- Chimera-users - RBVI Mailing Lists

Saving Output From Match Align
by Muk, Sanychen 22 Dec '16

22 Dec '16

Hello, I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays. Best, Sanychen Muk --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) ---------------------------------------------------------------------

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ChimeraX daily builds available!
by Elaine Meng 22 Dec '16

22 Dec '16

Prerelease daily builds of UCSF ChimeraX are now available to the public! UCSF ChimeraX home: http://www.rbvi.ucsf.edu/chimerax/ Download: http://www.rbvi.ucsf.edu/chimerax/download.html Please keep in mind that ChimeraX features are currently quite limited, that ChimeraX may not work on older machines and/or graphics cards, and that due to the upcoming holidays, responses may be slow if you contact us. On behalf of the Chimera/ChimeraX team, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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change default color maps
by Michał Kadlof 21 Dec '16

21 Dec '16

I found Palette Editor Tool, but I don't know how to use it. How can I apply chosen pallete in Surface Color Tool or load colors from palette into rainbow tool? -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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Crossfade and disp
by Daniel Asarnow 21 Dec '16

21 Dec '16

Hello Chimera experts, Here is another movie making question. I noticed that disp and ~disp trigger frames to be recorded, without a call to wait. For example: disp #2 movie crossfade 25 ~disp #2 disp #3 This would produce a movie that crossfades from model #2 to blank, with #3 suddenly appearing. To get crossfades between two ligands, I had to use: disp #2 movie crossfade 25 perframe "~disp #2" frames 1 disp #3 movie crossfade 25 Based on the documentation I wasn't sure if this was intended behavior or a bug. Did I miss a more elegant way to crossfade between two models? Thanks, -da

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Multiscale models command
by Ian Holmes 20 Dec '16

20 Dec '16

Hello Chimera gurus, I am using multiscale models to view a virus capsid (PDB 2QA0) in Chimera. I would like to create a Python script to render the capsid as a multiscale model and then highlight (i.e. select) certain residues. However, I can't figure out the command-line syntax to create a multiscale model. The docs also suggest the Midas Python module as an alternative way of scripting Chimera in Python, but I haven't yet found that module. Here is the rough order of what I am doing from the graphical user interface: Open model 2QA0 Tools menu -> Higher-order structure -> Multiscale Models panel (The following actions are all in the Multiscale Models panel) Click "Make models" button in "Models from molecules and matrices" section Click "All" button in "Select chains:" section Click "Hide" button in "Act on selected chains" section, "Selected chains" subsection Click "All" button in "Select chains:" section (again) Select "Ribbon" from "Style" menu in "Act on selected chains" section (then back to the main view) Zoom out (with mouse wheel) Favorites menu -> Command Line Type "select :10,20,30" (amino acids I want to highlight) Here is what I've got so far in terms of equivalent Python code: import os from chimera import runCommand as rc rc("open 2QA0") # make multiscale model here? rc("select :10,20,30") # select some residues Your help would be appreciated - thanks! Ian

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(no subject)
by Kartheek 19 Dec '16

19 Dec '16

Hi UCSF CHIMERA users, I am trying to make a movie in chimera using MD movie and pdb option. However I have been stumbled with the following error "Residue 256.C not in first model on line 20792 of /tmp/tmpvr4a2t.pdb". I do not have any end records, how can I rectify the error ?? -- Sincerely, P.Kartheek, Research Scholar, IIIT-H, Hyderabad, INDIA.

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Surface clip coloring
by Michał Kadlof 16 Dec '16

16 Dec '16

How can color volume by value with binning several values into single color? I achived the effect partialy by opening several times the same map. set different thresholds and colors to each one and playing with Per-Model Clipping tool, but it have some drawbacks. Planes can't be at exact same level because I observe artifacts. So I tried to move slightly inner layers upp, but still I observe "staris" effect. I also tried with Surface color tool, but it uses interpolation and blends colors togather. In other words I need something like this: https://1.bp.blogspot.com/-5B5ueLHCBPY/T4II4IddvwI/AAAAAAAAB_w/rYwqsJNldY0/… instead of something like this: https://i.stack.imgur.com/hQmry.png -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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probably a bug
by Michał Kadlof 16 Dec '16

16 Dec '16

Hello, I visualize density of my data two different way with the same thresholds and observe different sizes of regions. Isn't it a bug? -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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Hide side chain
by Zhu, Xiaoyan 12 Dec '16

12 Dec '16

Hello, I am using UCSF Chimera to generate figures of protein crystal structures. Some crystals, if open in Chimera, automatically show the side chains of some amino acids. I want to hide those side chains in my figures. I wonder if there's an easy way to do it. Thank you! Have a good one, Xiaoyan Zhu Ph.D. Candidate Department of Biological Sciences, Marquette University

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Multiple transparent objects
by Daniel Asarnow 12 Dec '16

12 Dec '16

Hi, I'm having some trouble with a movie of a morph between structures of the same protein bound to two different ligands. The basic idea is a closeup of the binding pocket, and as the morph progresses the initial ligand becomes transparent while the second one becomes opaque. The result is a similar effect to crossfade, only the morph animation is playing simultaneously. I've tried both the screen capture and ray tracing methods, with the following results: Screen capture - When a ligand is almost entirely transparent, a white silhouette is shown at the highest z-order, blocking what's behind. - There is a "pop up" effect when the ligands suddenly switch z-order at the beginning and end of my animation. - Single-layer and flat transparency options don't help. Ray tracing - Multiple transparency is fine. - Reflections and shadows are not made transparent. - E.g. when one ligand is 100% transparent, the reflections and shadows are still visible as white lines and dark spots. Maybe someone here has some insights on my transparency problems? A way to use crossfade instead would be even better. I can record movies with the two ligands separately and then crossfade them manually with ffmpeg. However, it would be nice to have this working entirely in chimera, especially for some more complicated animations I have in the works. Best, -da

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.pyc session file
by Luca Pellegrini 12 Dec '16

12 Dec '16

Hi, How can I open in Chimera a saved .pyc session file? When I try, Chimera reports the following error message: Error while processing /Users/lp212/Dropbox/<filename.pyc>: .pyc files are not portable; please use .py file instead Unfortunately I don’t have the .py file, Chimera doesn’t seem to have saved it (not sure why). Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

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Selective lighting
by Oliver Grant 12 Dec '16

12 Dec '16

Hi all, Is it possible to use the lighting command and have it apply only to particular models? I'd like my ligand to "pop" out by having a light that only shines on it, and not the protein. Oliver

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Fit-to-window for procedurally generated images
by Mike Sivley 09 Dec '16

09 Dec '16

I am procedurally generating images of protein structures using a Chimera python script. I can center the protein structure within the viewing window, align the protein to emphasize certain elements, set the output size of the final image, and manually apply a scale factor to the view, but I have not found a way to ensure that the protein structure is maximized (but fully contained) within the final image. Is there a "fit-to-window" command that will automatically scale the view in this way? Thanks! Mike Sivley

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How to find symmetry parameters for icosahedral molecule
by Haselbach, David 08 Dec '16

08 Dec '16

Hi everyone, sorry to ask such a basic question. I have a cryo EM density map 3.2 A of a icosahedral molecule and I already build the model of the monomer. I would like to place the remaining 59 copies and calculate the BioMT matrix for it. I started playing around with the sym command, but I couldn't get it working nicely. It's probably a problem of the coordinate system, but I couldn't figure it out. Than I thought there must be an automatic way and I tried Multifit but also this failed me miserably as the runs fail continuously with "stderr". So I was wondering is there a protocol to do this? Already thank you for any suggestions, David Dr. David Haselbach Max-Planck-Institute for biophysical Chemistry Department for structural Dynamics Am Fassberg 11 37077 Germany Tel. +495512011302

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symmetry axis
by chemocev marker 08 Dec '16

08 Dec '16

Hi All I am interested to measure the symmetry axis of individual sub-unit (chain A & chain B) along with the symmetry axis of the heterodimer (AB). Each chain has 2 domains and 2 fold rotations axis, and I can measure by removing 1 chain and measure for the other. Is there way to measure the inter-domain symmetry axis of the heterodimer molecule. best Jiri

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Fwd: chimera minimize option
by Jacqueline Vitali 07 Dec '16

07 Dec '16

It puckers ASN and ASP (and probably other amino acids). (I run it to relieve steric conflicts only) How do you fix this? And can you run it with the whole protein selected?

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question
by A G Szabo 06 Dec '16

06 Dec '16

You have been very helpful in explaining different items that use the command line. I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc. So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number. I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model. Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K. The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec <frameatom_spec.html> I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1. So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly. Thank you Arthur G. Szabo

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Re: [Chimera-users] Chimera -> Povray
by Elaine Meng 05 Dec '16

05 Dec '16

Hi Lothar, If you use "File… Export Scene” (instead of Save Image) or the “export” command, there is an option to save a file for POV-Ray without rendering: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> 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 > On Dec 5, 2016, at 3:07 PM, esserlo(a)helix.nih.gov wrote: > > Hi, > currently, I am using chimera to make a figure for publication and render > the result in povray. However the figure is a bit complex - with a gradient > background just to mention one thing- so that I have to edit the .pov file. > Is there a way to ask chimera to output the .pov file but not render it in > povray right away (that would save time as I need to edit it first!). > > Unfortunately in the "save image" menu, using povray, I did not find a > checkbox that would enable chimera to write out .pov only. > Thanks for any advice. > Lothar >

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difficulty in using chimera for large PDB files
by Shruti Khare 05 Dec '16

05 Dec '16

Dear Sir/Madam, When we use chimera to visualize PDB files with ~18,000 atoms (PDB ID 5FUU) even rotating the molecule is slow in chimera. The computer has 6GB RAM. Would upgrading RAM help or we need to get a graphics card installed? Graphics card capacity should be 2GB or higher? Could you please tell me the minimum computer configuration required by chimera to handle large PDB files? Also what is chimera's maximum limit for handling PDB files given a computer with very good configuration? Thank you. -- Shruti Khare Graduate Student Prof. Raghavan Varadarajan Lab Molecular Biophysics Unit Indian Institute of Science Bangalore +91-80-2293-2612 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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pipes and planks
by Kyle Morris 02 Dec '16

02 Dec '16

Dear Chimera dev, I am using the pipes representation. In this case is it still possible to color/highlight a segment by residue number? Using the normal commands when displaying pipes doesn’t update the color, only on the original model. Thanks for your help! Best wishes, Kyle

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Selected measure angles
by Soumya Govinda Remesh 01 Dec '16

01 Dec '16

Hello, I have just modified the loop script available here ( http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html) to measure certain angles and distances. I just want to know if there is a way to export the individual values of angles and distances to a file other than parsing from the reply-log. Thank you. Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh(a)lbl.gov

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saving pdb with transformed coordinates
by Michael Elbaum 01 Dec '16

01 Dec '16

Dear Chimera people, I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates. I've tried the following: for i in xrange(0,90,10): rc("rock " + "y " + str(i) + " 1") fn = basefn + str(i) + '.pdb' rc("write format pdb 0 " + fn) and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11. thanks for your help, Michael

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Unit cell
by Neha Gandhi 01 Dec '16

01 Dec '16

Hi Elaine, I have tried to look at the unit cell information of pdb Id :3HR2. It is a fiber diffraction structure of collagen with only CA coordinates. I tried using different programs like VMD to visualise unit cell, the unit cell is at the beginning of N terminus in agreement with experimental paper. Whereas in Chimera it is not the case. How can I visualize the unit cell of 3HR2 structure in Chimera and also number of molecules within one unit cell? Many thanks, Neha -- 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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Re: [Chimera-users] failing to open saved PDBs
by Healey, Joe 30 Nov '16

30 Nov '16

Hi Elaine, OK, that is what I had expected to happen yes - and that NMR ensemble looks to be what I was anticipating. I've attached the PDB chimera created here. I'm no expert on PDB internal formatting but it at least looks to me like there are coordinates, sequence information etc etc. I had thought that I had taken care to make sure whole models were saved (not just sel atoms), but I'll replicate it to make sure. Applying the preset in any event didn't work. Maybe you can spot what's wrong with it? Joe Healey M.Sc. B.Sc. (Hons) 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>

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more questions about visualizing the backbone.
by A G Szabo 30 Nov '16

30 Nov '16

Last week I asked a question regarding about how to visualize the backbone atoms. I have figured that out. I am working with a peptide that forms an amyloid structure. The peptide strands form a beta sheet. When I select two of the peptide units that are hydrogen bonded to form two strands in the beta sheet, the strands are shown as a coil type structure rather than a flat beta strand. How can I change the coil backbone to a beta strand structure? Second part is there a simple way to suppress the side chains but leaving the backbone atoms? I have included two peptide units that are hydrogen bonded to one another. Thanks Arthur G. Szabo

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