- Chimera-users - RBVI Mailing Lists

Centering Origin Index on Command Line
by Yong Zi Tan 10 Jul '17

10 Jul '17

Hi, Could I check if there is a command line version of the "center" button under Origin Index in the Volume Viewer? Thank you! [cid:image001.png@01D2F697.ECEEC010] Warmest Regards, Yong Zi Tan

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large datasets
by Arthur Szabo 10 Jul '17

10 Jul '17

I am trying to work with a data set that has three copies of a protein complex per asymetric unit in the cell. It is a rather large complex. I can delete two of the copies and work with only one complex. There are 9 chains in each complex. 3 oligonucleotide sequences, and 6 proteins of different sizes, the largest having about 1400 residues. The way in which I selected only one complex to visualize was to delete the other 18 chains one at a time. There must be a way of deleting each of the other two copies all at once but I did not try to find it in the Chimera tutorial list. The deletion only eliminates the image of each complex. Both complexes are still there in the total data set. The result is that saving a session takes about three minutes because it saving all the coordinates of the three copies of the complex. How can I make the process more efficient and delete two copies from the coordinate data set. Thank you Arthur G. Szabo

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software for protein 3D structure visualization
by fateme shaki 08 Jul '17

08 Jul '17

Dear Sir/Madam, I am looking for a program which could transform enzyme activity to a 3-dimentional form of the enzyme. I am not sure about such a program and I am not sure whether there is such program or not. I just saw the software for protein 3D structure visualization on your website and I assumed that this program might be useful. Could you please assist me in this case. Thank you in advance. Fateme

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Can I attach images when asking Chimera users mailing list?
by Jun Song 07 Jul '17

07 Jul '17

Hello, I have been looking at the archived discussions, and I have never seen a single discussion that had any images. Is it just archived transaction that is lacking images, or is it not possible to attach images to this email? Best, Jun Ha Song.

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Define Plane
by Catherine Jenifer Rajam Rajendran 01 Jul '17

01 Jul '17

Hi, I am trying to understand how the plane is defined in chimera. Can you please help me with that? "Define a plane for the specified <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> atoms. Eigenvectors/values are calculated from the atomic coordinates after subtracting the position of their non-mass-weighted centroid. The plane is anchored at the centroid and aligned with the first two eigenvectors (the third eigenvector is normal to the plane)." Define a plane for the specified <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> atoms. - specified atoms, i use 'sel protein' Eigenvectors/values are calculated from the atomic coordinates - atomic coordinates, so x,y,z coordinates of all atoms. (Can you please explain a bit more like how and what you read from PDB file to define plane). after subtracting the position of their non-mass-weighted centroid - how is non-mass-weighted centroid is calculated The plane is anchored at the centroid - which centroid is this? Is the protein moved to the origin(0,0,0) position? Thanks, Catherine

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Fwd: pdb-l: EMBL-EBI user survey
by Eric Pettersen 28 Jun '17

28 Jun '17

> Begin forwarded message: > > From: Gerard DVD Kleywegt <gerard(a)xray.bmc.uu.se> > Subject: pdb-l: EMBL-EBI user survey > Date: June 27, 2017 at 3:30:30 AM PDT > To: pdb-l(a)ucsd.edu > Cc: Gerard Kleywegt <gerard(a)xray.bmc.uu.se>, "Gerard Kleywegt \(EBI account\)" <gerard(a)ebi.ac.uk> > > Dear colleagues, > > EMBL-EBI (http://www.ebi.ac.uk/) is running a worldwide survey to understand > usage of its resources (there are several dozen, including UniProt, Ensembl, > ChEMBL, EuropePMC, PDBe, EMDB/EMPIAR and many more). We would like to ask you > to forward this request within your department, company or institution. We are > interested in responses from a wide range of scientists, in particular those > who do not think of themselves as bioinformaticians. The results are extremely > valuable to EBI in helping us to understand our users, and our users' needs. > > Here is the link to the survey: > https://www.surveymonkey.co.uk/r/2017_EBI_survey > > Many thanks! > > --Gerard > > --- > Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK > Head of Molecular and Cellular Structure > gerard(a)ebi.ac.uk pdbe.org emdb-empiar.org > PA: Pauline Haslam pdbe_admin(a)ebi.ac.uk > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > https://lists.sdsc.edu/mailman/listinfo/pdb-l .

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Difference between Chimera and ChimeraX
by Bon Ikwuagwu 26 Jun '17

26 Jun '17

Hello, I'm a first year graduate student and I am wondering what the differences are between Chimera and ChimeraX? I want to use the tools that are present in Chimera, but I don't know if those tools are also present in ChimeraX. Any feedback would be helpful. Best, Bon Ikwuagwu -- Bon Ikwuagwu PhD Student, Chemical and Biological Engineering Northwestern University

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Libfftw3.so.3
by Robert Waugh 26 Jun '17

26 Jun '17

Hello, I am a Masters Student from Kingston University, I am currently using Chimera as part of a Bioinformatics Project. For this project, I have decided to use IMP to integrate the data I have to make a coarse grained model. Unfortunately, upon using MultiFit I receive the error which I have posted below which states that I cannot open the shared object file libfftw3.so.3. I was wondering if it would be possible if you were to make this file available so that I can complete my Multifit Modelling. https://pastebin.com/kkRW6X3U Thank you, It would be much appreciated, Robert Waugh

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Trying to change dihedrals: ValueError: bond is part of a cycle
by Nikolaos Bismpikos 26 Jun '17

26 Jun '17

Hey, my goal is to change the dihedrals of an already existing pdb template in order to find low-energy protein conformations. The issue I have here is that for some residues the dihedrals phi and psi cannot be changed. That's the error I get: Traceback (most recent call last): File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line 683, in init chimera.openModels.open(a, prefixableType=1) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1929, in open models = func(filename, *args, **kw) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1299, in _openPython loadFunc(sandboxName, fileName, f) File "predictor.py", line 40, in <module> es.main_loop(); File "/home/nick/Python/pdb/AbstractOptimizer.py", line 97, in main_loop self.fs, self.evals, self.terminate = self.eval_pop(self.eval_func,self.pop,self.evals,self.eval_budget,self.extra_par) File "/home/nick/Python/pdb/eval_energy.py", line 20, in eval_energy allR[j].phi = pop[i,j]; File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py", line 98, in setPhi _setAngle(bond, phi, getPhi(res, missingIsError=True), "phi", anchorSide) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py", line 147, in _setAngle br = BondRot(bond) ValueError: bond is part of a cycle Is there a way to determine beforehand which bonds are part of circle and hence which residues' dihedral information cannot be changed? Thank you in advanced for your time, Nikolaos Bismpikos

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Chimera to Excel
by Fábio Pereira 24 Jun '17

24 Jun '17

Good Afternoon, I would like to know if i can to export informations opened in View Dock to Microsoft Excel. If this is possible, how can i do ? great!

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