- Chimera-users - RBVI Mailing Lists

Scripting commands for existing morph
by Cristina Paulino 29 Mar '17

29 Mar '17

Dear all, I would like to create a movie from an existing morph between two pdb coordinates. I was able to create a movie via the GUI as described in the manual. However I prefer to use scripts as it allows me to control every single step. I would like to be able to define exactly which frames should be shown when. For example, I would like to define in a script that it should wait at endpoint one (first structure) for x number of movie frames. Then interpolate (morph) to the other endpoint (second structure) for x number of movie frames and then wait again for a specified number of movie frames. Or even more complicated rotate the molecule or superimpose something else while it is interpolating/morphing between the pdb coordinates. Can anyone help me out? I couldn't find any good description for this. Many thanks in advance Cristina

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Re: [Chimera-users] [chimera-dev] (no subject)
by Elaine Meng 29 Mar '17

29 Mar '17

> On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > Hi, > Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. > Thank you. > Regards, > Kavya Shankar Hi Kavya, Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues

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ChimeraX Alpha release
by Eric Pettersen 28 Mar '17

28 Mar '17

Hi all, We have released an alpha version of ChimeraX. While it still lacks many features, it has enough useful new and fun features that you might want to take it out for a spin even if it doesn’t prove ready to be your day-to-day workhorse yet. Hope you like it! Home page: http://www.cgl.ucsf.edu/chimerax/ <http://www.cgl.ucsf.edu/chimerax/> Download page: http://www.cgl.ucsf.edu/chimerax/download.html <http://www.cgl.ucsf.edu/chimerax/download.html> —Eric Eric Pettersen UCSF Computer Graphics Lab

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来自"高振飞" <16110440015@fudan.edu.cn>的邮件
by 高振飞 28 Mar '17

28 Mar '17

Dear professor: I'm a student from Fudan University, I want use the software -- chimera. But I can't download it, can you send it to me by using E-mail? thank you very much. with my best regards yours sincerely Zhenfei Gao -- Zhenfei Gao(高振飞) Department of Macromolecular Science Fudan University 310 Yuejin Hall 220 Handan Rd. Shanghai, China 200433 M: +86-18516637266 QQ: 7693692

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Create an entire virus from Octant
by Li, Zongli 27 Mar '17

27 Mar '17

Hello, I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? Thanks, Zongli

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MD analysis outputting to file
by Neha Gandhi 23 Mar '17

23 Mar '17

Dear Chimera support, I want to calculate the centroid of the sugar ring and the distance from the centroid to another atom of amino-acid. I know this can be done using the Structure analysis tools in Chimera. I want to use distance command in the MD ensemble analysis and output it to the analysis to the text file. How can I write output per frame to a text file in Chimera? Your insight is appreciated. -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate

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Ensemble models
by Mohamed Noor 20 Mar '17

20 Mar '17

Hello. I have an ensemble of models from phenix.ensemble_refinement. I notice that Chimera automatically loads the models and displays only a subset of atoms as "atoms/bonds". Can I save this as a preset while changing other settings manually so that I can go back to the automatic preset if I make a mistake somewhere? Secondly, is it possible for Chimera to calculate rmsf of each residue and output the values to a CSV file? I would like to replot them in Excel. Thanks. Mohamed

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Looking at docked data with the receptor shows as surface
by Jonathan Y Wang 20 Mar '17

20 Mar '17

To whom it may concern, Hi! I recently docked a ligand onto a receptor using the AutodockVina tool and when I opened the data the ligand seemed to be placed in the middle of the trimer. I showed the receptor as surface and it seems as if the ligand is too big to fit inside any of the holes surrounding the trimer, but somehow it has placed itself inside. I additionally opened it using PyMol to double check the file, but it also seems too small to fit inside any of the holes. My inquiry is this: Does AutodockVina take into account surface projections when performing docking? Thank you so much for your time, Jonathan Wang

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Getting names of selected atoms and renaming
by Vladyslav Dziuba 17 Mar '17

17 Mar '17

Dear Sir or Madam, I have some difficulties with using ORCA and UCSF Chimera together. Let me describe my problem first. I need to freeze some atoms (actually, a lot of atoms) in my calculations (geometry optimization), e.g. make their coordinates constant. To do that I need to specify numbers of atoms from xyz file, which is obtained from pdb-file. The problem is that for every atom in pdb-file OpenBabel generates a new number (for example H27 may become 100th atom in xyz file), so that specifying atoms that must be frozen becomes much more complicated. Given that, I'd like to ask to help me find answer on some questions: 1. How can I rename atoms? It would greatly help me identificate atoms that must be frozen. Can I rename only all selected atoms? 2.Can I modify names of selected atoms? 3. How can I get list of numbers of selected atoms? For instance I've chosen some aminoacids residues and I want to get names or numbers of all atoms chosen. Because if I one wants to get a list of atoms in xyz file, he needs names or numbers of atoms in pdb file, but the last ones are disordered. Manual atom picking and comparison in pdb- and xyz-files is very time-consuming. UCSF Chimera is a truly powerful program so I believe there must exist an elegant solution to my problem. Hope to receive a letter from you soon. Thanks in advance! Best regards, Vladislav Dziuba

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Re: [Chimera-users] Smoothing and binning volume data
by Tom Goddard 16 Mar '17

16 Mar '17

Set "step 1” above the histogram in the Volume Viewer window to display the full resolution of the data. If step is 2 that means only every other density map grid point is shown along each axis. The step gets set automatically to values greater than 1 when the map is large to avoid slowing down the graphics (rotating, zooming…). The initial step it chooses is controlled by the volume viewer menu Features / Data Display Options… , “Adjust step to show at most [N] Mvoxels”. Tom > On Mar 16, 2017, at 11:41 AM, Andrea Fera <andrea.fera(a)gmail.com> wrote: > > Hi Tom! > > Tank you for your information. > Let me try to explain better what I asked. > > What I seem to have revised is that the virtual sections of my maps have a much higher resolution than the rendered images by Chimera. > This should be because, evidently, I didn't understand yet how to control the default smoothing and/or binning in the volume viewer, of which I used until now the default value. > Can you tell me how to do, or what to vary? > > Thank you for the tip about using two colors in the rendering. Going to try immediately. > Thanks, > Andrea > > > > > > > > > > -- > Andrea Fera, PhD – [Senior Research Scientist] > Advanced Molecular Imaging ; DUNS 824-XXX-XXX > Unit for Cytoskeletal Dynamics , NICHD, National Institute of Health > Email: andrea.fera(a)gmail.com <mailto:andrea.fera@gmail.com> > > > On 16 March 2017 at 14:28, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Not sure what you are asking. You can do Gaussian filtering to smooth a map, or binning to average 2x2x2 voxels together producing a smaller smoother map using the Volume Filter tool. > > To color “solid” style map rendering different colors at different data values click the nodes on the yellow line on the volume viewer histogram and then click the color button below the histogram to change the colors. > > Tom > > >> On Mar 15, 2017, at 7:49 PM, Andrea Fera wrote: >> >> Dear Tom, >> >> How are you? >> I am using Chimera more and more recently, and I have come to the point where I need to be able to control the amount of smoothing and/or binning that it inserts passing from the virtual sections to the rendering. >> >> Could you please send me some information on where I could look for this information? >> >> Another, related, thing. Is there a way that I can color in red or brighter color the part of the rendering including voxels below (or above) a certain threshold value? >> >> I hope that I am not asking anything too strange. >> Especially the first thing would help me greatly. >> >> Thank you, >> Andrea >> >> -- >> Andrea Fera, PhD – [Senior Research Scientist] >> Advanced Molecular Imaging ; DUNS 824-XXX-XXX >> Unit for Cytoskeletal Dynamics , NICHD, National Institute of Health

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