- Chimera-users - RBVI Mailing Lists

Saving images of all scenes in session?
by Oliver Clarke 02 Oct '15

02 Oct '15

Hi all, Apologies for yet another post and thank you for your patience! :-) Feature suggestion (or maybe this exists already?): I would like a way to iterate over all scenes in a session and save an image at each scene, with the same display settings (e.g keep background or make transparent, image format, wall-eye/cross-eye stereo, etc). This would be really very helpful when making, remaking and updating figures. Most of the time, I will have a session, say “Fig1.py”, within which I will have a bunch of scenes corresponding to each panel. It would be really advantageous to be able to take images of each scene all at once, saving each as (for example) Fig1_scene_name.jpg, Fig1_scene_name2.jpg etc. This could work in the same way as saving series of maps or models does now - just have a checkbox in the Save Image dialog for “save images for all scenes in session”, or something similar. It can take quite a while to save each image when on a slow computer, or when using graphics intensive settings such as silhouettes and shadows, so being able to save matched sets of images (e.g. low and hi-res versions, stereo versions, etc) with a couple of clicks would save a lot of time, particularly for example if you realize that the versions you saved the first time were all too low res and you want to go back and save a higher res version of every panel. I realize you guys might not have time to implement this for Chimera 1, as development of Chimera 2 is top priority, so maybe I can write a script to do this in the meantime? Is there any way to return a list of scene names using one of the built in python functions? I guess something in Animate.Scenes ought to do this, but not being much of a python programmer I can’t quite figure it out - any tips much appreciated. Cheers, Oli.

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Problems detecting h-bonds
by Felipe Vasquez 02 Oct '15

02 Oct '15

Hi, I have recently obtained some docking results (I have a complex) and I am trying to detect any protein-ligand h-bonds. Soon, I faced a first problem when I obtain this error message: "More than 2 coplanar positions specified!", and I think I solved it once my ligand was selected and I enter into the command line: "setattr a idatmType sel". However, I obtained later an entire panel (with a big list in it) asking me to indicate the expetd geometries and number of substituents for a large list of atoms, from both ligand and protein. How could I overcome this issue knowing that there is several expected h-bonds to be detected in my complex? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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Morphs
by Dr Kereiche 02 Oct '15

02 Oct '15

Dear Chimera team, lately I am facing some problems for creating a movie in which I would like to combine 2 morphs with each other. To make it clearer, I hope, I have 2 Em maps representing 2 states of my structure (vol #1 & vol #2) I did a morph maps (volume/ Morph map) after having recenter and align the 2 maps. it works perfectly. I did similar procedure with 2 pdb files (1.pdb & 2.pdb), corresponding to the fitted molecular structures of the 2 states (vol#1 & vol #2) , using the tool/Structures comparison/ morph conformation. The pbds are aligned with the EM map using VOP command. Now I would like to combine the 2 morphs together to have a final morph of the EM maps with the molecular structure, but I could not find a way to combine them. Thus I would like to know if it is possible to do it ? and if yes how to do it. Moreover is it possible to play the morph of the pdbs in way of the morph of the EM maps back and forth? Thank you in advance, Sincerely Sami

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Angle between pseudobond and principal axis
by Yasser Almeida Hernández 01 Oct '15

01 Oct '15

Hi all, I want to measure the angle between a pseudobond and the X, Y, Z axis. How can I do so? Best Yasser

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Re: [Chimera-users] metal coordination to display off
by Eric Pettersen 30 Sep '15

30 Sep '15

On 9/28/15 6:13 PM, "Luigi Di Costanzo" <dicostanzo(a)rcsb.rutgers.edu <mailto:dicostanzo@rcsb.rutgers.edu>> wrote: > > We have fetched 2MHR with Chimera and noticed that the middle nitrogen > of azide is bonded through a dashed line as following: > > FE2 FEO A 119 N2 AZI A 120 > > From the "structure analysis" tool and "metal geometry" window we are > unable to display off that dashed lines that is incorrect. > > The coordination table does not show that particular link and we can not > deselect it. > > Could you please look into it and provide some suggestions? > > Thanks. Hi Luigi, The spurious dashed line is due to a corresponding CONECT record in the PDB file. So one option is to locate that CONECT record and delete it. The other is to use the Metal Coordination tool to clean up the coordination of that iron. First, it is highly unlikely that the histidine nitrogens coordinating the iron are protonated, so you should select those hydrogens and “del sel” to get rid of them. Then if you bring up the metal coordination tool for the iron it will properly show the nitrogens as coordinating. If you already had the tool up when you deleted the hydrogens then you will have to force the tool to consider the newly deprotonated nitrogens by selecting them and clicking the “Add atoms selected in the graphics window" button. You can now remove the spurious coordination you noted above by first clicking the last atom in the coordination table (HIS 25.A NE2) and then clicking the “Create/Update metal-complex pseudobonds” button. I hope this helps. Let me know if you have any questions. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Chimera
by Scapin, Giovanna 30 Sep '15

30 Sep '15

Good afternoon I am interested in downloading and installing CHIMERA. Could you let me know if there is any licensing cost involved and if so whom I should contact? Thank you very much Giovanna Scapin Giovanna Scapin Principal Scientist Structural Chemistry Merck & Co., Inc. 2000 Galloping Hill Rd K15-1800 Room B133C Kenilworth NJ 07033 Phone +1 908 740 3632 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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Proportional representation of missing segments?
by Oliver Clarke 28 Sep '15

28 Sep '15

Hi all, I think it would be handy, in a future version of chimera, to have an option to represent missing segments in a manner that is proportional to the volume of protein missing - this would be very useful for getting a sense of which chain breaks correspond to very large missing regions (e.g. whole domains), and which correspond to short linkers or loops that are missing. For example, in the structure of the ryanodine receptor, there are missing segments ranging in length from ~5-250 residues in length - it would be very handy to be able to get a quick sense, upon first opening a structure, about what fraction of the crystallized or reconstructed protein is actually present in the model. I can think of a couple of ways of doing this. One way would be to associate an attribute with each missing segment, corresponding to the number of missing residues, and allow the user to scale the radius, color or opacity of the missing segments in proportion to this value (maybe this attribute already exists somewhere internally?). Another way might be to create a completely different missing segment representation - perhaps an ellipsoid, with the ends of the ellipsoid at the N and C-terminal breakpoints, and the volume of the ellipsoid scaled to the volume of a random polymer of the known number of missing residues. I would try to do this myself by creating an extension, but I don’t really know where to start to get the information that would be required - I don’t know how to iterate over all missing segments, calculate the number of residues in each, and create a new representation. I guess there is probably a list somewhere in Chimera corresponding to the missing segments and their properties, but I have no idea how to find it. Cheers, Oliver.

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Forcefields and Molecular Radii
by Cale Martin 25 Sep '15

25 Sep '15

Dear Chimera users, Over the last few days I have been using Chimera 1.9 to model the Poisson-Boltzmann surface potential of a protein. I have been using the APBS software and the two main forcefields I have been using are the TYL06 and AMBER. When I model the chemokine using the AMBER forcefield the result seems to be normal and as expected, but when using the TYL06 forcefield, the final molecule surface seems to have larger molecule radii almost making it look a little more "bubbly" for lack of a better term. Is this a function of the forcefield in any way? Should this be expected from these two different forcefields? Another issue that I have had along the same line involves the APBS program. The settings allow for the selection of a "Smoothed Molecular Surface" and one that is just "Molecular Surface" but when I run the program with every thing the same except these settings, the results look exactly the same. Should this setting affect the visualization of my molecule surface in any way? Thank you, Cale Martin

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FW: How can I find H-bond between ligand and protein residues within selected angstrom?
by Williams, Joanne 25 Sep '15

25 Sep '15

On 9/19/15 1:29 AM, "高木友理子" <kagaribi-firefly(a)bs.s.u-tokyo.ac.jp> wrote: > Dear Chimera creator, > > I use Chimera to analyse protein-ligand interaction. > Especially, I would like to find H-bond between these. > I clicked HBonds and tried to search H-bond within selected distance. > However,I could not. > I guess the reason is that I was not able to understand "Relax > constraints" in H-Bond parameter window. > I ,of course, checked chimera's help. > What is relax constraints? > What does 0.4 angstroms indicate? Is this the Max distance between ligand > and protein residue? > I would like to find H-bond between them within selected angstrom. > What should I do to know that? > Please teach me how to do. > Thank you for being patient with my English. > > Best regards, > > Yuriko Takagi > Tokyo university student

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Way to extract path to file from model ID
by Oliver Clarke 24 Sep '15

24 Sep '15

Hi all, I’m wondering, is there any way (presumably via a python function) to get the path to the original file from the model ID? I’ve written a little python jiffy (below) so I can lowpass filter maps to a specified resolution on the fly inside chimera using EMAN, but is quite slow because I need to first write a copy of the map out (so I know where it is) and then modify it. If anyone knows of an easier way to do such things I would be most grateful. Cheers, Oli. Script: def cmd_lowpass(lowpass,args): from Midas.midas_text import doExtensionFunc def lowpass(model,resol): import os from chimera import runCommand import subprocess import sys #You may need to change the below to .bash_profile if on mac. #You must have EMAN2 in your bash path for this to work correctly. #If running multiple times, you need to close the first instance of lowpass.mrc before creating a second. bashrc_path=os.path.expanduser("~/.bashrc") freq=1.0/resol command="cd ~; system mkdir chimera_tmp; cd chimera_tmp; volume "+model+" save ./tmp1.mrc" runCommand(command) pathvar=os.path.expanduser("~/chimera_tmp") os.chdir(pathvar) e2string="--process=filter.lowpass.gauss:cutoff_freq="+str(freq) print(e2string) mrc_in=pathvar+"/tmp1.mrc" mrc_out=pathvar+"/lowpass.mrc" e2command="source "+bashrc_path+"; bash -c \"e2proc3d.py"+" "+mrc_in+" "+mrc_out+" "+e2string+"\"" print(e2command) proc=subprocess.Popen(e2command,stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True) out, err = proc.communicate() print 'stdout:', out print 'stderr:', err runCommand("open lowpass.mrc") doExtensionFunc(lowpass,args) from Midas.midas_text import addCommand addCommand("lowpass", cmd_lowpass, help=False)

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