- Chimera-users - RBVI Mailing Lists

Running Mole - error
by Radkov, Atanas 09 Dec '19

09 Dec '19

Hello, My name is Atanas Radkov, postdoc in Seemay Chou's lab at UCSF. I was wondering if you could help me set up Mole on Chimera. I installed it, as well as Mono, but I keep seeing the error below. Could you please let me know if there is a way to address this error? Thank you so much for your time and help! Best wishes, Atanas Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/toolbar.py", line 26, in _guard func() File "/Users/atanasdradkov/Downloads/Mole2_plugin/MOLE2_5/MainWindow.py", line 954, in <lambda> icon, lambda d=chimera.dialogs.display, n=MainWindow.name: d(n), 'MOLE 2.5', None) File "/Applications/Chimera.app/Contents/Resources/share/chimera/dialogs.py", line 76, in display dialog = find(name, create=1) File "/Applications/Chimera.app/Contents/Resources/share/chimera/dialogs.py", line 61, in find return d() File "/Users/atanasdradkov/Downloads/Mole2_plugin/MOLE2_5/MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' Error in toolbar callback: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' File "/Users/atanasdradkov/Downloads/Mole2_plugin/MOLE2_5/MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: See reply log for Python traceback. Atanas Radkov, PhD Postdoctoral Scholar Adviser: Professor Seemay Chou Biophysics and Biochemistry Department University of California - San Francisco Genentech Hall 600 16th str San Francisco, CA 94158

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error de descarga
by Zayra Delgado Izquierdo 09 Dec '19

09 Dec '19

Buenas tardes, Estoy intentando descargar vuestro programa y me es imposible porque cuando acepto vuestras condiciones me salta un mensaje que dice: “Gracias por considerar la quimera UCSF. Por favor, háganos saber qué parte del acuerdo de licencia UCSF Quimera que encontró inaceptable.” No entiendo porqué sucede esto si yo estoy aceptando las condiciones y necesito urgentemente el programa. Por favor, necesito su ayuda. Gracias Enviado desde Correo para Windows 10

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Re: [Chimera-users] transposing a pdb structure ("copy & paste")
by simon two 09 Dec '19

09 Dec '19

Hello Elaine. Has there been any development of this problem since the 2007 post? I’m trying to duplicate a small group in a large molecule and use the copy to substitute it an existing group of very similar size in the same molecule. Best wishes Simon Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Contact_area Arguments
by Kevin Wang 06 Dec '19

06 Dec '19

Hi, I am using python to calculate contact area between 2 chains. My code is as follows p1, p2 = [s.surface_piece for s in openModels.list(modelTypes=[MSMSModel])] y = measure.contact_area(p1, p2, 2.5) However, this returns the error: TypeError: contact_area() takes at least 4 arguments (3 given) This is the function for contact_area def contact_area(p1, p2, d, color = None, offset = None, slab = None, smooth = False, optimize = True): What is the 4th required argument? Best, Kevin

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pseudobond problem while writing mol2 format
by Palani, Kirubakaran 06 Dec '19

06 Dec '19

Hi All, I have a PDB file and want to convert the PDB to MOL2 format. The PDB has missing residues which is not a problem but when I write to MOL2 format it assigns the pseudobond and I really no need of it. I tried to solve it by checking the thread but I am not getting a clear solution for my problem. Last, I am doing this by using the script as I have >1000 PDBs to process the same way so the command line would be preferred. PS: I send you the molecule in PDB format as an example case. Thanks in advance, Kiruba ________________________________ This electronic message is intended to be for the use of the named recipient, and may contain information that is confidential or privileged. This communication may contain protected health information (PHI) that is legally protected from inappropriate disclosure by the Privacy Standards of the Health Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania Laws. You can direct questions concerning PHI or HIPAA to the Corporate Compliance and Privacy Officer at (215) 707-5605. If you are not the intended recipient, please note that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this message in error, you should notify the sender immediately by telephone or by return e-mail and delete and destroy all copies of this message.

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Opening Amira segmentations
by Tom Goddard 06 Dec '19

06 Dec '19

Unfortunately Chimera does not handle Amira segmentation files. Maybe we can add that to ChimeraX or next generation program. What kind of segmentations do you have? Are they surfaces? Or are the per-voxel index maps? Tom > On Dec 5, 2019, at 12:02 PM, Guo, Wangbiao <wangbiao.guo(a)yale.edu> wrote: > > Thank you, Tom. So, what kind of Amira segment files can I open with Chimera? > >> On Dec 5, 2019, at 3:00 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> The error message says your Amira file does not contain BoundingBox in the header. That line tells ChimeraX the size of the 3D image data in the file. I suspect it means your Amira file does not contain 3D image data (instead it might have segmentation surfaces or some other Amira objects). The Chimera Amira reader only handles 3d image data. >> >> Tom >> >> >>> On Dec 5, 2019, at 11:36 AM, Guo, Wangbiao <wangbiao.guo(a)yale.edu> wrote: >>> >>> >>> >>> >>> <Screen Shot 2019-12-05 at 2.32.48 PM.png> >>> >>> >>> >>> >>> >>> >>> >>> >>> Hi: >>> When I open my Amira label file by Chimera, I always come out with an error: cannot find “bounding box” line, can u help me to figure out? >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.… <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.…>

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Video about masking
by Krishan Pandey 05 Dec '19

05 Dec '19

Hi I am kind of new to Chimera and was wondering if there is a video tutorial about creating a mask in Chimera. I intend to use the mask for local resolution or multi body refinement. To experienced users this may be a novice question. I tried to search online but could find any. When I use volume eraser to delete part of EM map, it does not do anything, nothing is deleted. I am using Chimera 1.13.1 (build 41965). Any help is appreciated. Thank you Krishan Pandey

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Fitting ligands/substrates to protein structure
by Jason Jeffrey Rodencal 05 Dec '19

05 Dec '19

Hello chimera users! I've been browsing the various tutorials for chimera and I've seen a lot of amazing models of proteins bound to DNA, ligands, etc. I have a pdb file for my protein of interest and its substrate, and I have the active site of the protein. I was wondering if there's any way of predicting how the substrate fits into the catalytic cleft. Is there some easy code or application that can do this in chimera or is this a far more challenging task than I appreciate? Thank you! Jason Rodencal Dixon Lab Stanford University

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(no subject)
by Guo, Wangbiao 05 Dec '19

05 Dec '19

[cid:8911DAA1-04B5-48F5-9F7E-D075345E38BE@its.yale.internal] Hi: When I open my Amira label file by Chimera, I always come out with an error: cannot find “bounding box” line, can u help me to figure out?

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secondary structure restraints and crosslink restraints
by Fränze Müller 27 Nov '19

27 Nov '19

Dear Chimera developers, I would like to perform homology modelling using Modeller in Chimera. At the moment I am using just distance restraints formatted like in the Chimera documentation (res1 res2 dist stdev). This file only contains crosslinking data. Is there a way to also include secondary structure restraints, that can serve as additional information during homology modelling? Or can I provide some were another file including this information separate from the crosslink information? Best wishes and Thanks for your help, -- *Fränze Müller* Postdoctoral Researcher *Biochemistry and Functional Proteomics, Warscheid Lab* University of Freiburg|Schänzlestr. 1|79104 Freiburg|Germany Phone +49 761 203 2681

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Undo option?
by Luca Pellegrini 27 Nov '19

27 Nov '19

I was wondering if there are any plans for an Undo option? I just managed to wipe a detailed view of an active site with lots of side chains, by selecting one more amino acid on the ribbon drawing and then picking by mistake ’show only’ rather than ’show’ (slip of the finger). ps: I found an old post on this in 2004, explaining that there is no such option, but perhaps the Chimera authors are open to changing their mind? After all, we are using Chimera to make ever more complex drawings. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Modification of paths
by Reza Khayat 27 Nov '19

27 Nov '19

?Hi, I've installed the headless version of Chimera and have realized that it inserts the location of the headless binary into the PATH variable. Unfortunately, I can't figure out what system file has been modified. I use a tcsh shell and the .cshrc is not modified. Any help in identifying the modified system file would be greatly appreciated. Thanks. Best wishes, Rez Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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Save pdb problem
by Rui Chen 25 Nov '19

25 Nov '19

Hello, I docked a ligand into a monomer, now I want to save a new pdb file. In the new pdb file, chian A will be docked monomer, chain B will be the chain B of homodimer. I already superimposed the two PDB files and deleted chain A of homodimer. I also used change chain ID to add chain IDs to the combined PDB file. However I got the following problems: 1. In my system, there are glycans (residue name: 0YB), *I cannot add chain ID to the glycans* (residue 209-216 belongs to chain A, residue 425-432 belongs to chain B) 2. In my system, I also have a small molecule docked in chain A, I realized only *the last line of the ligand was given a chain ID "h"*, is this a problem? 3. I want to *save these two PDB files as two chains, not two models* (actually it's a homodimer except for the ligand) 4. Can I manually *delete all the connections*? Looking forward to your reply. Best regards, Rui

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Cntrl+shift + left selection makes screen go blank
by Dominique Gutierrez 25 Nov '19

25 Nov '19

Hello, Cntrl+shift + left selection makes screen go blank where I only see the green box and the pdb or map disappears until releasing the mouse. Are there any settings that prevent that in chimera or any display settings? Best, Dominique Gutierrez

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Extract a chain in cryo-EM map
by bahareh behkamal 25 Nov '19

25 Nov '19

Dear secretariat, Would you please say to me how I can extract a chain in the cryo-EM map and save it separately as a ".mrc" file? For example, I need to select chain R in protein EMD-5030 which is attached at the following link. EMD-5030.map <https://drive.google.com/file/d/1ittGPj4s26H3AE2EAjXt5sSGSW4NbrQb/view?usp=…> I am grateful if you could help me regard this issue. Sincerely, Bahareh Behkamal Ph. D. Candidate of Computer Engineering Dept. of Computer Engineering - System Software Researcher in Structural Bioinformatics *Ph. D visiting student in Politecnico di Torino, Italy* Dept. of Applied Science and Technology [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 11/25/19, 03:23:52 AM

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Re: [Chimera-users] How to make trimer by Chimara?
by Elaine Meng 23 Nov '19

23 Nov '19

Dear Wisoot Chanit, If you’re using ChimeraX there is another address: chimerax-users(a)cgl.ucsf.edu Besides the ChimeraX Modeller tool link I sent earlier > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> … there is also an example here <http://www.rbvi.ucsf.edu/chimerax/features.html#multichain-modeller> Also we are not the Modeller developers, so depending on the question you may need to look at the Modeller help at their website: <https://salilab.org/modeller/discussion_forum.html> Best, Elaine > On Nov 23, 2019, at 9:39 AM, Wisoot Chanit <wchanit(a)yahoo.com> wrote: > > Dear Dr.Eliane Meng, > > Thank you very much for your reply and recommendations, which are really helpful. I have tried using ChimeraX a few days ago. It is very simpler than Chimera. By following the instructions you recommended, I believe I can make it although it may take some time and effort as you mentioned. I used to use Modeller 5-6 years ago for my Ph.D. papers and now I need to go back to my knowledge. If I have questions, I will send it directly to chimera-users(a)cgl.ucsf.edu . > > Thank you very much again for this help. > > Wisoot Chanit > > On Sunday, November 24, 2019, 12:19:19 AM GMT+7, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > Dear Wisoot Chanit, > It is recommended to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d here). > > As mentioned in the manual page, the Modeller interface in Chimera can only be used to make monomers. Although Modeller by itself can model multimers, the GUI to run it in Chimera is simpler and only has the most common options. > > So if you are using Chimera, you could first model a monomer and save it to a file. Then you could open 3 copies of that monomer model and match them onto the 3 chains in a trimer structure. There is a manual page for the Modeller tool in Chimera and also a tutorial with an example. See also the manual page on superposition (matching structures in 3D). > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> > > Our newer ChimeraX program has an improved Modeller interface that can model a trimer, however, if the template is a trimer. So another possibility is to use the ChimeraX program instead of Chimera. > <http://www.rbvi.ucsf.edu/chimerax/> > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> > > Yet another possibility is to download Modeller and learn how to use it directly, but that would take more time and effort. > <https://salilab.org/modeller/> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > > On Nov 23, 2019, at 6:10 AM, Wisoot Chanit <wchanit(a)yahoo.com> wrote: > > > > Dear Dr.Elaine Meng, > > > > I am a new user of Chimera and have been searching for methods to do comparative modeling of rotavirus structure. > > > > I have read your post (CCL: Monomer to Trimer), but I still questions. > > > > My aim is to make a homology modeling protein of VP7 protein of rotavirus using 3FMG pdb as a template. I do not know how to impose three monomers into the template. > > > > My amino acid sequence is > > > > Rotavirus G3 : > > TSTLCLYYPSEAATEINDNSWKDTLSQLFLTKGWSTGSVYFKEYTDIASFSVDPQLYCDYNVVLMKYDATLQLDMSELADLILNEWLCNPMDITLYYYQQTDEANKWISMGSSCTIKVCPLNTQTLGIGCLTTDATTFEEVATAEKLVITDVVDGVNHKLDVTTATCTIRNCKKLGPRENVAVIQVGGSDVLDITADPTTAPQTERMMRINWKKWWQVFYTVVDYVNQIIQAMSK > > > > Could you please guide me how I can find a protocol to make a homology model? I tried to follow the attached paper. > > > > Thank you very much. > > > > Sincerely, > > Wisoot Chanit > > > > > > > > > > CCL: Monomer to Trimer > > > > > > > > > <High prevalence of G3 rotavirus in hospitalized children in Rawalpindi, Pakistan during 2014.pdf> >

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Re: [Chimera-users] How to make trimer by Chimara?
by Elaine Meng 23 Nov '19

23 Nov '19

Dear Wisoot Chanit, It is recommended to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d here). As mentioned in the manual page, the Modeller interface in Chimera can only be used to make monomers. Although Modeller by itself can model multimers, the GUI to run it in Chimera is simpler and only has the most common options. So if you are using Chimera, you could first model a monomer and save it to a file. Then you could open 3 copies of that monomer model and match them onto the 3 chains in a trimer structure. There is a manual page for the Modeller tool in Chimera and also a tutorial with an example. See also the manual page on superposition (matching structures in 3D). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> Our newer ChimeraX program has an improved Modeller interface that can model a trimer, however, if the template is a trimer. So another possibility is to use the ChimeraX program instead of Chimera. <http://www.rbvi.ucsf.edu/chimerax/> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> Yet another possibility is to download Modeller and learn how to use it directly, but that would take more time and effort. <https://salilab.org/modeller/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 23, 2019, at 6:10 AM, Wisoot Chanit <wchanit(a)yahoo.com> wrote: > > Dear Dr.Elaine Meng, > > I am a new user of Chimera and have been searching for methods to do comparative modeling of rotavirus structure. > > I have read your post (CCL: Monomer to Trimer), but I still questions. > > My aim is to make a homology modeling protein of VP7 protein of rotavirus using 3FMG pdb as a template. I do not know how to impose three monomers into the template. > > My amino acid sequence is > > Rotavirus G3 : > TSTLCLYYPSEAATEINDNSWKDTLSQLFLTKGWSTGSVYFKEYTDIASFSVDPQLYCDYNVVLMKYDATLQLDMSELADLILNEWLCNPMDITLYYYQQTDEANKWISMGSSCTIKVCPLNTQTLGIGCLTTDATTFEEVATAEKLVITDVVDGVNHKLDVTTATCTIRNCKKLGPRENVAVIQVGGSDVLDITADPTTAPQTERMMRINWKKWWQVFYTVVDYVNQIIQAMSK > > Could you please guide me how I can find a protocol to make a homology model? I tried to follow the attached paper. > > Thank you very much. > > Sincerely, > Wisoot Chanit > > > > > CCL: Monomer to Trimer > > > > <High prevalence of G3 rotavirus in hospitalized children in Rawalpindi, Pakistan during 2014.pdf>

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Fw: To add hydrogen atoms for a dataset
by Williams, Joanne 21 Nov '19

21 Nov '19

-- JoAnne Williams | Executive Analyst to: Matt Jacobson, Professor and Department Chair Pam England, Professor Zev Gartner, Professor Tom Ferrin, Professor Department of Pharmaceutical Chemistry Wallace Marshall, Professor Center for Cellular Construction | Department of Biochemistry & Biophysics 600 16th Street, Room N372 | UCSF MC2200 | San Francisco, CA 94158 Phone: (415) 418-3079 | Email: joanne.williams(a)ucsf.edu ________________________________ From: 周盛福 <zhousf(a)szbl.ac.cn> Sent: Tuesday, November 19, 2019 1:33 AM To: chimera <chimera(a)cgl.ucsf.edu> Subject: To add hydrogen atoms for a dataset Hi all, I have used UCSF Chimera for several years and find that Chimera has a perfect behavior in adding hydrogen atoms for small molecules. It is easier to add wrong hydrogen atoms onto nitrogen heterocycles groups with other software, including openbabel, MGLTools, PyMol, etc. Now I want to add hydrogen atoms for a dataset, which contains more than 10 thousands ligands for virtual screening. And a great number of compounds in this dataset have nitrogen heterocycle groups. So I want to add hydrogen atoms for all these compounds by Chimera. When I try to run a script in Favorites > Command line by read a MOL, addh and delete the MOL in cycle. I found that the memory usage of Chimera keep growing although I have delete the previous MOLs. My question is: How can I avoid this problem while I want to handle numerous molecules with Chimera? If there is a way to run Chimera in a real terminal without run Chimera in graphic interface? Or Which bin file in Chimera_HOME can add hydrogen atoms for a molecule? Sincerely look forward to your reply. Thanks Best Shengfu Zhou 2019.11.19

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How to draw a longer vector in visualization mode
by Byrd, Robert A. (NIH/NCI) [E] 20 Nov '19

20 Nov '19

I would like to draw a vector that would extend the connection of two points in a model. This would allow better visualization. The current status is a line that joins between the centroid of a plane of atoms to another atom that is above the plane. I would like to extend this vector out into space for say 5 or 10 angstroms. This would allow visualization of the direction relative to the remainder of the molecule. All that I have been able to do is draw a line between the centroid and the atom. This does not give the perspective to other parts of the overall scene. In the attached image this would be the red bar connecting the centroid of the purple plane to the green atom. How would one extend this out 5-10 Angstroms? Ideas? Thanks Andy Byrd

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Problem with swapaa
by Dan Kool 20 Nov '19

20 Nov '19

I am having problems mutating some residues with the 'swapaa' command. How do I mutate to 'A' or 'G' or 'I' for example? I always get an error that the rotamer library doesn't support it. Is there a workaround or is it actually not possible to simply mutate a residue to one of those? I tried changing the rotamer library, but I get the same error. Best, Dan ---------------------------------------------------- Daniel Kool Graduate Assistant, Jernigan Lab, 335 Kildee Bioinformatics and Computational Biology Iowa State University kool(a)iastate.edu

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Programmatic trimming of PDB files based on alignment with reference structure
by Zachariah Schuurs 19 Nov '19

19 Nov '19

Dear Chimera Team, I have a reference protein domain and then a series of PDB files which all contain the same domain. I have programmatically been able to script an alignment of the reference to the same domain in the other files whereby he domain in the proteins of interest are isolated using the zone select method. This however leaves me with fragments and often misses some of the domain features of the interest proteins that occur outside of the specified zone. I am wondering if it is possible to write a python script that selects the area on the protein of interest by selecting the residues in the sequence alignment after MatchMaker is conducted. For instance - protein #0 is my reference protein, which is 150 residues long. My protein of interest contains the same domain as the reference, but is 500 residues long. Upon conducting MatchMaker and getting an output sequence alignment, the 150 residues of #0 (the reference) are selected, along with the aligned residues in the protein of interest. It is possible to select the residues in the sequence alignment window (as in the picture) but I wish to be able to script it. The selected 150 residues (or so) in the protein of interest are then saved as their own trimmed file. I have been able to write a python script for completing the MatchMaker etc, but I am not sure how to achieve the selection of residues in #1 based of the alignment with #0, or if it is even possible. Thanks Zachariah Schuurs | PhD Candidate CARP - Cancer & Ageing Research Program Institute of Health and Biomedical Innovation | Queensland University of Technology Level 6 | Translational Research Institute | 37 Kent St | Woolloongabba QLD 4102 T: +61 7 3443 7296 | E: zachariah.schuurs(a)hdr.qut.edu.au | Web: www.carp.org.au<http://www.carp.org.au/> [email] I acknowledge the Turrbal and Yugara, as the First Nations owners of the lands where QUT now stands. I pay respect to their Elders, lores, customs and creation spirits. I recognise that these lands have always been places of teaching, research and learning. This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email. [cid:image004.png@01D59AF3.602278E0]

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Re: [Chimera-users] setting zoom with a specific window size.
by Elaine Meng 19 Nov '19

19 Nov '19

> On Nov 19, 2019, at 5:56 AM, JOHN FLANAGAN <jmf27(a)psu.edu> wrote: > > Hi > I am trying to compare several negative stain em maps to make a figure. For what I want to do its easier not to have all of the maps loaded at the same time. However, I am having trouble keeping everything on the same scale. I am able to set the windowsize, center the maps but the zoom is not always the same. I searched the web and found that there used to be zoom and setzoom commands that should do the trick, but neither is recognized in my version of chimera (commands I mean). All of the maps have the same starting A/px but what I want to do is take the map with the largest extent and set that and whatever its being aligned too to fill the window then for every other session have the same windowsize and effective zoom. Pardon my inelegant description but I hope that provides sufficient explanation for what I am trying to do. > > Cheers > John Hi John, Sending this to chimera-users(a)cgl.ucsf.edu, the recommended address for Chimera questions. That way, whoever has the expertise can answer, and others can benefit. This previous post may answer your question. It says you have to download the setzoom command code separately and provides a link. <http://www.cgl.ucsf.edu/pipermail/chimera-users/2017-January/013091.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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exit code -1073741819 + debug
by Fatemeh Haghighi 18 Nov '19

18 Nov '19

Hi I have tried to make a movie of MD simulation by Chimera. I could be done one time, then for other MD’s it exits abnormally with the code -1073741819. Even I have decreased the size of .xtc file, it exits abnormally yet. I have reinstalled chimera, but the problem did not resolve. The debug report was: Cannot execute 'gzip': no automatic decompression of .Z files Best Regards

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Elliptical cylinders
by John Hackett 14 Nov '19

14 Nov '19

Good morning, is to possible to draw capped elliptical cylinders in Chimera? I would like to render elliptical cylinder representations of nanodiscs together with a membrane protein to visualize results from small-angle scattering experiments. Thanks, -jch ________________________________ John C Hackett, PhD, RPh Associate Professor, Physiology & Biophysics VCU School of Medicine Goodwin Research Laboratory Rm. 165 Massey Cancer Center 401 College St. Richmond, Virginia 23298-0035 Telephone: +1.804.828.5679 ________________________________

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problem picking atoms in graphic window
by Wartell, Roger M 14 Nov '19

14 Nov '19

Hi, I have a peculiar but simple problem using Chimera [version 1.13.1(build 41965)] on a Windows 10 PC-computer]. Using it to model docking of small molecules to an RNA using autodock vina. This has worked fine. Recently wanted to measure distances by control-click on atom 1 and control-shift-click on atom 2 (picking the atoms in graphic window). Nothing came up in 'Structure Measurement' box when I 'picked' the atoms and clicked on Create except for it telling me I had to pick atom 1 and atom 2. If I hold the 'control' key of the keyboard down and move the mouse's hand symbol around an atom, the green outlined shape does not remain when I lift my finger from the mouse. On the right side of the bottom bar of the screen it says 'selection cleared' which disappears in a few seconds. When one holds both control and shift keys down and encircle the green shape around an atom, the outline remains. Control click in an empty area removes it, as it should. A postdoc in an adjacent lab who uses Chimera took a look and was puzzled since her downloaded version on her computer works fine in picking atoms etc. She also was puzzled since my mouse arrow when moved over an atom/residue did not show what residue it was, which apparently it should. We tried several pdb files (proteins and an RNA) and they all behave the same. We checked under Preferences that the matrix of radio buttons for my mouse's actions were set the same as hers. Is there some other preference setting I do not have set properly? Everything the mouse should be doing with regard to moving/rotating molecules is as expected, and the program otherwise appears to work fine. Any/all suggestions on solving this 'picking' atoms problem are most welcome. Thank you and the others at UCSF who have developed Chimera. Best Roger

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