with the “models” option of “turn” (or “roll”) or with the mouse after freezing some models by unchecking their “A”ctive buttons in the Model Panel. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2018, at 11:56 AM, Dmitry Semchonok <semchonok(a)gmail.com> wrote: > > Dear Elaine, > > Thank you for your answer. > > I read the last link > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting > > but I still can not save the map > > <F8EED359A67845868DD4F80A9DAF3499.png> > > If I put onGrid I get this > > <B7696E2A55B04A298BEB09E32A85BDF2.png> > > Could you please briefly tell how to make it work? > > Thank you. > > > Sincerely, > Dmitry > > > Sent from Mail for Windows 10 > > From: Elaine Meng > Sent: Thursday, May 10, 2018 5:59 PM > To: Dmitry Semchonok > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] saving new position of the model > > Dear Dmitry, > For atomic models, of course: you can just specify saving transformed coordinates in the Save PDB or Save Mol2 dialog (or “write” command). > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> > > The rotating could be done by hand with the mouse or with commands “turn” or “roll." > > However, I’m guessing you probably mean a map since that is more complicated. As explained in the “Saving Maps After Fitting” link below, you would generally have to resample the map onto a different grid that has the axes oriented how you want: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On May 10, 2018, at 8:34 AM, Dmitry Semchonok <semchonok(a)gmail.com> wrote: > > > > Dear colleagues, > > Is there a way to rotate the model and than save it with a new x y z? > > Thank you > > Sincerely, > > Dmitry > > > <F8EED359A67845868DD4F80A9DAF3499.png><B7696E2A55B04A298BEB09E32A85BDF2.png>

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saving new position of the model
by Dmitry Semchonok 10 May '18

10 May '18

Dear colleagues, Is there a way to rotate the model and than save it with a new x y z? Thank you Sincerely, Dmitry Sent from Mail for Windows 10

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Setting map origin index to 0 while keeping fitted structures
by Ahmad Abdelzaher 08 May '18

08 May '18

Hello, I have spent some time fitting structures to my map. I want to set the origin to 0, however, that will lose me all the work I did. Any suggestions? Regards.

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Help
by Kimberley Perry 08 May '18

08 May '18

Hello! I am trying to model molecular structures for a Python course I am taking. I tried your online water example, and it looked like it ran, but I am not seeing the structure. Am I doing something wrong? Kim

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join models
by VALENTINA BRANDI 08 May '18

08 May '18

Hi, I’m a Phd student and I need to join different domains of a protein. I have used the tool “join models” of Chimera, but unfortunately after the union there is a partial superimposition between the two models. How can I solve this problem? Thank you so much, Valentina Brandi Inviato da Posta<https://go.microsoft.com/fwlink/?LinkId=550986> per Windows 10

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movie recording
by Michał Kadlof 04 May '18

04 May '18

Hello, I would like to make a movie using Chimera. I need to interpolate between key frames. I know how to do it using Animation tool, but I would like to do it for thousands of frames and clicking it all by hand is not doable. Is there any magic command for making timeline automatic way? -- best regards, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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trying to use per-frame pdb 'CONECT' information in movie maker
by Black, Kersey 04 May '18

04 May '18

Hi, Just recently back to using Chimera after a long time, so a bit rusty on this. I am reading in a trajectory of a small hydrocarbon for a single pdb file, and with each fram I include the geometry and the connectivity I want with ‘CONECT’ lines. But, when I use the Movie Maker tool to read it in, it seems to using one or more frames (perhaps the last one? to detect connectivity to auto detect connectivity and then applying it to all geometries, and this is putting bonds in places where I do not want them. Does movie maker honor CONECT information for each step? Is there a way to have it do so? Or is connectivity set once for the entire trajectory? Thanks much for any help on this, Kersey

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Coloring ensemble atoms by distance from mean structure
by Tom Goddard 03 May '18

03 May '18

Hi David, I’ve attached a Python script mean_distance.py that can compute the distance of each atom in an ensemble from the mean structure. Then you can color using that distance. Here’s an example set of Chimera commands. open 1mtx show open mean_distance.py rangecolor distance_from_mean 0 blue 3 white 6 red The script uses all open molecules as the ensemble. The coloring can also be done with menu Tools / Depiction / Render by Attribute. Tom > On May 3, 2018, at 10:10 AM, Morgan, David Gene wrote: > > Tom, > > Hope you are doing well. Jim Powers and I here at IU keep thinking we need to invite you and/or the team back for another chimera workshop, but we haven't done the ground work to see how possible that would really be. But I keep hoping! > > In the meantime, I have a question about whether chimera can do something, and if not, I have a feature request... I was watching a grad student give a talk showing lots of superposed atomic structures. The structures included some molecular dynamics simulations and some crystal structures of the same protein in subtly different conformations (packing into a viral capsid, where the different subunits in the asymmetric unit have slightly different conformations). It occurred to me that _after_ showing the mess of spaghetti he had, the points he needed to make would be better served with a different visual: If he were to average the ensemble of MD atomic positions to a single chain (and color-code by the ensemble RMS difference from the average) and do the same for all his ensemble of X-ray structures, it would be much easier to talk about and show the consistencies and inconsistencies in the atomic co-ordinates from all the data. This same sort of averaging an ensemble of atomic co-ordinates is sometimes done with NMR structure ensembles (but I don't know about the color coding with the RMS). > > I have looked at lots of packages that manipulate atomic co-ordinates, but haven't found anything that seems to actually do what I want to do. For example, gromacs is supposed to do the averaging but it really wants to work with MD data and at a minimum, I'm not smart enough to make it work with a series of standard PDB files. My NMR colleague suggested molmol for the averaging, and I need to explore that more. But there doesn't seem to be a recent linux version nor does it seem to be "scriptable" (i.e., if I wanted to do this for a dozen different ensembles, I would have to painfully mouse click my way through the process). On top of all that, I ran into numerous on-line discussions about how averaging was "the wrong thing to do." All those people had valid reasons for saying so, but right now, I'm really talking about a more simple visual that conveys some of the information contained in any sort of ensemble of atomic co-ordinates. > > So my first question is: does chimera have a utility that would do this sort of thing? I looked at various commands but did not see anything that looked like it would do this. If not, can I put a feature request into the queue? > > Looking forward to hearing from you and chatting some more. > > -- > politics is more difficult than physics. > A. Einstein > > David Gene Morgan > Electron Microscopy Center > 047D Simon Hall > IU Bloomington > 812 856 1457 (office) > 812 856 3221 (3200) > http://iubemcenter.indiana.edu >

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Question regarding rotating dihedrals
by Rodrigo Galindo-Murillo 02 May '18

02 May '18

Hello! I need to do a dihedral scan around the phi/psi angles of alanine dipeptide and to create the input files to later do single point calculations I am using the cmd script: open ../scan.pdb rotation 0 @/serialNumber=7 @/serialNumber=9 rotation 0 180 write format pdb #0 test.pdb I need to use atom serial numbers since the idea is later do the scan with non-canonical peptides that will not work with the native phi/psi descriptions. The script is not modifying any angle but I can see that is generating test.pdb correctly. Could you please orient me if this is the correct set of instructions? Thank you! Rodrigo.

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Changing depth cue to side to side from front to back
by Trevor Harris 02 May '18

02 May '18

Hello, I would like to know if it is possible to change the depth cue to side to side rather than front to back. I don’t want to change the position of the molecule. Is it possible? Thanks, Trevor

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Label hydrogen bonds
by Pawan Mainkar 30 Apr '18

30 Apr '18

The following bug report has been submitted: Platform: windows_x86_64 Chimera Version: 1.11.2 Description Respected sir, I am a PhD student in the discipline of Biotechnology, actually sir i am working on Enzyme-inhibitor docking study and i did docking using Cluspro and then i want to check how much interaction by visualizing the inter molecular hydrogen bonds with proper labeling (like in structure hydrogen bond between D45-S89 with 2.3 Angstron) ,but sir am only able visualize only hydrogen bonds in Your software UCSF Chimera but am unable to label it with proper amino acid along with distance so i request you sir please tell me how to do that or provide me any video file regarding the same File attachment: Docking complex.docx

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Important Query
by Rida Zainab 30 Apr '18

30 Apr '18

Respected Sir, I am a research student trying to use chimera but I am having difficulties. Whenever I give an operation or task in chimera, the replylog opens always giving error. Suppose I tried to convert PDB file to Mol2 and there was error of replylog. I tried to do docking using autodock vina and it is not happening too. I am unable to do anything. Please tell me what's wrong? Big help needed. Regards, Rida.

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Suggestion for adding a volume map to morph conformation
by Trevor Harris 25 Apr '18

25 Apr '18

Hello, I would like to use the Morph Conformation show the changes of the molecular orbitals from starting material to transition state to product. I can show the changes structurally of the atoms which is great, but this would be amazing with the molecular orbitals overlaid the structures. If this option is available to add volumes into morph conformation, then I couldn’t find it. Would it be possible to add this feature? It would be similar to IBOView. Thank you! Trevor Harris Postdoctoral Fellow UPenn Chemistry, Chenoweth Group

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Problem running Modellerfrom Chimera (versión 1.11.2(build 41380) 2016-12-05 19:45 UTC. Platform Linux64)
by Sergio Garay 23 Apr '18

23 Apr '18

Hi all I've tried to run Modeller locally from Chimera (versión 1.11.2(build 41380) 2016-12-05 19:45 UTC. Platform Linux64. Windowing system: x11), but when it finishes, the model is not loaded inside Chimera. The log window give me the following output: *Model 0 (model1.pdb) appears to be a protein without secondary structure assignments.* *Automatically computing assignments using 'ksdssp' and parameter values:* * energy cutoff -0.5* * minimum helix length 3* * minimum strand length 3* *Use command 'help ksdssp' for more information.* *seq (len 437): added* *target (len 437): model1.pdb (#0) chain A* *seq (len 437): model1.pdb (#0) chain A* *target (len 437): added* *Target seq: added* *Template structures: * * model1.pdb (#0)* *Run locally, the Modeller binary location: /usr/bin/mod9.19* *Now, modeller is running locally...* *Wrote /tmp/tmp73g3JY/template_struc/model1.pdb_0_0.pdb* *MODELLER process output* *-----------------------* *-----------------------* *MODELLER process errors* *-----------------------* *Could not find platform independent libraries <prefix>* *Could not find platform dependent libraries <exec_prefix>* *Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]* *'import site' failed; use -v for traceback* The problem seems to be that Chimera can not load the models obtained . I can find the model inside the directory: /tmp/tmp73g3JY/template_struc/*model1.pdb_0_0.pdb* Thank you in advance. Sergio -- *Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Fwd: Re: run chimera remotely over nice dcv
by Greg Couch 23 Apr '18

23 Apr '18

Solution found! -------- Forwarded Message -------- Subject: Re: [Chimera-users] run chimera remotely over nice dcv Date: Sat, 21 Apr 2018 13:20:11 +0200 From: Mihajlo Vanevic <m.vanevic(a)uu.nl> To: Greg Couch <gregc(a)cgl.ucsf.edu> Dear Greg, Thank you very much for the prompt reply. About ssh -X, indeed putting the compatible libGL.so from local machine to Chimera's lib folder does the trick. About Nice DCV, I have contacted Nice DCV developers and will let you know if the problem is solved. With best wishes, Mihajlo On 04/20/2018 07:54 PM, Greg Couch wrote: > > Hi Mihajlo, > > We don't have any experience with Nice DCV, perhaps some other user on > the mailing list can help. But guessing at possible problems, make > sure that Chimera is displaying locally in Nice DCV virtual machine > (the DISPLAY environment variable should be ":0"), and the remote > display is done using the Nice DCV client. > > If, instead, you're using X11's remote display capability, then you > wouldn't need to use Nice DCV, any virtual machine technology would do > (or not do) -- the trick there is to have compatible OpenGL drivers on > both the virtual machine and your local computer (running the X11 > server). Assuming compatible versions of Linux on both ends, you > could copy libGL.so from your local machine to the Chimera's lib > directory on the remote machine, and it should work. > > Good luck, > > Greg > > On 4/20/2018 5:07 AM, Mihajlo Vanevic wrote: >> >> Dear Chimera users and developers, >> >> We are trying to run Chimera remotely on our cluster via Nice DCV >> visualization software: >> >> https://www.nice-software.com/products/dcv >> >> This package provides GPU acceleration for OpenGL and >> DirectX applications. It indeed works for most of apps, however with >> Chimera >> we get the following startup error >> >> X Error of failed request: GLXBadContext >> Major opcode of failed request: 152 (GLX) >> Minor opcode of failed request: 5 (X_GLXMakeCurrent) >> Serial number of failed request: 73 >> Current serial number in output stream: 73 >> >> Our cluster visualization node has nvidia GeForce GTX 1080 Ti cards >> and nvidia drivers 384.81 >> >> Chimera works if we use software mesa rendering, but it would be great if >> we can make it work remotely with hardware rendering. >> >> With kind regards, >> Mihajlo Vanevic >> Cryo-EM group, Utrecht University >>

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Error in Windows saving a session
by Joel Mackay 21 Apr '18

21 Apr '18

Hi all Have other people seen (and solved!) this error before (below)? I'm having it crop up pretty much all the time now when I try to save a session (on my Win7 machine - running Chimera 1.11.2. Thanks Joel WindowsError Exception in Tk callback Function: <function command at 0x00000000155434A8> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save getattr(self, self.keepEquiv())() File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK self.Apply() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply self.command(1, self) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB saveSession(paths[0], **kw) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) WindowsError: [Error 32] The process cannot access the file because it is being used by another process WindowsError: [Error 32] The process cannot access the file because it is being used by another process File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) See reply log for Python traceback. ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay(a)sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/

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run chimera remotely over nice dcv
by Mihajlo Vanevic 20 Apr '18

20 Apr '18

Dear Chimera users and developers, We are trying to run Chimera remotely on our cluster via Nice DCV visualization software: https://www.nice-software.com/products/dcv This package provides GPU acceleration for OpenGL and DirectX applications. It indeed works for most of apps, however with Chimera we get the following startup error X Error of failed request: GLXBadContext Major opcode of failed request: 152 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 73 Current serial number in output stream: 73 Our cluster visualization node has nvidia GeForce GTX 1080 Ti cards and nvidia drivers 384.81 Chimera works if we use software mesa rendering, but it would be great if we can make it work remotely with hardware rendering. With kind regards, Mihajlo Vanevic Cryo-EM group, Utrecht University

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Adding quadrant lines to atoms
by Trevor Harris 20 Apr '18

20 Apr '18

Hi, Is there a way to add quadrant lines to atoms similar to how Houkview does it in CylView, pictured below. If not, could you add this feature as an option? All the best, Trevor Harris

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