- Chimera-users - RBVI Mailing Lists

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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Support for Chimera1.13.1
by Mr 13 Nov '19

13 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 03 Nov '19

03 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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