- 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 06 Dec '19

06 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 26 Nov '19

26 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 26 Nov '19

26 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 15 Nov '19

15 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 15 Nov '19

15 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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Support for Chimera1.13.1
by Mr 14 Nov '19

14 Nov '19

HI Developer I am about to purchase and use the software of Chimera1.13.1 . I need to configure a workstation for processing. I have a long-term plan. Do you have a recommended computer hardware configuration here? I will also use the following program in this workstation: Software: Discovery studio (version 2.5); MOE (version 2015); PyMOL (version 2.3); Amber (version 14); Schrodinger (version 2018-4x64); RStudio (3.5), etc.; Database: Microarry; TCGA; NCBI; RNA-seq; RCSB PDB; NONCODE, etc.; Which operating system can run these software perfectly and let them not conflict with your company's software. Sorry to ask so many questions, I hope you can reply to me. Thank you!

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Shiny cilnders
by Luca Pellegrini 13 Nov '19

13 Nov '19

Hello, I have prepared a ribbons drawing for my structure, with axes for the helices in it (Tools -> Structure Analysis -> Axes/Planes/Centroids). When I try to reduce the shininess of the figure, I can change it for the ribbons (Viewing -> Lightning -> Shininess) but not for the axes, that remain unchanged (very shiny). Is there a way to change the shininess for all objects, ribbons and axes? 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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Re: [Chimera-users] images from ChimeraX
by Tom Goddard 12 Nov '19

12 Nov '19

Hi Mike, Neither Chimera nor ChimeraX can output CMYK images. Your computer screen is RGB and the CMYK color space and RGB color space includes colors that the CMYK color space of a specific printer cannot duplicate as shown in this wikipedia color space image https://en.wikipedia.org/wiki/Color_space#/media/File:CIE1931xy_gamut_compa… <https://en.wikipedia.org/wiki/Color_space#/media/File:CIE1931xy_gamut_compa…> The colors can be quite different as shown in the the comparison below also from wikipedia color space. So you should convert the image yourself in Photoshop or Gimp or other photo-editor so you can see what it will look like. It would be helpful if ChimeraX was able to show you what your image would look like when limited to CMYK and help you pick colors that can be exactly represented in CMYK that most printers will handle, but we don't have that capability. Tom > On Nov 12, 2019, at 10:20 AM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu> wrote: > > Hi- > Another last thought… > The company I sent the left and right eye views to said there was a problem converting the .png RGB files to CMYK for printing. Is there a way (ChimeraX) to output CMYK, or do I have to find someone with Photoshop or something to convert it? > This is their email: > > Hello and thank you for your business. We are happy to help you. Our production department is stating that the artwork we received was submitted in RGB color format. > When we convert your file to the required CMYK color book we use for printing. There is a drastic change in color. > > We would suggest converting your artwork to CMYK then color adjusting your artwork so that your order prints accurately. > > Please revise and resend us your artwork saved in CMYK color format. Once we receive your updated artwork, we will review and respond to you right away. > > We are here to review and answer any questions you have. Please let us know anything we may help you with. > > Thanks. > > From: Tom Goddard <goddard(a)sonic.net> > Date: Thursday, November 7, 2019 at 2:57 PM > To: "Schmid, Michael F." <m-schmid(a)slac.stanford.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] images from ChimeraX > > Hi Mike, > > One last thought (I hope it is the last!). ChimeraX has a camera mode called side by side, enabled with command "camera sbs". This shows left and right eye images and is for recording videos that use SBS format. It behaves just like wall eye stereo. There is a parameter that controls the depth of field (which adjust the angle of rotation between the left/right views), "camera sbs eyeSeparation 10". Here the number 10 is in Angstroms, the separation of the left and right cameras in the scene. You can preview this cross-eye but the depth will be inverted because the left and right eye images need swapping from cross eye. If it worked you could swap left and right panels by just cutting each out in a photo editing program. Alternatively you could use negative eye separation, then it seems to work as cross-eye but the image separation is bit weird. > > There were errors when I used ChimeraX camera sbs and resized the window. I fixed those today. The errors are harmless -- just warning that OpenGL resources were not deleted. But tonight's ChimeraX won't have those errors. > > Tom > > > > On Nov 7, 2019, at 1:59 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > > Hi Mike, > > I just noticed the subject of your message said ChimeraX. All my answer was about Chimera, not ChimeraX. (There is a separate ChimeraX mailing list chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>). > > Here are ChimeraX tips. So in ChimeraX there is no cross-eye stereo mode (yet). So I would suggest using the two side-by-side ChimeraX windows. There is an icon in the lower right corner that hides all the tool panels at the right edge so the graphics is the full window width. Use the windowsize command to get the right aspect ratio (e.g. windowsize 900 1200). Use a saved session. Rotate one image with "turn y 6". Use the File / Save... dialog and choose PNG image and set pixel size to be 300 times desired print width in inches. One thing that could be a bit weird is if you use full lighting then it casts a direct shadow and the left and right eye direct shadows won't match since the light direction is fixed to the view direction (ie the light does not rotate 6 degrees, so the left and right eye won't see the same lighting). Soft lighting only has isotropic shadows so won't have that problem. If the direct shadow is a problem you could rotate the light using the "lighting" command. Use lighting with no options to show the current direction vector for the light, then calculate a rotated direction 6 degrees and set it with the "lighting direction x,y,z" command. > > Tom > > > > On Nov 7, 2019, at 1:47 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > > You might also set "supersample 1x1". The default 3x3 setting makes the image 3 times bigger on each axis and then bins down by a factor of 3. Making it 3 times larger make cause the graphics to fail on such a large image. And at 300 dots per inch the 3x3 supersample won't have a visible effect. > > Tom > > > > On Nov 7, 2019, at 1:45 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > > Hi Mike, > > The panel shown by File / Save Image... says pixels "Units pixels". > > Tom > > <Screen Shot 2019-11-07 at 1.44.52 PM.png> > > On Nov 7, 2019, at 1:34 PM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu <mailto:m-schmid@slac.stanford.edu>> wrote: > > Hi- > Thanks. That really helps! So the “width” and “height”, if just given as 5400 and 7200, respectively, will be understood as pixels, or do you have to say “5400 pixels”? > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Date: Thursday, November 7, 2019 at 1:28 PM > To: "Schmid, Michael F." <m-schmid(a)slac.stanford.edu <mailto:m-schmid@slac.stanford.edu>> > Cc: "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: Re: [Chimera-users] images from ChimeraX > > Hi Mike, > > To avoid pixelation make sure to save the left and right eye images at high resolution. Using Chimera File / Save Image... you would set the image size in pixels to be maybe 300 times the number of inches wide you will make the image (so if one eye image is 18 inches wide that use image width 5400 pixels). > > For surface rendering of the tomogram make sure step is 1 in volume viewer so it is using the full resolution data. > > For getting the right angle of rotation between the two images I would suggest that you display it on a large flat panel screen (e.g. 50" TV) if you have one at the size you want to print at and check visually how well the cross-eye stereo pair is working. Make the Chimera window aspect ratio exactly match what you will print (e.g. 36 x 24n inches would be 3 to 2), for example use Chimera command "windowsize 1800 1200". In Chimera you can use the "cross-eye stereo" camera in the side view (menu Favorites / Side View) Camera tab in the "camera mode" menu. Then you can fiddle a bit with the focal plane by going to the Side View tab, choose "Side: top" and drag the vertical dashed yellow line left or right. It represents the focal plane. I'm not sure what that means for cross-eyed stereo but it effects the angle of rotation between left and right images. I tried this on my 24 inch wide screen (so not as big as you will print) and I really have to stand far back (5 or 6 feet) to comfortably look at it, otherwise the floating image is too close to my face and I think my eyes don't like to converge that close while still focusing 5 feet away. If this cross-eye stereo mode works for you, you can use File / Save Image... and it will save the two eyes as a single image. > > If that cross-eye stereo mode isn't working well for you you could open two copies of Chimera side by side and rotate the image of one relative to the other with the command "turn y 6" to rotate one view by 6 degrees. You might first save a session in the desired orientation that you open in both Chimera copies then rotate just one of them. > > I think the key here is to try it on a screen to see if it is giving you what you want before you print. > > Tom > > > > > > > On Nov 7, 2019, at 9:48 AM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu <mailto:m-schmid@slac.stanford.edu>> wrote: > > Hi- > I am trying to make a high resolution image of a surface rendering of a tomogram. The final size of the image(s) will be 18 in x 24 in. It is for a wall display. How do I do it for the best (minimally pixelated) result? I presume I will have to adjust the triangle rendering of the maps to be included, and also the rendering of the final images (for a stereo pair). Also, I assume I have to render them at ~6 degrees total tilt with respect to each other. > Thanks, > Mike > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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Fetch by EMDB via GUI downloads first where before uncompressing in users downloads directory
by Ryan Harlich 08 Nov '19

08 Nov '19

Hi Chimera, If I fetch by EMDB via GUI and it downloads then decompresses and freezes where did it go? I know when it is done it goes to my download directory, but where does the gz get downloaded to and where does the partial uncompressed file end up. I cannot find ~5-~10 GB of this lost file. It was ~5 GB gz file so I think the gz is still on my computer. I searched for it to and my computer said no results found so I am not sure if it is named something else when you fetch by EMDB. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Re: [Chimera-users] images from ChimeraX
by Tom Goddard 07 Nov '19

07 Nov '19

Hi Mike, The panel shown by File / Save Image... says pixels "Units pixels". Tom > On Nov 7, 2019, at 1:34 PM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu> wrote: > > Hi- > Thanks. That really helps! So the “width” and “height”, if just given as 5400 and 7200, respectively, will be understood as pixels, or do you have to say “5400 pixels”? > > From: Tom Goddard <goddard(a)sonic.net> > Date: Thursday, November 7, 2019 at 1:28 PM > To: "Schmid, Michael F." <m-schmid(a)slac.stanford.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] images from ChimeraX > > Hi Mike, > > To avoid pixelation make sure to save the left and right eye images at high resolution. Using Chimera File / Save Image... you would set the image size in pixels to be maybe 300 times the number of inches wide you will make the image (so if one eye image is 18 inches wide that use image width 5400 pixels). > > For surface rendering of the tomogram make sure step is 1 in volume viewer so it is using the full resolution data. > > For getting the right angle of rotation between the two images I would suggest that you display it on a large flat panel screen (e.g. 50" TV) if you have one at the size you want to print at and check visually how well the cross-eye stereo pair is working. Make the Chimera window aspect ratio exactly match what you will print (e.g. 36 x 24n inches would be 3 to 2), for example use Chimera command "windowsize 1800 1200". In Chimera you can use the "cross-eye stereo" camera in the side view (menu Favorites / Side View) Camera tab in the "camera mode" menu. Then you can fiddle a bit with the focal plane by going to the Side View tab, choose "Side: top" and drag the vertical dashed yellow line left or right. It represents the focal plane. I'm not sure what that means for cross-eyed stereo but it effects the angle of rotation between left and right images. I tried this on my 24 inch wide screen (so not as big as you will print) and I really have to stand far back (5 or 6 feet) to comfortably look at it, otherwise the floating image is too close to my face and I think my eyes don't like to converge that close while still focusing 5 feet away. If this cross-eye stereo mode works for you, you can use File / Save Image... and it will save the two eyes as a single image. > > If that cross-eye stereo mode isn't working well for you you could open two copies of Chimera side by side and rotate the image of one relative to the other with the command "turn y 6" to rotate one view by 6 degrees. You might first save a session in the desired orientation that you open in both Chimera copies then rotate just one of them. > > I think the key here is to try it on a screen to see if it is giving you what you want before you print. > > Tom > > > > > > On Nov 7, 2019, at 9:48 AM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu <mailto:m-schmid@slac.stanford.edu>> wrote: > > Hi- > I am trying to make a high resolution image of a surface rendering of a tomogram. The final size of the image(s) will be 18 in x 24 in. It is for a wall display. How do I do it for the best (minimally pixelated) result? I presume I will have to adjust the triangle rendering of the maps to be included, and also the rendering of the final images (for a stereo pair). Also, I assume I have to render them at ~6 degrees total tilt with respect to each other. > Thanks, > Mike > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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images from ChimeraX
by Schmid, Michael F. 07 Nov '19

07 Nov '19

Hi- I am trying to make a high resolution image of a surface rendering of a tomogram. The final size of the image(s) will be 18 in x 24 in. It is for a wall display. How do I do it for the best (minimally pixelated) result? I presume I will have to adjust the triangle rendering of the maps to be included, and also the rendering of the final images (for a stereo pair). Also, I assume I have to render them at ~6 degrees total tilt with respect to each other. Thanks, Mike

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UCSF Chimera on Arm processors
by Dr. Santanu Roy 04 Nov '19

04 Nov '19

Dear Sir/Madam, I just wanted to know if there is any version of UCSF Chimera that can be run on Arm v8 based Single Board Computers like the Raspberry Pi 4 with 4 GB RAM. Thanks and Regards, S Roy Dr. Santanu Roy Department of Microbiology, Acharya Prafulla Chandra College, New Barrackpore, Kolkata - 700 131

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Atom box
by MARIA CLARA BLANES MIRA 04 Nov '19

04 Nov '19

Dear Chimera experts, I have been measuring surface volumes by using the atom box option in order to obtain a surface slice volume and then the volume measure. But how could I use the atom box in the command line? Thank you! clara import chimera import os from chimera import runCommand runCommand(’sel :2.A,19.A,25.A, 5.B, 23.B, 26.B’) # to define the box runCommand(‘atomBox ????’) runCommand('measure volume #0') runCommand('close all')

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Re: [Chimera-users] Coloring map by curvature
by Tom Goddard 04 Nov '19

04 Nov '19

Hi Shengyou, The curvature.py script was attached to the Chimera mailing list message you found. http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009580.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009580.html> It got renamed with a ".bin" suffix, so after you download you should change the file name to curvature.py. A similar capability is in ChimeraX, the "measure convexity" command https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#convexity <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#convexity> Here's an example image using "measure convexity #1" on EMDB 0074. Tom > On Oct 6, 2019, at 7:15 AM, huangsy(a)hust.edu.cn wrote: > > Hi Tom, > > > > I just noticed that you had helped a user about "Coloring EM map by curvature" in UCSF Chimera through some scripts like the following > > open 1grl > > molmap #0 15 grid 2 model #1 > select #1 > open ~/Desktop/curvature.py > Could you please send me the "curvature.py" file or tell me where to download it? > > > Thank you very much for your help! > > Best regards, > > > > Shengyou > > -- > > Shengyou Huang, PhD > > Professor of Biophysics > School of Physics > Huazhong University of Science and Technology > Email: huangsy(a)hust.edu.cn <mailto:huangsy@hust.edu.cn> > Lab web: http://huanglab.phys.hust.edu.cn/ <http://huanglab.phys.hust.edu.cn/>

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Can mouse preferences by set to specific UCSF Chimera function (ex. "Undo Move" under Movement Mouse Mode) ?
by Jun Ha Song 30 Oct '19

30 Oct '19

Dear RBVI, My current project involves modifying market set to better-fit the density map, and I use "*Undo Move*" function of "*Movement Mouse Mode*" window all the time (at least 100 times every hour). Although the "*Undo Move*" is already a godsend for my current project, I have to confess that I find moving my mouse all the way to "*Movement Mouse Mode*" window, then clicking "*Undo Move*" little bit tiring (especially after looking for "Movement Mouse Mode" Window over 10,000 times, at least). I have learned that there is also a way to use Undo Move via Toolbar, but the fact that I need to move my mouse from my model to click the Undo Move button remains the same. I want to ask the following question : "*Can Mouse button (ex. MMB), or a specific custom keyboard key (ex. Pause/Break), be assigned to activate a UCSF Chimera function that requires its button to be physically pressed?*" This is such a minor wish, as it would likely only benefit 1 person, I already feel guilty for asking this. That is why I want to know if mouse button can be assigned to actiavte UCSF Chimera function in general. Best, Junha Song.

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molecular dynamics simulation manual
by AYMAN NAEEM 29 Oct '19

29 Oct '19

Hello I want to use molecular dynamics simulation guideline by using chimera. I will be grateful for your attention. Best regards Ayman Naeem

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electron scattering factors
by Thomas Bick 29 Oct '19

29 Oct '19

Is it possible to create a density map based on a pdb using electron scattering factors rather then a sole gaussian distribution? The molmap command apparently doesn`t have a argument to include scattering factors? Are there maybe different possibilities do that in Chimera? Thanks for the help in advance! Best Thomas Bick

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Pov-Ray functionality
by Brown, Jeffrey 28 Oct '19

28 Oct '19

Hello, I like a lot about ChimeraX; however, I can’t figure out how to export to POV-RAY format. Has this functionality been removed? Although there is a pseudo ray trace function in Chimera X - it is impossible to add scenes like I did in this publication https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009406 In which I used Chimera to render all of the proteins and then moved them around and added membrane etc. Also there is a lot more control in POV-RAY as it is code that you can’t accidentally rotate with your mouse. Cheers, JWB Jeffrey Wade Brown, M.D., Ph.D. Instructor in Medicine Washington University School of Medicine Department of Gastroenterology 660 South Euclid, Campus Box 8124 St. Louis, MO 63110 Facsimile: (314) 362-3643 Office: (314) 454-8204 Pager: (314) 253-1585 E-Mail: brownjw(a)wustl.edu<mailto:brownjw@wustl.edu> http://independent.academia.edu/JeffreyWadeBrown ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Chimera-users] Creating movies with alpha channel / transparent background
by Tom Goddard 28 Oct '19

28 Oct '19

Hi Martin, It is possible that some Chimera movie encode command format option will put the transparency channel into the movie -- it all depends on what ffmpeg does and what those formats support. I don't know what ffmpeg supports nor what formats support transparency -- you could try to look that up online, or you could simply try each of the Chimera formats and see if it produces a movie with transparency. Chimera simply hands the sequence of PNG images to ffmpeg (which is bundled with Chimera, ffmpeg version 2.1). From what I saw in ffmpeg docs there is not a special include transparency option -- it is simply a matter of having a transparency channel in the images and having ffmpeg support for the specific output format. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#encode-op… Tom > On Oct 28, 2019, at 2:04 PM, Martin Textor <martin_textor(a)gmx.de> wrote: > > Hi Tom, > > thank you. I'm aware that Chimera can output a series of images with a transparent background, I have done this already (using png). As this is possible, and the "movie encode" command supports, besides other formats, .avi and .mov, both of which definitely support an alpha channel, I had hoped there might be some option for "movie encode" that's just not described in the documentation which allows obtaining a video with transparent background and spares me from having to use a third-party tool. > > With regards to Elaine's reply, I want to use the video overlaid to another one, so a static background image is not an option in this specific case, but thanks for the suggestion. > > Best, > Martin > > Am Mo., 28. Okt. 2019 um 20:05 Uhr schrieb Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>: > Hi Martin, > > You can have Chimera save a series of transparent background images using the movie command, for example, > > set bgtransp > movie record dir ~/Desktop/test format png ; turn y 1 90 ; wait 90 ; movie stop > > Then you would need to encode the PNG images in ~/Desktop/test into a movie using some encoding program. I doubt the Chimera "movie encode" command supports any video format that can handle transparent background. Chimera uses ffmpeg to encode movies and apparently ffmpeg can encode some video formats with transparency, for example, as described here the motion PNG format in .mov can handle transparency > > https://stackoverflow.com/questions/644684/turn-image-sequence-into-video-w… <https://stackoverflow.com/questions/644684/turn-image-sequence-into-video-w…> > > Tom > > > > >> On Oct 28, 2019, at 10:06 AM, Martin Textor wrote: >> >> Hello, >> >> I was wondering if it is possible to create movies with a transparent background? I know that it's possible to create images with a transparent background and that the video formats supported by Chimera to encode movies include avi and mov, both of which support an alpha channel as far as I know. >> >> Kind regards, >> Martin Textor >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > > > > -- > Martin Textor > 20 Elmer Mews, > Leatherhead, Surrey, > KT22 9DN, UK > > Fon: +49(0)178 3993650 <> > Mail: martin_textor(a)gmx.de <mailto:martin_textor@gmx.de>

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Creating movies with alpha channel / transparent background
by Martin Textor 28 Oct '19

28 Oct '19

Hello, I was wondering if it is possible to create movies with a transparent background? I know that it's possible to create images with a transparent background and that the video formats supported by Chimera to encode movies include avi and mov, both of which support an alpha channel as far as I know. Kind regards, Martin Textor

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Fit list behavior query
by Oliver Clarke 28 Oct '19

28 Oct '19

Hi, I often use fitmap with the “search” flag to find the orientation of a fragment (e.g. a single domain of a larger protein) in a cryoEM map - something like “fitmap #1 #0 search 100 radius 5”. Normally, a fit list table will appear and the model will reorient to match the highest scoring entry in the fit list. One thing I have noticed is that if I run a second such command after the first (e.g. to try a different radius or number of trials), the fit list is not updated - all the entries are identical, and the model is again reoriented to match the highest entry in the first list. I find I need to first manually clear all the fits from the first trial in order for it to correctly update with the results of the second run. I wonder if it would be possible to alter this behavior such that the fits from the first run are automatically cleared if a second fitmap command is issued? Cheers Oli

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Using Chimera on IOS devices
by Lytle, Ayren 23 Oct '19

23 Oct '19

Good afternoon, I've reviewed the list of supported operating systems<http://www.rbvi.ucsf.edu/chimera/download.html> on your website and did not see IOS listed. Do you have any experience using Chimera on iPads and if so do you recommend it for College Biology students? Our instructors have referenced some Galaxy Tab A (2019) Android tablets, but we would prefer to support IOS devices over Android due to our existing central support manage systems. I've included a link below to the Andriod tablet they are considering as well. I appreciate your time. Thanks. https://www.cdwg.com/product/samsung-galaxy-tab-a-2019-tablet-android-9.0-p… Best regards, Ayren Lytle Manager, User Services College of Southern Nevada | Department of Office of Technology Services 3200 E. Cheyenne | North Las Vegas, NV. 89030 Office: (702)-651-4450<a%20href=%22tel:%20(702)-651-4450%22%3e123-456-7890%3c/a> | ayren.lytle(a)csn.edu<mailto:ayren.lytle@csn.edu> www.csn.edu/ots<https://at.csn.edu/otsservices> [ConfidentialSignatureLine]

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50 chains structure numbering errors
by Ahmad Khalifa 23 Oct '19

23 Oct '19

Hello, I'm trying to deposit a PDB with 50 chains. My PDB has a lot of HETATM records and at some point it switches from HETATM"number" to HETATM*****. The PDB throws an error regarding HETATM*****. If you any suggestions regarding the error and / or processing the .pdb to make the deposition easier, please let me know. I also wonder if I can save my file as a cif by Chimera. Regards.

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could not access chimera webpage
by Sirin Theerawatanasirikul 23 Oct '19

23 Oct '19

Dear Chimera UCSF developers I am Sirin Theerawatanasirikul from Thailand. I am working on protein structures and use chimera every day. In a couple days, I tried to access your website via safari run in Mac Os Mojave ; https://www.cgl.ucsf.edu › chimera I could not access any topic or any feature. Could you please give me a suggestion? Sincerely yours, Sirin -- Sirin Theerawatanasirikul DVM (Hon.),PhD.(Pathobiology) Assistant Professor, Department of Anatomy Faculty of Veterinary Medicine, Kasetsart University THAILAND e-mail: fvetsrth(a)ku.ac.th, sirin.t(a)ku.ac.th, numilo(a)hotmail.com office phone: +66(0)2 942 8954

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Reassign chain ID letters
by Ahmad Khalifa 21 Oct '19

21 Oct '19

Hello, I have a structure with multiple chain IDs, some of them include number chain IDs and same letter small case and capital case chain IDs. I want to reassign the chain ID's randomly so that they are letters first then numbers, capital case then small case. How can I do that?! Best regards.

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Chimera
by Arnaout, M. Amin,M.D. 18 Oct '19

18 Oct '19

I<https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac64/c…>I downloaded chimera-1.14-mac64.dmg<https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac64/c…> on my iMAC with Catalina OS but cannot open Chimera (see attached).

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Chimera on macOS Catalina (10.15)
by Tom Goddard 16 Oct '19

16 Oct '19

Apple released their next version of macOS, version 10.15, called Catalina, a week ago. I have tested the Chimera 1.13.1 and Chimera 1.14 release candidate with Catalina and they worked without obvious problems. macOS Catalina has introduced new security measures where you must give permission to each application to allow it to access Desktop, Downloads and Documents folders and external disk drives. So you will see those permission dialogs appearing in Chimera and will need to press Allow. You only need to grant permission once for each folder when you try to open data from that folder and those permissions will apply to all future Chimera uses, so it is not too annoying. Tom

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depict hydrophobicity surface in super large molecules in chimera
by Marta Perez Illana 15 Oct '19

15 Oct '19

Hi all I was trying to analyze the hydrophobic surface of two very large structures ( 3 chainsx 900 aa each so 2.700aa). As expected the default surface calculation has failed. Normally for electrostatic potential what works for me is making a mol map (molmap #3 4 gridSpacing 0.5) and then calling the pdb2pqr and apbs servers directly from chimera, which is very convenient. However I cannot find an analogous way to make it with hydrophobicity... Since the surface fails for such big molecules, the straight forward way (present-3interactive surface hydrophobicity) does fail as well... Then... is there any server than can be called from chimera, to get hydrophobicity as an attribute to be depicted? Or alternatively could you suggest any server that gives output hydrophobic column, compatible to get it after to chimera attributes? Reading a bit I found that, not as electric fields, that can be computed for structures, hydrophobicity comes just for the sequence, without taking into account the neighbours and context... P.D: I have managed to represent in other programs the hydrophobic surface, but I really want to make it in chimera, to make it more consistent and easy to organize myself... Thanks a lot! and sorry if the question goes beyond Chimera... Marta

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Bond-type error
by Laia Ferrer Duran 15 Oct '19

15 Oct '19

Hi, I recently started using chimera for one project from university. At first I worked in the university computer that it had the program. Today, as I have to work from home I downloaded the latest version of chimera in the web page and I tried to do a dock prep in the protein from DB 2am9. With the receptor it worked well, but when I done it with the ligand TES it seems to have a problem with the add charges fase. I searched first in all you webs and all it seems to say is that the molecular structure isn't correct but I really think there isn't a problem with the structure because with exactly the same steps it used to work in the university computer. The error says: (TES) sh: 1: C:/Program: not found (TES) /usr/bin/antechamber: Fatal Error! (TES) Cannot properly run "C:/Program Files/Chimera 1.14rc/bin/amber18/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac". Failure running ANTECHAMBER for residue TES Check reply log for details I don't know if it could be some problem with my program or if I should change the configuration of the program or what it is that isn't working. Thanks in advanced and I look forward you answer.

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surface color
by Schmid, Michael F. 14 Oct '19

14 Oct '19

I’m trying to do the same thing as Chimera’s “Surface Color”, but in ChimeraX, on the command line. After reading the docs, I tried “color height #1 (the map designation) center 0,0,0 axis z rainbow”. It gave “expected a keyword”. What did I miss? Thanks, Mike

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