- Chimera-users - RBVI Mailing Lists

desinstallation
by Isabelle Fourré 18 Jul '18

18 Jul '18

Dear Chimera users, How to desinstall correctly Chimera? I forgot to install it as "root" so the executable file has not been copied in my /usr/local/bin directory, and I would like to restart all the process. I did not find any README file... Thanks a lot -- Isabelle FOURRÉ Maître de conférences (Assistant professor) Laboratoire de Chimie Théorique Sorbonne Université (campus Pierre et Marie Curie) 4 place Jussieu | Tour 12-13 4e étage Boite courrier 137 | Pièce 418 75252 PARIS Cedex 05 Tél : 01 44 27 96 59 --

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Movie question
by Yanhe Zhao 17 Jul '18

17 Jul '18

To whom may concern, This is Yanhe Zhao, from ut southwestern medical center. I am making a movie with Chimera, i know how to make it by saving different positions. Now I add 2d label in special position and make it again, no label in movie. Do we have way to copuling the position with our label or another different way? e.g. by saving scenes? The final movie version should have labels fade in and out at different time point. I really appreciate if someone can do me the favor. Best, Yanhe

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Include position from multiple frames in one image
by David Sáez 16 Jul '18

16 Jul '18

Hi, I have a molecular dynamics simulation created using Amber, and I visualize the result in Chimera using MD Movie. I would like to show the wandering of a small molecule inside the active site, but in just one picture. Is it possible to include all the positions sampled by some selected atoms in the exported image? Thanks for your help.

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turning kdssp off
by Mateusz Sikora 16 Jul '18

16 Jul '18

Dear Chimera users, is there any way to turn the secondary structure assignment (kdssp) off? I am transforming a set of coordinates from a MD trajectory into electron density. I collapsed many frames of the trajectory into a single file, meaning there are many unphysical overlaps (I only care about the density). Problem is, that the PDB file I am opening is rather large (couple of millions of atoms) and kdssp gets absolutely stuck on it. I would appreciate some help. Best regards, Matt

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MD movie error
by ChuHui Fu 16 Jul '18

16 Jul '18

Hi all, When I was trying to use MD Movie option on the attached pdb trajectory file, chimera kept telling me that there were missing residues. "Chimera Error Residue 3864.het not in first model on line 126754 of /homes/cfu/model1_sep_475.B_md_traj_system.pdb" But I checked that the number of atoms in each one of the pdb files and there didn't seem to be any missing. Then I separated the trajectory files and use vimdiff to compare the models pairwise, but doesn't seem like there are different residues, (unless I missed them). Can anyone suggest what I might have done wrong? model1_sep_475.B_md_traj_system.pdb <https://drive.google.com/a/haverford.edu/file/d/1w82K6a2FfLDzphcn6Jj2VwCjok…> Thanks!! -- ChuHui Fu B.S.Candidate in Chemistry Haverford College, Class of 2019 cfu(a)haverford.edu

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Coordset and reset bug
by Cristina Paulino 13 Jul '18

13 Jul '18

Dear Chimera team, I just stumbled on a bug that wasn’t present before (not sure from which version on). Chimera gets stuck if you try to make a movie were a specific set of frames of a morph is recalled and at the same time the camera position is reset to save position. Here the specific example that doesn’t work anymore, but did initially: coordset #3 1,61,1 reset morph2 90 wait 90 Now I had to change, so that both movements happen independent. coordset #3 1,61,1 wait 61 reset morph2 90 wait 90 Any change this bug could be fixed? It is a nice feature to be able to keep the morph going while it moves to another saved-position. Best, Cristina ____________________________________________________________________________________ Dr. Cristina Paulino Assistant Professor at the Department of Structural Biology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Faculty of Science and Engineering , University of Groningen Nijenborgh 7, 9747 AG Groningen, The Netherlands Room 5171-0054 Phone: +31 50 363 34 02 Email: c.paulino(a)rug.n <mailto:c.paulino@rug.nl>l https://www.rug.nl/research/electron-microscopy <https://www.rug.nl/research/electron-microscopy> http://www.membraneenzymology.com <http://www.membraneenzymology.com/> ____________________________________________________________________________________

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Delete pseudobonds
by Javier Marchena 12 Jul '18

12 Jul '18

Hi, A pseudobond has been automatically created in one of my structures, because of "missing segments". I want to delete the pseudobond in order to create a real covalent bond between those two atoms. But I have problems with deleting the pseudobond, I have not found a way to do it. Could you help me out? Thanks in advance. PS: I send you the molecule in pdb format just for you to see the pseudobond.

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Output chain sequences
by Healey, Joe 11 Jul '18

11 Jul '18

Hi Chimera Team, I've been experiencing issues with the "Align Chains" tools that connect to Clustal and Muscle - I think ostensibly this might be because the servers are no longer available or something. I'm happy to make the alignments myself, but to do this I'd like to try and simply export the sequences of all open models to a fasta file or similar. I know this can be done manually sequence-by-sequence thtrough the GUI. Could you tell me what the python (or chimera syntax) would be to do this if it's possible? I'm envisaging something to the effect of this, but I can't quite get what I need back in terms of the sequence (it returns a `bound object'?): ``` from chimera import openModels all_mods = chimera.openModels.list(modelTypes=[chimera.Molecule]) with open('output.fasta', 'w') as ofh: for mod in all_mods: ofh.write('>%s\n%s' % (mod.name, mod.sequence) ``` Thanks, 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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Use of sym command
by Lee A.G. 11 Jul '18

11 Jul '18

Hi Elaine I am trying to use the sym command to generate BIOMT-described copies of a protein. As a test I have used 2oli, as in your contribution of 12 Jan 2009. Having loaded 2oli and entered the command sym #0 #0 I get the error message "No symmetric molecule copies". Any help gratefully received Anthony Lee

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3D environment
by Heymann, Bernard (NIH/NIAMS) [E] 11 Jul '18

11 Jul '18

Hi I'm interested in acquiring a PC with capabilities to use ChimeraX for 3D VR visualization of large volumes (2k cube). What is the best configuration (CPU, GPU, VR hardware) for around a $5-10k budget? Bernard

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Clustering algorithm
by David Adrian Saez San Martin 10 Jul '18

10 Jul '18

Hello, I want to use Chimera to generate clusters of a molecular dynamics trajectory. I have been looking for info about the clustering algorithm it uses, but I was not able to find anything. I guess it employs a default technique, does anybody know which one? Regards. David-.

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Problem with netcdf trajectories
by David Sáez 09 Jul '18

09 Jul '18

Hello, I am using UCSF Chimera, candidate version 1.13 LInux64. When I load an MD Movie with prmtop and netcdf files (both created using Amber) the software crashes and gives segmentation fault error. In the trajectory dialog box the netcdf format is not shown as an option. With the previous version, I was able to open those files. Regards.

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Need your Kind help..
by Rajlakshmi Chetty 09 Jul '18

09 Jul '18

Dear Sir/Madam Greetings for the day!! Myself Rajlakshmi Chetty, is Doctoral student in field of Nanomaterials. I am self learning and using chimera since back few days with the help of website tutorials and am stuck with a problem which is described below: I have .pdb file format of docked complex (Hex software) in which their is H bond is missing between ligand and receptor when opened in chimera. I tried Tools>structure depiction>find H bond but in that parameters query when i apply I am getting H bond of the whole complex which I don't want. I want to visualize H bond or any bonding between ligand and receptor. Is their any other way or what parameters change i need to do? I have attached H bond parameters dialog box with this mail. This problem where I am stuck is need for the time for my research work. So your kind help will be a great blessings for me. Your help of gratitude will be highly appreciated. Thanking you and looking forward for your reply!! -- *Kind Regards* *Rajlakshmi Chetty* Doctoral Student School of Chemical Sciences Central University of Gujarat Gandhinagar 382030 India Mobile No :- * +91 9427178591* +91 8780155455 e_mail :- *rajlakshmi(a)cug.ac.in <rajlakshmi(a)cug.ac.in>* [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 07/07/18, 12:27:44 PM

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Interactions pairs
by Francesco Pappalardo 05 Jul '18

05 Jul '18

Dear All, We started to use Chimera since few time. I have, maybe, a very easy question. How we can visualise interactions pairs between the ligand and the receptor for which we computed blind docking. For the sake of clarity I attach a figure showing what we wish to get. Thank you. Francesco Pappalardo

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(no subject)
by Eslam Nofal 04 Jul '18

04 Jul '18

Hello Thanks a lot for your effort please help me to know how can I determine My Model for a certain mutated gene (like smn protein for normal sequences,type I,II,III,and IV Spinal muscular atrophy) How can I know the protein model for different seq is functional or non functional? I made models for different affected cases of SMA with A suitable template for pdb and Recorded The Qmean and GMQE number for each model with but till now I can not be able to determine this sequence produce good functional protein or not especially with gene have Frame shift mutation which produce new protein and also have a lot of stop codon in the sequence I hope you understand the meaning of my Question ? and hope to guide me to suitable tool or method Thanks

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What is exactly matchDist?
by Murpholino Peligro 04 Jul '18

04 Jul '18

Got 8 x-ray structures. Load them into Chimera and did Structure Comparison -> MatchMaker (with multiple sequence alignment). In the alignment I choose Structure-> Asses Match and it creates a residue attribute named matchDist. I guess is the Distance in angstroms for every alpha carbon in my ith structure (where i=1, 2, 3, ...7) to every matching alpha carbon in my reference structure? Thanks

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Horrible FPS Drop after Operation Chimera Update
by Bellamy Baron 04 Jul '18

04 Jul '18

Any of you got this problem? I had a Horrible FPS Drop after Operation Chimera Update. Thanks in advance for your assistance -------------------------------------------------------------------------------------------------------- Bellamy Specialist - iWYZE https://www.iwyze.co.za/products/car-insurance

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Please unbundle libRMF
by Yuri 02 Jul '18

02 Jul '18

Chimera installs lib/libRMF.so, and UCSF IMP also installs lib/libRMF.so, so that they can't be used together, despite the claim that "IMP can also be used from the Chimera <http://www.cgl.ucsf.edu/chimera/> molecular modeling system" (see https://integrativemodeling.org/) Please unbundle libRMF (https://github.com/salilab/rmf) and use an external package for it. Also imagine if some other software used libRMF too, how can they all be installed together? Bundling is a mess. Please never bundle software packages because this only causes problems down the road. I also asked IMP to unbundle libRMF.so: https://github.com/salilab/imp/issues/1005 Thanks, Yuri

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Chimera application questions
by Yanhe Zhao 02 Jul '18

02 Jul '18

To whom may concern, This is Yanhe Zhao from UT Southwestern Medical Center. I have to question when use Chimera as below, hopefully someone could do me a favor to answer it. 1, my crystal structure have four copies in one Asymmetrical structural unit. When I try to combine two of them by selection and combine command, always combine all of them. I pretty sure that I only select two of them; 2, I got one PDB from SASDB, how can I show it as a density map like CryoEM? When I open, it's shown as lines-like map so as to which couldn't be used for docking. I really appreciate it if someone could do me this favor. Thanks a lot. Best, Yanhe

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Chimera Through VirtualGL
by Logan Sweezy 28 Jun '18

28 Jun '18

Hello! I have been trying to get Chimera working through ssh, where the Chimera installation is located on a Red Hat based cluster, but the user is using a MacOS machine to access the cluster. Looking through the archives of the mailing list, I found a suggestion to use VirtualGL to run Chimera through ssh. VirtualGL seems to be running as intended, but isn't working entirely correctly with Chimera (it runs glxgears and other applications fine). It gets farther in start up than without VirtualGL, but crashes on the Initializing OpenGL step around 80% of the time. I have traced the point of failure to reside within a call to the makeGraphicsWindow function within the tkgui.py file. Specifically, it fails at the line within the makeGraphicsWindow function: graphics = Togl.Togl(parent, **kw) which is found somewhere around line 2690 within the try / except portion which is itself nested in the while 1 loop. I can't determine why exactly it is failing here, and trying to trace the problem to a specific line within the instantiation of the Togl object proved fruitless. I was wondering if anyone would be able to shed some light on what could be causing this issue, or know how to fix it? Alternatively, if anyone knows of another good solution for using Chimera through ssh on a Mac machine, that information would be greatly appreciated. Thanks for taking the time to read my inquiry! Best, Logan Sweezy Scientific Systems Admin Rockefeller University

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adding measurement to Angles/Torsions via command line
by Ryan Pavlovicz 28 Jun '18

28 Jun '18

Hi, Is there a way to add a torsion measurement to the Angles/Torsions table via command line so that i can create a .com file to more easily analyze multiple measurements upon opening my session? The best workaround I can think of is to just use the 'angle' command followed by 'start Reply Log'. Thanks, ryan

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Re: [Chimera-users] Display errors
by Elaine Meng 28 Jun '18

28 Jun '18

Hi Ahmad, To summarize for the others: this is not a display error but missing secondary structure information. The reason is that the multiple-model single-PDB format is technically only for multiple coordinate sets of the same set of atoms (like an NMR ensemble), and there is only one set of helix/strand information at the top of the file that is used for each of the models. Chimera includes only the information from the first model when writing the file. In your case, although the two models look like copies of each other, they actually have some different chain IDs. In the new single file, your second model is mostly lacking this information. As I mentioned before, you can simply calculate helix and strand after opening the file: ksdssp However (and you might not care about this anyway), the assignments might be slightly different than in the original files. If you want to keep exactly the original secondary structure assignments , the better way to make a single PDB file is to combine the two models into one model before saving. You can combine models using the Model Panel (open from Favorites menu): choose both models on the left, then click “copy/combine” on the right, or with the “combine” command, for example: combine #0,1 model #2 close true and then save only the new combined model (#2) to a PDB file. I hope this helps, Elaine > On Jun 28, 2018, at 11:01 AM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > Thanks a lot Elaine. I would appreciate you taking a look at my structures. Please find it in the attachments. > > Kind regards. > > On Thu, Jun 28, 2018 at 12:51 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Ahmad, > I do not have this problem when I just open two structures and save them as a single PDB. When I reopen the saved PDB it shows all the secondary structure of both structures. > > When you save make sure you are saving all of the atoms (do not use options “Save displayed atoms only” or “Save selected atoms only”). Other than that, I don’t have any idea what happened with your file, without seeing that file. You could send (attach) it to e-mail. You could send to just me if you don’t want to put it on the list. > Regards, > Elaine > > > > On Jun 27, 2018, at 5:30 PM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > > > I open the structures in the first image, which have the secondary structures displayed correctly. I click file save pdb as single file.That's the process I follow to save the file. How can I fix it? > > > > On Wed, Jun 27, 2018 at 4:54 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Ahmad, > > I don’t what process you used to save the structures in a single file, so I don’t know what went wrong. All I can tell from your images is that in the bottom image, some of the copies do not have secondary structure assignments, and that is why they show up as thin “coil” ribbon instead of the wider helix and strand ribbon. It might be that something is wrong about the format of your single file, or that some of the backbone atoms are missing. If you don’t think there are missing backbone atoms, you could try command “ksdssp” to reassign helix and strand, but the assignments probably won’t be exactly the same as from the original PDB file. > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html> > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Jun 27, 2018, at 8:24 AM, Ahmad Abdelzaher <underoath006(a)gmail.com> wrote: > > > > > > Hello, > > > > > > After saving the two side by side structures in a single file, I get the weird display errors in the picture shown below. How can I fix that? > > > > > > Regards. > > > <before_saving.png><after_Saving.png> > > > > > <A9_padded.pdb><A10_padded.pdb>

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Display errors
by Ahmad Abdelzaher 28 Jun '18

28 Jun '18

Hello, After saving the two side by side structures in a single file, I get the weird display errors in the picture shown below. How can I fix that? Regards.

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(no subject)
by Ahir Pushpanath 27 Jun '18

27 Jun '18

Dear Chimera Team/Users, I wanted to write a python script within chimera that aims to essentially print out a contact map of a selected chunk of residues on an open structure. However, before doing so, I wondered if there is any programmatic way to generate the rotamer library at every position (i.e when you open up the rotamer tool, you get an option of 5-6 conformations you can pick for a residue), I wanted to generate that for every residue in the protein programmatically (and save every rotamer possibility) (as an altlocation?) in the crystal structure. Only after that do I want to calculate the contact map, in essence, I am trying to be as expansive as possible for each residue's "possible" contacts with any other, taking into account the full rotamer ensemble. Any tips on how to manage this programmatically? -- Dr. Ahir Pushpanath* PhD.* Senior Biologist, Johnson Matthey.

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Chimera bug report submission
by Bharat Reddy 27 Jun '18

27 Jun '18

Is it possible to view more than three volumes in the volume viewer window? Whenever I open more than three, the least recent density contouring disappears. I can always go to the data tool bar and select it, but it gets teadious when you are juggling 4+ volumes classes and trying to observe the difference between them. Cheers, BR File attachment: volume_viewer.png

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SASA calculation per residue
by Andrew Macrae 25 Jun '18

25 Jun '18

Hello Chimera developers, I'm trying to calculate sasa scores for a list of individual residues in chimera and cant quite get it. Ive tried commands and the define attribute menu. The command ive been using is 0.23:23/areaSAS I've used similar things but I don't know what Im missing. Thanks for any help. Cheers, Andrew MacRae UCSC

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Exporting STL/COLLADA/OBJ with textures
by Healey, Joe 25 Jun '18

25 Jun '18

Hi, Is it possible for Chimera to somehow export the textures/colour mappings of the models when saving the scene as a .dea/.obj/.stl? At the moment I can export the models, including surfaces (with correct transparency) but I haven't found an option for texturing/colouring? Cheers 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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Structure measurements
by Healey, Joe 23 Jun '18

23 Jun '18

Hi Chimera Team, Is there a quick/automatic way to determine the largest dimensions of a model (maybe its minimal bounding box or similar?) without having to select 2 atoms specifically to draw the distance between? 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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Movie render issue
by BuddySphinx 23 Jun '18

23 Jun '18

Dear Chimera developer, I tried to use the animation to make movies. However, after recoding the output movie could not be seen (Can play but nothing shown). I was wondering what could be the issue? Thank you, Yangqi Sent from Mail for Windows 10

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different docking scores with SDFs and SMILES
by Kerr, Kelly E (HSC) 22 Jun '18

22 Jun '18

Hello, I have really enjoyed using your incredibly comprehensive and user-friendly program. I cannot overstate how much I appreciate it. I'm encountering a discrepancy though that I can't explain. It probably shows a lack of basic understanding on my part, but I would be grateful if you could help me figure this out. I have not been able to find 3D structure files for all of the ligands I'd like to run, so I have been using Chimera to build structures from the canonical SMILES presented on PubChem. I have also been using Chimera to minimize these structures. In order to be sure that the structures are completely minimized I've used the following... Steepest descent steps 1000 Steepest descent step size 0.02 Conjugate gradient steps 10000 Conjugate gradient step size 0.002 I ran this minimization and then AutoDock Vina for both the SDF and SMILES-built versions of several ligands. Both versions came from the same page (I was using PubChem) and both versions seemed to get minimized completely (the minimization outputs ended with many rows of RMSDs of zero). I'm confused that I'm getting different energy values (both initial and after minimization) for the two versions and I'm getting slightly different docking results as well. * Is it expected that SMILES and SDF files of the same chemical should have different energy values even after minimization? * Would you recommend using Zinc (aromatic) SMILES to build structures instead of the canonical smiles on PubChem? OR would you recommend using PubChem CIDs instead of SMILES? Thank you so much in advance for your time and guidance. Best regards, Kelly Kerr

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ChimeraX won't start on Ubuntu 16.04
by Petr Leiman 21 Jun '18

21 Jun '18

Dear ChimeraX users and Developers, ChimeraX v. 0.5 or 0.6 would not start on our stock Ubuntu 16.04 machines. The error message is as follows: This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, xcb. Reinstalling the application may fix this problem. Fatal Python error: Aborted Current thread 0x000014f406ce7740 (most recent call first): File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/chimerax/ui/gui.py", line 93 in __init__ File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", line 485 in init File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", line 788 in <module> File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line 85 in _run_code File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line 193 in _run_module_as_main Aborted (core dumped) A few more errors while checking for missing libraries (ldd) of ChimeraX-supplied libqxcb.so, libqxcb-glx-integration.so or libqxcb-egl-integration.so /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.9' not found /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5' not found /usr/lib/x86_64-linux-gnu/libQt5XcbQpa.so.5: version `Qt_5_PRIVATE_API' not found /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5: version `Qt_5' not found /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5 Do I need to do a system-wide replacement of Qt5 for a different flavor (OpenGLES)? Thanks, Petr

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来自pengweiyucas的邮件
by pengweiyucas 21 Jun '18

21 Jun '18

Dear sir: I want to know how to show the disulfide bond ? Thank you !

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extract parts of a map based on 'volume data gradient norm'
by Dieter Blaas 18 Jun '18

18 Jun '18

Hi, I want to segment a map based on differences in 'volume data gradient norm' which I can adjust as to color the part of the volume I am interested in in blue and the one I want to get rid of in red. Is there a way of doing so? I admit that I never used the segger tool and do not know whether it would be appropriate for this task. The final aim is it to write out the blue volume! Thanks for hints, bw, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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one more suggestion in chimera
by GLY 15 Jun '18

15 Jun '18

dear Eric I sorry to trouble you. Could you just give a more function in Distances of structure analysis, please? When count the distance, we must select 2 atoms exactly. For example, use the command 'select #0:2@CA #1:3@CA' and then click create button, so that we will get the distance between the CA of residue 2 in model 0 and the CA of residue 3 in model 1. HOWEVER, if we type 'select #0:@CA #1:@CA', we can't get all the distances between all CA in model 0 and all CA in model 1! :( So, how about just adding one function, so that the Create button could count serial distance? Maybe it will just be 2 buttons, one for 'select #0:@CA' and the other for 'select #1:@CA'. I am sorry to trouble you, and many thanks. best wishes! Guo NOTE: Maybe you recommend me multiple distance! But I try a lot, such as 'measure distance #0:@CA #1:@CA multiple true'. This command just result the minimum distances between all CA in model 0 and CA in model 1, not all distances! In addition, I see the site 'http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-May/009922.html', <http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-May/009922.html',> too. I am sorry, it doesn't work for we don't know how small the overlap should be. (the smaller overlap, the more contacts would be detected)

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Nucleotide Mutagenesis in Chimera
by Elhajjajy, Shaimae Imane 14 Jun '18

14 Jun '18

Hello, I am trying to mutate nucleotide residues in RNA using Chimera, and I've seen previous posts about using the "swapna" command. However, Chimera is giving the error message "Unrecognized command: swapna". Is there a way for me to enable swapna for Chimera to recognize so that I may use it? Thank you, Shaimae

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Showing/Hiding/Fading
by Gustaf Olsson 14 Jun '18

14 Jun '18

Hello Chimera users and developers, I’m back again. So my movie rendering is progressing though I have of course run into more problems. I have one PDB file open, I need to create a surface around one molecule that is close to other molecules so running the surface command directly does not work as intended. I therefore have to split the PDB file and calculate a surface around a single molecule. All is well, however after this I run into some problems trying to clean up the script. I assume that I am defining the modelID incorrectly though I cannot figure out how. The following works: split #0 atoms :17.het surface probeRadius 0.5 vertexDensity 20.0 :17.het coulombic -5 red 0 white 5 blue :17.het wait combine #0.1-2 modelId 0 close true surftransparency 100 #0.1 This splits the model putting one residue (17) in a separate model, I calculate the surface without issue, color it by coulombic charges. I then have to combine the models (the single residue (17) and the rest of the residues) and close the old “residue 17” model. I then need to hide the newly created surface to display it at a later point in the movie. The script above works, however this does not seem very neat. I have experimented with different other commands, including transparency transp 100,s #0.1 Which also works well, as long as I split and combined the models. However, I have to combine the model for this to work! split #0 atoms :17.het surface probeRadius 0.5 vertexDensity 20.0 :17.het coulombic -5 red 0 white 5 blue :17.het wait combine #0.1-2 modelId 0 close true surftransparency 100 #0.1 Everything but hiding the surface works. transp 100,s #0.1 This does not work either in this case. I am assuming that I am not defining the model ID correctly for the surface and this is why I cannot hide it? I also tried using surfcat: surfcat templ :17.het surf probeRadius 0.5 vertexDensity 20.0 templ coulombic -5 red 0 white 5 blue templ wait surftransparency 100 templ or any of the following: surftransparency 100 #0 surftransparency 100 :17.het surftransparency 100 #0:17.het transp 100,s #0 Hides the created surface, what am I doing wrong in defining the surface to hide it and show it again? Thank you for any input and best regards // Gustaf

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select a specified residue
by 张征锋 13 Jun '18

13 Jun '18

Dear Sir, It is nice to use the amaizing software of UCSF Chimera. I can select a kind of residue such as all 'SER's and label them, while I am able to select a specified number of residue, such as the 200th residue 'Ser'. Could you please show me how to do with this? Thanks a lot. Best, zhengfeng ------------------ Zhengfeng Zhang School of Life Science Central China Normal University. NO.152 Luoyu Road, Wuhan,Hubei, P.R.China 430079

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Symmetry operation calculations for multimeric fibrillar assemblies
by Einav Tayeb-Fligelman 13 Jun '18

13 Jun '18

Dear Chimera support team, I am trying to deposit to the PDB an X-ray crystal structure I solved, and came across with the need to calculate its biological assembly, which is pretty tricky in my case, and so I wondered if Chimera could help me with that. I am working on fibrils made out of repeating units of peptides. The asymmetric unit in my structures usually contains only a monomer, whereas the structure of the fibril is obtained by drawing the copies of this monomer along the fibril axis (potentially there are tens of thousands of those copies), based on the unit cell parameters (the copies are packed within the unit cell). After choosing and drawing an arbitrary number of copies along the axis of fibrillation I would like to get the output of the symmetry operations resulting in this desired representation of the fibril, in order to deposit them as the biological assembly of my structure. I would appreciate if you could advice me to how to obtain those symmetry operations so to define my biomt. Thank you in advance, Einav -- Einav Tayeb-Fligelman, PhD The Landau lab Faculty of Biology Technion, Israel Institute of Technology Haifa, Israel E-mail :einavtf@campus.technion.ac.il Tel at the lab:+972-77-8871964 <+972%2077-887-1964>

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make helical filament model using command sym
by Yaowang Li 13 Jun '18

13 Jun '18

Dear all, I have built a model from cryo-em density map, now I am going to create a model of a filament (have a length of the pitch, over 1000 A) from it. I think the command 'sym' can do it, but not easy for me. I have tried many times. sym #0 group h,rise,twist,100 or sym #0 group c2*h,rise,twist,100 coord #1 or sym #0 group h,2.292,179.6,100 coord #1 the model is wrong I also try to measure the symmetry first and sym #0 group #1 it is almost right, but I need much longer, how set it? using the 'n' parameter? and how? and if I want to set rise and twist myself, how to do it? Best wishes, Yaowang

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FindHBond tool not finding H-bonds with sulfur?
by Gustavo Seabra 12 Jun '18

12 Jun '18

Hi there, I’m trying to use the findHBond tool to count Hbonds in a system. However, I noticed ti does not find any HB involving sulfur atoms in my system. I’ve put together a simple example system here to show what I mean. After opening the files, I do: 1. Select the ligand (Select > Residue > LIG) 2. Tools > Surface/Binding Analysis > FindHBonds 3. Find These Bonds: Both 4. Relax H-bond constraints: (I tried even relaxing to 1A and 30deg, with no change) 5. Select “Only find H-bonds with at least one end selected” 6. Hit Apply. Chimera does find some HBonds involving nitrogen and oxygen, but no HBond is found involving the sulfur atom on the ligand, even though there is a serine (Ser525) close enough to make a HBond to the ligand S atom. So, I wonder what I am doing wrong here? Am I skipping any steps? I have checked in a different program (PoseView) and it can find the bond with no problem. Thank you very much, -- Gustavo Seabra

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Fading structures/surfaces in/out
by Gustaf Olsson 12 Jun '18

12 Jun '18

Making a movie using a CMD script I am using something like the following to fade structures in/out transparency 95 :17.het; wait 8 transparency 90 :17.het; wait 8 transparency 85 :17.het; wait 8 transparency 80 :17.het; wait 8 transparency 75 :17.het; wait 8 transparency 70 :17.het; wait 8 transparency 65 :17.het; wait 8 transparency 60 :17.het; wait 8 transparency 55 :17.het; wait 8 transparency 50 :17.het; wait 8 transparency 45 :17.het; wait 8 transparency 40 :17.het; wait 8 transparency 35 :17.het; wait 8 transparency 30 :17.het; wait 8 transparency 25 :17.het; wait 8 transparency 20 :17.het; wait 8 transparency 15 :17.het; wait 8 transparency 10 :17.het; wait 8 transparency 5 :17.het; wait 8 transparency 0 :17.het; wait 8 Is it possible to use the “frames” function in transparency to achieve the same? Assuming that transparency is set to 100% and I want to fade in of course. transp 0,a :17.het frames 160 Best regards // Gustaf

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making a movie of sliding through contours
by Pranav Shah 10 Jun '18

10 Jun '18

Dear Developers, Would it be possible to make movie clips of electron density map at different density thresholds in chimera. Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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scolor filament (geometry cylindrical)
by René Frank 08 Jun '18

08 Jun '18

Hello People, I would like to surface colour a filament within an EM map using cylindrical geometry (scolor geometry cylindrical). However, the electron density of the filament does not lie perfectly on the x, y or z axis. Is there a way of using two marker points placed at each end (on the longitudinal axis) of the filament to define the orientation of the cylindrical geometry and scolor the filament accordingly? My attempts to do this whilst executing the following command didn’t seem to work: scolor #0 geometry cylindrical axis sel cmap 5,gold:10,red:15,blue Many thanks for any suggestions/help, R. ====================== Dr René Frank ======================

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Re: [Chimera-users] Question Regarding on Finding Distances
by Tom Goddard 05 Jun '18

05 Jun '18

Hi Padua, Search online to find how to update your Windows graphics driver. Unfortunately for old laptops, there may not be any new graphics driver. Tom > On Jun 5, 2018, at 1:01 PM, Xiong, Padua L wrote: > > Hi Tom, > > After following what you have said, under the Gathered Information provided from the Bug Report Dialog I have found: > > OpenGL Vendor: Microscoft Corporation > OpenGL Renderer: GDI Generic > OpenGL Version: 1.1.0 > > Because everything is listed as you have said, I can see that this problem is occurring because of the graphics driver. > > Thank you so much for your fast response. > > Padua > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, June 5, 2018 1:48:07 PM > To: Xiong, Padua L > Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > Subject: Re: [Chimera-users] Question Regarding on Finding Distances > > Probably your graphics driver is not adequate. You can check what driver Chimera is using with Chimera menu Help / Report a Bug under “Gathered information” it will list OpenGL Renderer and Version. If it says Microsoft GDI 1.1 then you are using 1990s graphics and Chimera won’t do selection. You would need to update your driver. > > Tom > > >> On Jun 5, 2018, at 12:26 PM, Xiong, Padua L wrote: >> >> Hi there, >> >> My name is Padua and I'm an undergraduate research assistant working on pharmacogenomics. To do this, I have been using your program UCSF Chimera. >> >> I've been trying to find the distances between a protein and a drug but keep running into problems with selecting an atom in the graphics. When I try doing Ctrl-click or Shift-Ctrl-click to select an atom, I don't select anything at all (nothing is highlighted green as its supposed to when something is selected). >> >> My professor I'm working under has tried changing the mouse settings as well. Is there something I'm missing that's not listed in the User's Guide and tutorials? >> >> Much thanks, >> >> Padua >> _______________________________________________ >> 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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Question Regarding on Finding Distances
by Xiong, Padua L 05 Jun '18

05 Jun '18

Hi there, My name is Padua and I'm an undergraduate research assistant working on pharmacogenomics. To do this, I have been using your program UCSF Chimera. I've been trying to find the distances between a protein and a drug but keep running into problems with selecting an atom in the graphics. When I try doing Ctrl-click or Shift-Ctrl-click to select an atom, I don't select anything at all (nothing is highlighted green as its supposed to when something is selected). My professor I'm working under has tried changing the mouse settings as well. Is there something I'm missing that's not listed in the User's Guide and tutorials? Much thanks, Padua

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Atom Specification not working in exported PDB
by Gustaf Olsson 03 Jun '18

03 Jun '18

Hello again Chimera Users So now that I have the “movie” command working decently, it turns out that I cannot export a PDB file from my MD simulation and retain the ability to select by residue or atom number. PDB files generated by other software (PACKMOL, AMBER) works fine though when I exported a PDB file from a fram in an AMBER MD simulation using chimera, I can open the file, I can select using residue names though trying to refer to atom or molecule numbers does not work. To be clear, the exported PDB file contains multiple molecules and solvent, all ar present and the file loads though trying to run commands like show :17 ~show @536-593 Affects EVERY atom and molecule in the system when it should only affect residue 17 (by specifying residue number OR all atoms in that residue). Using the show :XXX works as intended though this affects all residues XXX and I only want to affect residue 17. Am I doing something wrong or can I solve this in a simple way? Best regards // Gustaf

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Place marker at centre of volume box python command
by Kyle Morris 01 Jun '18

01 Jun '18

Hi Chimera dev, Is there a python command to place a marker at the precise centre of a volume’s box, regardless of the centre of mass of the volume in the box? I have played with creating dummy volumes and measuring their centres but it’s clunky and got a bit stuck with doing this. A single command would be cleaner, if it’s possible. As always thanks for your help! Best wishes, Kyle

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Command line syntax questions
by Divita Mathur, Contractor Code 6910, FN 01 Jun '18

01 Jun '18

Hi I am trying to write an alias and am curious if I can do the following using command line (in order to include them in the alias): 1. Separate chains that belong to the same model – can I change the model # on a single chain from an existing model? For example, I built a DNA duplex, selected one chain (sel :.A) and tried to change the model # (combine sel model 8 close true) but the new model also includes chain B. 2. Change residue number of a residue in a chain. I combined a small molecule to a DNA chain between residues 18 and 19, but after combining, the molecule’s residue number remains 1. I would like to change it to 19 or 18. 3. Following point #2, I also want to assign the new molecule the same chain ID – A. In the pdb file, the chain ID is blank for the newly inserted molecule. Thank you for your help. I also want to mention that the Chimera user discussion portal has been very helpful otherwise! Best, -- Divita Mathur Postdoctoral Research Fellow Center for Bio/Molecular Science and Engineering Naval Research Laboratory Washington DC 20375 (202) 767-0687 (Office) divita.mathur.ctr.in(a)nrl.navy.mil

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Recording a movie of an MD simulation
by Gustaf Olsson 30 May '18

30 May '18

Hello everyone First time posting, looking for some advice. I have an MD simulation that was produced with the AMBER software package and I want to record a movie (MP4) file of the simulation. I wanted to use a CMD file and not go through the GUI since this would be a step in a series of steps and I was also hoping to perform some “in movie” modifications to the structure though I quickly ran into a huge issue, the frame rate. So basically i tried something like this: movie record size 3840,2160 format png supersample 3 coordset #0 1,-1 wait 10 movie stop movie encode output /Users/guolaa/Desktop/Arbete/Konferenser/MIP2018/Presentation/myMovieFolder/mdSimulationBox.mp4 format mp4 quality highest >From this I received what looked like a single frame of “movie”. This seemed very strange to me since I assumed that this would be 500 PNG images resulting in a 20 second movie at 25 fps. It seems I’m missing something in the process since MD iterations, frames and frame-rates does not seem to match up. I’ve gone through the documentation regarding maxFramerate, movie, coordset and so forth and I can’t work out a decent strategy. I have 500 iterations (MD-frames) loaded, I want to record a smooth 10 seconds (-ish) long MP4 movie file covering the entire range of MD-iterations (first frame to last frame though not necessarily every frame in between) and I want to do this in a CMD script and not using the GUI menu system since I plan to do more things while recording at some point (manipulating representations). Thank you in advance for any input, best regards // Gustaf

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chimera clear selection
by Brian Ondek 29 May '18

29 May '18

Hi chimera help,I have been using chimera and find it extremely useful. I was finding particular protein sequences within my structures and hit clear selection under the select tab.Now whenever I try and find a seq, it wdoes not show up and "selection cleared" appears in the bottom right corner of the window. I tried to reboot and the issue persists.Interestingly I can still see amino acid and chain selections just fine.How can I undo this "clear selection" issue I inadvertently caused? Thank you in advance for your help.Brian Ondek

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