July 2018 - Chimera-users - RBVI Mailing Lists

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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Chimera-users July 2018