- Chimera-users - RBVI Mailing Lists

Including halogen atoms in findHBond tool?
by Nawel Mele 23 Jul '18

23 Jul '18

Dear Chimera users, I am looking for hydrogen bonds between a receptor and an ensemble of docked ligands with different structures including halogen atoms. I would like to know if there is a way to include halogen atoms in the hydrogen bond (findHBond) facility ? Best regards, Nawel -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK)

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Question about disulfide bonds and energy minimization
by Steven Douglas Aird 23 Jul '18

23 Jul '18

Dear Elaine, For the first time in about three years, I need to do a little more modeling. We sequenced an NADase and I used Galaxy to create a model using a known CD38 structure as a template (attached). Chimera displayed everything, but the disulfide bonds, of course. So I entered the specifications for those manually into the PDB file (attached). Two of the disulfides displayed properly, but four appear as thin dashed lines. At least one, at the C-terminus is clearly way too long. I tried to do an energy minimization, but while Chimera executed the steps, nothing in the structure moved. It used to be that one could watch the structure flex as it assumed the most energetically favorable conformation, but not this time, yet some of the disulfide bond lengths are clearly wrong. I also tried to use the set length command, in the forms: set length 2.05 / Set Length [2.05] but Chimera does not like either of these commands. If the manual included examples of the command format for each command, that would be really useful, because it is not clear where the syntax problem lies. As always, thanks for your help! Sincerely yours, Steve Steven D. Aird Technical Editor Faculty Affairs Office 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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Morph Conformations tool doesn't produce a model with ribbons + *atoms*.
by Alex Nazlidis 22 Jul '18

22 Jul '18

Hello, I am trying to use morph conformation tool to produce a morph in a ribbon + atoms representation. While my 2 models are represented exactly as I want, when I create the morph the atoms diasappear and I'm left with the ribbon representation. Is there a way to create what I want? Regards, Alex

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Truncating fitted structures using a map mask
by Ahmad Khalifa 20 Jul '18

20 Jul '18

Hello, I have a tubulin lattice (sheet) fitted into a microtubule map. I want to generate a structure that has only one dimer, surrounded by only fragments from the other dimers on the top, bottom and sides. Is there a way to do that in chimera? Regards.

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Problems with V1.13
by Stefan Kunert 20 Jul '18

20 Jul '18

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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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