- Chimera-users - RBVI Mailing Lists

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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Ca-Ca difference plot
by Luca Pellegrini 30 Nov '16

30 Nov '16

Hi, I have superimposed two structures of the same protein in two different conformations, and now I would like to calculate a plot of the distances between alpha carbons for each residue in the two conformations, to quantify the relative movement of different domains in the protein structure. Can anyone please explain a simple way of doing this in Chimera? Apologies if I missed something obvious, I tried 'RR distance maps' but couldn’t figure out how to do this simple task. Best regards, 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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Visualizing Orientation of Side Chains
by Christian Bock 30 Nov '16

30 Nov '16

Hello, I am new to Chimera and want to visualize how the side chain orientation for a specific residue changes in different structure predictions. Means I have a correct structure and several predictions and I want to see how different the orientations are among the predictions with reference to the correct structure. I was looking at the MD movie but I am not sure if it's smart to put the correct structure and all predictions into one .pdb file to make a movie. Does anyone has other suggestions? Thanks, Christian

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using Chimera to superimpose structures using sequence alignments
by Elaine Meng 28 Nov '16

28 Nov '16

Hi Deepak, You would still have to show the Chimera GUI (it cannot be done running Chimera with no GUI), but if you mean using a script instead of interactively choosing menu items, it may be possible. However, there is no Chimera command to do this. It would require a Python script. For future reference, we recommend sending Chimera questions to the chimera-users(a)cgl.ucsf.edu list (which I CC’d here, so you do not need to re-send this question). Since today is a holiday, and I do not know Python, somebody may be able to help you with this question next week. Best, 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 Nov 24, 2016, at 3:08 PM, Deepak Kumar <deepakk1(a)andrew.cmu.edu> wrote: > Dear Dr. Meng, > I am a Bioinformatician at the Computational Biology Department of Carnegie Mellon University. I have been using Chimera for visualization purposes and for many other of its features. I got to learn about your expertise from here: > > http://www.cgl.ucsf.edu/home/meng/index.html > > May I please request you to give your suggestions on this problem mentioned below: > > I know of one feature "multialign viewer" which uses a fasta alignment file to superimpose two pdb structures in Chimera. However, I have been using this feature through the GUI of Chimera. I am in need of using this feature standalone i.e superimpose two pdb structures based on a fasta alignment file. May I please request you to let me know, how can I perform this step standalone and not through Chimera GUI. > > Thank you so much for your time and consideration. > Yours Sincerely, > Deepak

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On the adding of the dynamics effect on the static structure
by James Starlight 28 Nov '16

28 Nov '16

Dear Chimera Users! I am interesting whether it possible to add some impression of the dynamics to some static elements of the pdb? Assuming that I am working with the visualisation of static x-ray structure and would like via some vizualisation trick to add some element of the conformational dynamism (like what can be obtained from the md trajectory or nmr ensemble) to the selected fragment of the structure (e.g loops or alpha-helix) eventually making impression of the several conformers superimposed on the structure? Thanks so much for any suggestions! James

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FW: Channel and normal mode calculations
by Williams, Joanne 28 Nov '16

28 Nov '16

On 11/28/16, 8:43 AM, "Mohamed Noor" <mohamed.noor(a)ul.ie> wrote: >Hello. > >I am wondering whether Chimera can do these calculations natively? Or do >I need some plug ins? > >Thanks. >Mohamed

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failing to open saved PDBs
by Healey, Joe 28 Nov '16

28 Nov '16

Hi (again) Chimera Team! Encountered a problem where chimera seems to fail to open PDBs that it created. I saved multiple PDBs to a single file as I wanted to open them and have them behave like a single structure. I started a new session with another PDB open that I want to compare the multiple PDBs to, went to open the multiple PDBs from before that I saved as a single file and nothing appears. Chimera claims to have opened the files successfully and I get no errors etc. Am I maybe misunderstanding the point/use of the multiPDB file form? 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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Fit in map equivalent for surfaces?
by Healey, Joe 28 Nov '16

28 Nov '16

Hi Chimera Team, Is it possible/does a function exist to fit one structure inside the calculated surface of another? To be clear, i don't mean inside a density map, I mean an MSMS surface calculated from a PDB inside chimera itself. I have 2 proteins that are sequentially very different, but I suspect fulfilling the same role. They don't overlay via MatchMaker well, but they look to have quite similar space occupation, so I'd like to see how well they fit in one anothers 'map'. Any alternative suggestions appreciated! Thanks, Joe 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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angle between subunits
by chemocev marker 26 Nov '16

26 Nov '16

Hi All I am interested to measure the angle between chain A and chain B of heterodimer, and both sequence identity is around 14%. I can measure the angle by selecting 3 atoms on chain A and chain B but this is bias because, if I change the residues then the angle will be different. I can also measure by structure measurement options and defining the axes and all the create axes for all the helices in the chain A and chain B and measure the angle between two helices on chain A and chain B. I am not sure if its a right way to claim the angle between chain A and chain B in one PDB file. I also try to use the "match :.A at CA <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> :.B at CA <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> move false show true" But it gives the rotation angle. As I am comparing the different homologous structureswhere chain B shows more identity but the each structure have a different state giving a unique angle between chains. What can be best option to measure this??? best Jiri

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simple question
by A G Szabo 25 Nov '16

25 Nov '16

I should be able to find this but haven't looked too hard. I am interested in a salt bridge between the C-terminal carboxylate and a Lys residue in the protein. I know how to visualize the Lys side chain, and the C-terminal residue. How do I visualize the carboxylate terminus? I tried backbone only actions, but nothing worked. Thanks AGSzabo

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