- 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

2 1

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

2 1

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

2 1

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

2 2

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

2 1

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

2 2

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> >

1 0

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>

1 0

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

3 3

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

2 1

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

2 1

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]

2 6

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

2 1

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

2 1

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 ________________________________

3 3

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

2 1

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!

2 1

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

3 2

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>

1 0

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

5 5

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>

1 3

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

2 1

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

2 1

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')

3 4

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/>

2 1

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.

2 2

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

2 2

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

2 1

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.

3 3

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>

1 0

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

3 2

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

2 1

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]

2 1

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.

2 1

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

2 1

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.

2 1

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).

2 1

Chimera on macOS Catalina (10.15)
by Tom Goddard 15 Oct '19

15 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

1 0

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

3 4

Bond-type error
by Laia Ferrer Duran 14 Oct '19

14 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.

3 4

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

2 1

FAD binding site on Cryptochrome
by Margiotta, Joseph 11 Oct '19

11 Oct '19

Hi-> I am very new to molecular modeling and have a very basic novice user issue. We are studying cryptochrome proteins some of which are known to bind the chromophore Flavin adenine dinucleotide (FAD) and for this and other reasons are considered photopigments. We have looked at a cryptochrome in chicken that binds FAD and is light sensitive (GallusCRY4) and have sent the AA sequence to Zhang’s COACH site for Protein-ligand binding site prediction (https://zhanglab.ccmb.med.umich.edu/COACH/) at the University of Michigan. The results come up with a C-score confidence prediction of 0.59 with a cluster size of 63 for FAD binding to GallusCRY4. The results allow you to download the 3D model and the residue-specific binding probability, which is estimated by SVM, the predicted bound ligands and detailed prediction summary, and the templates clustering results. We’d now like to extend this modeling to GallusCRY1 and GallusCRY2 to see get a FAD binding prediction and the complex structure with the most representative ligand in the cluster. The COACH site lets you export the model and complex structure in PDB format and I downloaded Chimera to visualize and analyze the PDB results. I would like to be able to label the structures using the binding probabilities, and template clustering results to include the predicted FAD binding pocket on the three CRY proteins and also label a tetrad of Trp residues that are thought to be responsible for electron transfer. Can you give me some general guidance on how to start this analysis? -- Joseph F. Margiotta, PhD Professor of Neurosciences UT College of Medicine & Life Sciences Block HS 120A Mail Stop 1007 Toledo, OH 43614 419-383-4119

2 2

Centroid/axis question
by Luca Pellegrini 08 Oct '19

08 Oct '19

Hello, I have generated a bunch of axes and centroids for my protein complex structure. Now I would like to change their appearance by changing their radius, to make them the size I want for a picture. Is there a way to do this for an existing axis/centroid, or do I need to create them again? I have got quite a lot of them… Thanks, 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

2 2

Question about electron density map
by Zhang, Bixia 04 Oct '19

04 Oct '19

Dear Developer, I want to have a figure of my ligand only and its electron density, and I used my protein mtz file to generate a CCD4 map in phenix and then open in chimera. I tried fit in map but it does not fit well. Could you please help me out? And after I have the electron density, how to hide the backbone electron density? Thanks a lot! Best, Bixia

2 1

next/previous buttons suggestion
by Oliver Clarke 04 Oct '19

04 Oct '19

Hi, I like and frequently use the next/previous buttons (present in the daily builds) for sequential model display or activation. They are very useful for quickly comparing multiple 3D classes, or multiple aligned atomic models. One thing that would make this feature even more useful would be the capacity to lock display of a model - that is, temporarily remove it from the next/previous sequence. This would be useful, for example, when one wants to keep a single “reference” atomic model (or density map) displayed, but sequentially compare with multiple other maps/models. Would this be possible to add? Either as a command, or adding another checkbox that controls the lock/unlock status of the currently displayed model. Cheers Oli

1 0

[ Asking how to combine loops of models after refinement ]
by Hồ Phương Dung 03 Oct '19

03 Oct '19

Dear Sir/Madam, I am Dung. I am currently using Chimera to do the refinement for my protein because it has some large missing residues segments. I use Tools/ Loops- Model refinement of Chimera software to do that task. As it was failed to generate models if I performed refinements for all missing residues segments. Thus, I decided to refine them not at once. The problem is that I could not find how to combine the separated loops from models after refinement. I am new to Chimera so I hope that my description can be useful for you to imagine my problem. I hope that you could support me to solve this problem. I really appreciate it. Thank you for spending your valuable time. Yours sincerely, Dung Hồ Ngọc Phương Dung International University - Vietnam National University Email: phuongdunghongoc(a)gmail.com

2 2

PROBLEM IN ENERGY MINIMIZATION
by Prabuddha Bhattacharya 02 Oct '19

02 Oct '19

Dear Chimera, I have been facing a problem recently while using UCSF Chimera. After opening the structure of ligands in the chimera window as .pdb file, when ever I am trying to minimize the energy (Tools-->Structure Editing-->Minimize Structure) of that ligand in (which is in .pdb form), I am getting the following error message: "Failure running ANTECHAMBER for residue". I am using "AMBER ff14SB" (for standard residues) and "Gasteiger" (for other non-standard residues). Upon trying out with "AM1-BCC" (for other non-standard residues), I am getting an altered compound so that cannot be perhaps tried. Kindly find attached the .pdb files for the ligands I am trying to minimize the energy, and a word file containing the screen shots of the step-by-step messages leading to the error message that I am getting. I will be highly grateful if you can help me in sorting out the problem. Thanks in advance, Best Regards, *Prabuddha Bhattacharya * *Assistant Professor* *Adamas University* *Kolkata 700126* *India*

3 5

Re: [Chimera-users] Selecting residues with zones when reference is absent
by Elaine Meng 02 Oct '19

02 Oct '19

> On Oct 1, 2019, at 11:39 AM, Carlos G. Oliver <cgoliver(a)protonmail.com> wrote: > > Hi Elaine, > I just have a follow-up question on this topic. > Specifically the command: > > select ligand & nucleic acid z<10 > > I'm not sure how the & operator is working here but it seems that it considers the two selections independently and then takes the intersection. > > However it would be faster to first select the ligands and then within the ligand atoms find the ones that satisfy the second condition. > > When I tested it on 6s0z knowing beforehand the name of the residue: > > select #0:ery z<10 > > The computation is much faster. > Wondering if there is a way to more efficiently combine the selection conditions similar to this. > Thanks again! > Best, > Carlos G. Oliver Hi Carlos, Sending questions to chimera-users (CC’d here) is recommended unless involving private data. Others may know the answer when I don’t, and messages may fall through the cracks if you them only to my individual address. I’m not a programmer and don’t know the code structure, so I don’t know if there is any ingenious way of structuring your specification to make it faster. There might not be a way. However, your two commands seem to be doing totally different things. Is ERY the ligand? In that case your second command is lacking the “nucleic acid” part. The documentation says that & has highest priority, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combi…> … so your second command > select ligand & nucleic acid z<10 > intersects ligand with all residues within 10 angstroms of nucleic acid. is that what you are trying to do, find all ligands within 10 A of nucleic acids? Naturally this is going to take much longer than your first command > select #0:ery z<10 … which just finds all residues within 10 A of ligand ERY. It’s looking at a zone from one residue instead of a zone from many (hundreds?) of nucleic acid residues. The comparison should instead be to select #0:ery & nucleic acid z<10 … which I suspect would be just as slow. There are various ways to split up the selection process but I don’t have any reason to believe that they would be faster. In general, ChimeraX is much faster than Chimera for working with large structures (say ribosome), at least in rendering, and allows using parentheses in command-line specifications so it’s clearer what you will get. In ChimeraX, the command could be something like select ligand & (nucleic :<10) ...which takes 1 second on my laptop with structure 6s0z, whereas Chimera with your first example command is just hanging on that same structure and had to be force-quit. However, maybe ChimeraX doesn’t do all of the other things you are currently trying to do. ChimeraX is available under similar licensing conditions as Chimera (free for noncommercial use): <http://www.rbvi.ucsf.edu/chimerax/index.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

4 6

Gaussian filter prior to fitmap?
by Oliver Clarke 02 Oct '19

02 Oct '19

Hi, Would it be possible to add an option to fitmap (in either/both chimera/chimerax) to restrict the spatial frequencies used for fitting? That is, to fit gaussian filtered versions of the input maps behind the scenes, but apply the resulting transform to the unfiltered maps? Filtering maps to say 15 Å gives a much better radius of convergence in my experience - much less prone to getting stuck in local minima. In general I also wish that when applying a gaussian filter in Chimera (or chimerax), the approximate equivalent in spatial frequency terms was indicated - e.g. if I am applying a gaussian filter of sdev x to a map of pixel size y, what lowpass filter does this effectively equate to? Also, when one wants to fit multiple maps to a single reference (quite common when inspecting results of 3D classification), Chimera gives an error message indicating that multiple maps have been input. There is an “eachmodel true” option one can set to allow fitting of multiple maps to a single reference, but the default value is false. It seems to me that the default value for this should be true, as if the user is specifying a wildcard or model ID range for the maps to fit, this is probably the behavior they are after I think. Or maybe the error message could be altered to indicate that if this is what one wants to do the eachmodel keyword needs to be specified? Cheers Oli

2 1

How to launch chimera in a remote server
by Sun Yeping 01 Oct '19

01 Oct '19

Dear everyone, Chimera is installed in a remote CentOS 7 server, and it works properly if working directly on the server. However, when I login to that server from my local machine (also centos 7 system) wish ssh and try to launch chimera, an error information window appears which reads: "Display misconfiguration. Please Increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera Installation Instructions" I googled this error and find that someone solve it by installing virtualGL, so I also installed virtualGL and try to launch chimera with: $vglrun chimera But get the following errorL # vglrun chimera [VGL] WARNING: The OpenGL rendering context obtained on X display [VGL] :0 is indirect, which may cause performance to suffer. [VGL] If :0 is a local X display, then the framebuffer device [VGL] permissions may be set incorrectly. [VGL] WARNING: The OpenGL rendering context obtained on X display [VGL] :0 is indirect, which may cause performance to suffer. [VGL] If :0 is a local X display, then the framebuffer device [VGL] permissions may be set incorrectly. X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 154 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 36 Current serial number in output stream: 36 Do you know what the error is about and how to solve it? Thanks in advacnce Yeping Sun

2 1

Download chimney
by sergio Bertel Perez 01 Oct '19

01 Oct '19

It does not allow me to download the program, I accept the terms and it sends me a message (Thank you for considering UCSF Chimera. Please let us know what part of the UCSF Chimera license agreement you found unacceptable). <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

Re: [Chimera-users] Question about selecting residues
by Zhang, Bixia 27 Sep '19

27 Sep '19

Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia ________________________________ From: Zhang, Bixia <bixia.zhang(a)wsu.edu> Sent: Friday, September 27, 2019 10:11 To: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> Subject: Re: Question about selecting residues Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia ________________________________ From: Zhang, Bixia Sent: Friday, September 27, 2019 10:06 To: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> Subject: Question about selecting residues Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia

2 2

Docking with UCSF Chimera
by Su Datt Lam 25 Sep '19

25 Sep '19

Dear Chimera, Dear Chimera, I am trying to use your software to run molecular docking of sucrose onto a structure. I've provided the ligand and also the receptor structure in the email. I've added the charge for the ligand (using Tools->Structure editing-> Add charge) and selected Gasteiger ad the charge method. After that, I prep the ligand (using Tools -> Structure editing-> Dock Prep). Then, I performed the docking thru Tools ->Surface/Binding Analysis ->AutoDock Vina. Vina program managed to run, but with some errors. The ligand bound to the structure is not the right structure of sucrose, but a hairball. I suspect there's something wrong with the Ligand prepping method in chimera that causes the structure to go crazy. Can you help me with this problem? Many thanks, Su

2 1

Re: [Chimera-users] polar and nonpolar surface area
by Susy López 24 Sep '19

24 Sep '19

Dear all This does not answer my question. Maybe, I don't explain it properly. I would just like to know if there is any command in Chimera, which allows me to identify the atoms that are part of the total solvent accessible surface area (SAS). I will try to explain my question with an example. First, Commands: open 121p select :62 show sel Select>residue>all nonstandard Actions>Atoms/Bonds>delete select :62@OE1 surface sel [image: image.png] As shown in the image, I have identified an atom that forms the surface accessible to the solvent. However, to identify the total atoms of that protein I have to select atom by atom, which implies a lot of time and more if I have several proteins. So, I would like to know, if it´s possible to obtain a command that allows me to select all the atoms at the same time, specifying the atoms that are part of the total solvent accessible surface area(SAS). Thank you (: kind regards, Susanna El lun., 23 sept. 2019 a las 17:33, Susy López (<susannalopez18(a)gmail.com>) escribió: > Dear all > > > > This does not answer my question. Maybe, I don't explain it properly. > > I would just like to know if there is any command in Chimera, which allows > me to identify the atoms that are part of the total solvent accessible > surface area (SAS). > > > > I will try to explain my question with an example. > > First, > > Commands: > > open 121p > > select :62 > > show sel > > Select>residue>all nonstandard > > Actions>Atoms/Bonds>delete > > select :62@OE1 > > surface sel > > > > As shown in the image, I have identified an atom that forms the surface > accessible to the solvent. However, to identify the total atoms of that > protein I have to select atom by atom, which implies a lot of time and more > if I have several proteins. > > So, I would like to know, if it´s possible to obtain a command that allows > me to select all the atoms at the same time, specifying the atoms that are > part of the total solvent accessible surface area(SAS). > > > > Thank you (: > > > > kind regards, > > Susanna > > > > > > > > > > El lun., 23 sept. 2019 a las 11:54, Elaine Meng (<meng(a)cgl.ucsf.edu>) > escribió: > >> Dear Susanna, >> This sounds like the same question others have been asking recently… >> maybe a class assignment. If so, you can tell the others in the class so >> that they don’t have to ask here again! :-) >> >> Please see this recent response, and links therein: >> < >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016160.html >> > >> >> …including the following, which has with more details starting at the >> fifth paragraph, “However, you can get the total surface area given some >> range of hydrophobicity values…” >> < >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016140.html >> > >> >> …or a web server you could try instead of Chimera: >> < >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016141.html >> > >> >> These answers suggest selecting polar and nonpolar residues, giving a few >> different options for deciding which ones are polar and nonpolar, and then >> just adding up the surface area from the selection. Maybe by “customize” >> you meant deciding for yourself which is polar and nonpolar? You can just >> select a list of whatever residue types you want, e.g. command: select >> :asp,glu,his,lys,arg >> >> You don’t have to worry about selecting only the atoms on the surface, >> because if they are not on the surface they will just add zero area to the >> total and the result will be the same. Selecting a residue selects all the >> atoms in that residue. >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> > On Sep 21, 2019, at 3:12 PM, Susy López <susannalopez18(a)gmail.com> >> wrote: >> > >> > Dear all >> > I am starting to use Chimera as a master's student and I have some >> difficulties. >> > >> > I know how to select the amino acids that are part of the surface of my >> protein. However, I don't know how to select the atoms of the surface. >> Specifically, the atoms accessible to the solvent. >> > >> > My second question is: >> > >> > I would like to know how polar amino acids (arginine, asparagine, >> aspartic acid, cysteine, etc.) and non-polar amino acids (alanine, glycine, >> isoleucine, leucine, etc.) can appear. Is there any configuration that >> allows me to identify polar and non-polar amino acids for edit them? Is it >> possible to customize those amino acids when I select them? >> > >> > I would be grateful if someone could help me, thank you. >> > >> > Best regards, >> > >> > >> > Susanna >> >>

2 2

(no subject)
by Susy López 24 Sep '19

24 Sep '19

Dear Tom Goddard I would just like to know if there is any command in Chimera, which allows me to identify the atoms that are part of the total solvent accessible surface area (SAS). I will try to explain my question with an example. First, Commands: open 121p select :62 show sel Select>residue>all nonstandard Actions>Atoms/Bonds>delete select :62@OE1 surface sel [image: image.png] As shown in the image, I have identified an atom that forms the surface accessible to the solvent. However, to identify the total atoms of that protein I have to select atom by atom, which implies a lot of time and more if I have several proteins. So, I would like to know, if it´s possible to obtain a command that allows me to select all the atoms at the same time, specifying the atoms that are part of the total solvent accessible surface area(SAS). Thank you (: kind regards, Susanna

2 1

calculating virus surface in prep for radial color display
by Gampe, Robert 24 Sep '19

24 Sep '19

Hi Chimera Users I need to calculate a radial distance plot from a surface representation of an Adeno Associated Virus structure as shown from literature below. However the: 1. Action, Surface, Show command fails, reporting CHIMERA often fails for large structures ( AAV is easily over 200K atoms ) with multiple chain IDs ( I have 60 individual chain IDs for each of the 60 capsid proteins ). Other CHIMERA popup suggestions did not resolve the problem either ( changing molecular surface parameters in the Inspect Selection ( actually didn't see anything to change ) or in PREFERENCES - NEW SURFACES. I tried using CHIMERA, Structure editing, change chain IDs to all chain A, but that was disallowed. Summary: could not figure out how to get CHIMERA to calculate and display a surface representation of an AAV virus and then use that display to calculate radial coloring as shown below. Any solutions greatly appreciated and thanks. Rob [cid:image003.jpg@01D56FE1.62351B70] [cid:image004.jpg@01D56FE1.62351B70] _________________________ Robert Gampe, MS | Senior Scientist | RDRU Structural Biology| Pfizer Inc. 7030 Kit Creek Rd, Morrisville, NC 27560 Office: 919-666-5969| Robert.Gampe(a)pfizer.com<mailto:Robert.Gampe@pfizer.com> [cid:image006.jpg@01D4D043.EB786830] _________________________

2 1

calculating virus surface in prep for radial color display
by Gampe, Robert 23 Sep '19

23 Sep '19

Hi Chimera Users This is 2nd send to you after I enrolled as a CHIMERA user :), thanks. I need to calculate a radial distance plot from a surface representation of an Adeno Associated Virus structure as shown from literature below. However the: 1. Action, Surface, Show command fails, reporting CHIMERA often fails for large structures ( AAV is easily over 200K atoms ) with multiple chain IDs ( I have 60 individual chain IDs for each of the 60 capsid proteins ). Other CHIMERA popup suggestions did not resolve the problem either ( changing molecular surface parameters in the Inspect Selection ( actually didn't see anything to change ) or in PREFERENCES - NEW SURFACES. I tried using CHIMERA, Structure editing, change chain IDs to all chain A, but that was disallowed. Summary: could not figure out how to get CHIMERA to calculate and display a surface representation of an AAV virus and then use that display to calculate radial coloring as shown below. Any solutions greatly appreciated and thanks. Rob [cid:image001.jpg@01D56FEE.1FF9C5A0][cid:image002.jpg@01D56FEE.1FF9C5A0] _________________________ Robert Gampe, MS | Senior Scientist | RDRU Structural Biology| Pfizer Inc. 7030 Kit Creek Rd, Morrisville, NC 27560 Office: 919-666-5969| Robert.Gampe(a)pfizer.com<mailto:Robert.Gampe@pfizer.com> [cid:image006.jpg@01D4D043.EB786830] _________________________

3 2

(no subject)
by Susy López 23 Sep '19

23 Sep '19

Dear all I am starting to use Chimera as a master's student and I have some difficulties. I know how to select the amino acids that are part of the surface of my protein. However, I don't know how to select the atoms of the surface. Specifically, the atoms accessible to the solvent. My second question is: I would like to know how polar amino acids (arginine, asparagine, aspartic acid, cysteine, etc.) and non-polar amino acids (alanine, glycine, isoleucine, leucine, etc.) can appear. Is there any configuration that allows me to identify polar and non-polar amino acids for edit them? Is it possible to customize those amino acids when I select them? I would be grateful if someone could help me, thank you. Best regards, Susanna

2 1

Chimera laptop features required
by Aron Singletary 19 Sep '19

19 Sep '19

I was looking for system specs and ran across this comment: "I don't think you can buy one anymore, but the best laptops were those with NVIDIA Quadro (not NVS) graphics and a 3D stereo display (120Mhz, 3D glasses). Chimera needs workstation graphics (NVIDIA Quadro or AMD FirePro/FireGL), to support 3D stereo viewing." Just wanted to let you know there are still many great systems available with Quadro and FirePro graphics, they will usually be a good bit more expensive than traditional consumer laptops though. Our older GoBOXX SLM available in 15" with the Quadro P3200. https://www.boxx.com/systems/mobile-workstations/goboxx-slm/goboxx-slm-vr Our newer GoBOXX SLM available in 15" or 17" with Quadro RTX300-, RTX4000 or RTX5000. https://www.boxx.com/systems/mobile-workstations/goboxx-slm/goboxx-slm-15 Or if you are looking for a true desktop replacement we have our GoBOXX MXL. https://www.boxx.com/systems/mobile-workstations/goboxx-mxl Thank you, Aron Singletary Enterprise Representative BOXX Technologies 10435 Burnet Road, Austin, TX 78758 Work: (512) 852-3347 Toll Free: (877)877-2699 x347 Fax: (512) 835-0434 Email: asingletary(a)boxx.com<mailto:asingletary@boxx.com> www.boxx.com<http://www.boxx.com/> [BOXX_Logo_email]

1 0

Fwd: chimera install problem
by Elaine Meng 18 Sep '19

18 Sep '19

Oh sorry, I was waiting for someone else to answer because I didn’t realize until now that you sent this message to only me. I don’t know anything about this subject, so I’m forwarding your message to the chimera-users mailing list for somebody else to reply. We recommend sending Chimera questions to this list instead of to individual developers. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: 陈柳青 <519198561(a)163.com> > Subject: chimera install problem > Date: September 17, 2019 at 5:31:06 AM PDT > To: meng(a)cgl.ucsf.edu > > Hi! > I have a problem when install chimera-1.13.1-linux_x86_64.bin <http://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x8…> in my computer, its opensuse system. > can you tell me how to solve this problem? as i am not familiar with linux system. > sincerely! > Liuqing Chen > >

2 1

Chimera inquiry
by Danny Turin 18 Sep '19

18 Sep '19

Dear Sirs and Madames, I first want to start by sharing my appreciation with you for creating this program. It has been very helpful in my biochemistry course. I have been using the program to compute the total area and volume. Is there a way to only select either the polar or non-polar residue in the surface structure to determine volume and area. Thank you for your time. Sincerely, *--Daniel Turin * University of Minnesota Class of 2021, B.S. Health Sciences l turin005(a)umn.edu l (651)-600-0805 l

2 1

Unable to Find Function
by Bailey Onken 17 Sep '19

17 Sep '19

Hello, I am currently a student in Biochemistry. I have a protein and I am trying to separate polar and nonpolar residues located on the surface of these molecules and then finding the values for the surface area associated with polar and nonpolar areas. If you can help me get to this function I would be very grateful. Thank you very much, Bailey -- *Bailey Onken *| Student, University of Minnesota Rochester 507.329.7409 | onken031(a)umn.edu

2 3

How to draw 3-fold axis of a Icosahedron
by sunyeping 17 Sep '19

17 Sep '19

Dear everyone, I created an icoshedron with "Tool>high-order structre>Icoshedron surface" menu. Do you know how to draw 3-fold axis of a Icosahedron so that I can see the 3-fold symmetry center on the icoshedron surface? Thank you in advacne.

2 1

Command line equivalence for Render by Attribute radii
by Sygusch Jurgen 16 Sep '19

16 Sep '19

Hello, I cannot seem to find the command line equivalence for Render by Attribute radii. I am trying to display a tunnel where the atom B-factors represent the tunnel radius. I am able to display the tunnel as expected by using the GUI. In the GUI, when I do Tools --> Depiction --> Render by Attribute --> atoms --> My Model; then Render Attribute --> bfactor; Radii --> Atom Style --> Sphere, I get the expected result of the tunnel diameter varying according to Bfactor (tunnel radius). What is the command line equivalence for doing this? I cannot seem to find it. Thank you for looking into this.

3 3

Selecting residues with zones when reference is absent
by Carlos G. Oliver 16 Sep '19

16 Sep '19

Hello, I would like to select all ligands that are within a distance of nucleic acids but above a distance from proteins. The selection command I have so far is: `select nucleic acid z<10 & protein z>10 & ligand` This works for PDBs that contain both nucleic acids and protein. However, some will only contain nucleic acids, and in this case the `protein z>10` condition will result in an empty selection even when there is a valid ligand. I was wondering if there was a way to check whether the model contains protein to run a different selection command for each case, or to use a different selection command which handles both cases. Thanks! Carlos G. Oliver

2 2

Dockprep OT2 C terminal question
by Danilo Boškovic 16 Sep '19

16 Sep '19

Dear caretakers, I have a non-standard residue OT2 (C terminus last O atom) that does not get recognized in the amber force field (everything else is fine). How do i rename this residue so it is properly accounted when adding charge? Sincerely, D. Boskovic

2 1

Max 100 residues for local bug?
by Danilo Boškovic 16 Sep '19

16 Sep '19

Dear caretakers, I tried to do autodock vina but as soon as i did i got an error that i can only do max 100 residues. I use a local installation of AVina. Is this a bug or is there somewhere something im missing? 41965 build number 1.13.1 version Sincerely, D. B.

2 1

Where is the radius.nc map file in the Semliki Forest virus?
by sunyeping 16 Sep '19

16 Sep '19

Dear everyone, The Semliki Forest virus tutorial (https://www.cgl.ucsf.edu/chimera/data/tutorials/semliki/semliki.html) mentioned a radius.nc which is used for visualization of the layer. However, the tutorial doesn't describe where the reader can download it. Do you know where to get thid file? Thank you in advance. Yeping Sun

2 1

Re: [Chimera-users] Electrostatic potential molecular surfaces
by Elaine Meng 11 Sep '19

11 Sep '19

Hi Fernando, Our resources don’t allow spending much time on consulting with individual research projects, sorry, and I can only answer mostly as it pertains to Chimera as I don’t know the details of parameters developed by other people or other programs. Also Chimera questions should be sent to this mailing list instead of to me directly so that other people can also benefit, unless private data are discussed or attached. You found an old script that is really special-purpose, finding the surface area that is more red than blue after coloring by electrostatic potential. Note that this would include surface that looks white but has a tiny, tiny tint of pinkishness. Also, the surface area that is more blue than red is just the complement of the surface that is more red than blue. In other words, if the surface is 75% red>blue then it is 25% blue>red because very little if any will be pure white. They always add up to the total surface. So no, you cannot use these scripts to figure out how much of the surface is polar or nonpolar. It may not matter given the above, but which method, set of charges, and what parameter values to use for electrostatic potential (ESP) calculations are research decisions that I cannot make for you. There are always tradeoffs, and different people have different opinions, etc. I don’t know python, but your generalization to coloring by hydrophobicity by identifying cornflower blue vs.goldenrod might be wrong. Red vs. blue is simpler since they are RGB color components. However, even if the color comparison is done correctly, the logical problem is the same, they always add up to the whole surface, and nearly white areas will always be combined with one side or the other. However, you can get the total surface area given some range of hydrophobicity values independent of any coloring. Hydrophobicity in this case is just a constant lookup value for each type of amino acid, according to this table (kdHydrophobicity column): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> You would have to decide yourself which range of values is polar or nonpolar, but then you could just select all the residues that are less than or more than a certain value, e.g. command: select :/kdHydrophobicity>0.0 Alternatively you could just use command: select polar select ~polar …but you might not agree with what amino acids are considered polar, as shown in a table in this page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/resprop/resprop.h…> Then if surface is shown you could add up the area for the selected residues, e.g. menu: Tools… Structure Analysis… Attribute Calculator, and in that tool calculate attribute named whatever you want for “molecules” with Formula: sum(areaSAS.residue) (… or SES instead of SAS, to be compared with the corresponding total area given in the Reply Log when you show the surface) with option to “Restrict formula domain to current selection” and “Show calculation results in Reply Log" turned on, other options turned off, click Apply. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calcul…> Totally separate and not related to Chimera, but I happen to know of this web server you might be interested in, for comparing ESP of related proteins: <https://pipsa.h-its.org/pipsa/> Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 11, 2019, at 2:16 PM, Fernando Villa <fer.vdl1928(a)gmail.com> wrote: > > > Dear Elaine C. Meng, Ph.D > > I have some questions about electrostatic potential molecular surfaces and protein comparison. > > 1. The following scripts are added, edited from the redarea.py script of link http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts, considering that the script allows reading the surface in Å2 colored more red than blue area. > > 1. Add scripts: > > Command: > > > open > > -blue_area_03.py > > -cornflowerblue_area_03.py > > -goldenrod_area_02.py > > -red_area_02.py > > (the scripts are attached) > > > 2. I used the following commands: > > > open 4MZ2 > > > delete solvent > > > addh > > > addcharge > > > Surface > > coulombic -10 red 0 white 10 blue > > > The electrostatic potential surface is presented by Coulombing coloring Surface: > > > > <image.png> > I execute the commands: > > > redarea #0 > > red area 3562, total area 5730, ratio 0.6217 > > > bluearea #0 > > blue area 2168, total area 5730, ratio 0.3783 > > > The dominant areas of both colors are obtained. > > The following command is input: > > > rangecolor kdHydrophobicity min cornflowerblue 0 white max goldenrod > > > > <image.png> > Next: > > > cornflowerbluearea # 0 > > cornflowerblue area 4109, total area 5730, ratio 0.7171 > > > > goldenrodarea # 0 > > Goldenrod area 1621, total area 5730, ratio 0.2829 > > > So, I believe (I'm not sure): > > Blue area + Red area = PSA ß Is correct? > > White area = NPSA ß Is correct? > > > So, the real blue and red areas would be (not sure): > > > (Redarea * PSA) / Total surf = Real Red area > > (Bluearea * PSA) / Total surf = Real Blue area > > So: > > Bluearea = 1554.6792 > > Redarea = 2554.3208 > > > Is this calculation correct? > > > Could I apply these calculations to compare them with other proteins of the same family? > > For example: > > Protein members of the immunoglobulin family. > > > > In the Chimera version 1.14, I Download the following programs pdb2pqr-windows-bin64-2.1.1 > > apbs1.5_win64 > > Downloaded from the website: http://www.poissonboltzmann.org > > Next, I assign charges and radii with the following parameters of PDB2PQR > > > <image.png> > And I saved the file. Pqr > > > <image.png> > Later I opened the file 001_B4.pqr with Chimera 1.14 > > > <image.png> > I use the following command: > > > surface > > And run the APBS interface with the following default parameters: > > <image.png> > > As a result, the color gradient of the molecular surface appeared as shown: > > > <image.png> > <image.png> > > > However, my question is: > > Are these parameters correct using the force field PARSE of PDB2PQR? Or, is it necessary to use a different force field? > > > Could I apply the scripts: > > -blue_area_03.py > > -cornflowerblue_area_03.py > > -goldenrod_area_02.py > > -red_area_02.py > > > to calculate the redarea and bluearea and compare it with other proteins? > > > Is there a script that gives me the correct areas of both red and blue colors? > > > Sorry for my long email, as I am new to this area. And I really need help. > > I apologize for so many questions. > > I would greatly appreciate your help. > > > Best regards, > > Fer. > > > > > <blue_area_03.py><red_area_02.py><goldenrod_area_02.py><cornflowerblue_area_03.py>

2 3

How to analyze cryo-EM reconstruction map of virus and prepare publishable figures?
by sunyeping 11 Sep '19

11 Sep '19

Dear all, I am new to cryo-EM structural biology. Now I have a cryo-EM reconstruction map for a virus particle. I wish to analyze the characteristics of the virus, such as the h, k and t number, the component of an cryo-EM asymmetric unit of the capid and prepare some publishable figures. I have no idea how to do these things. Could all these be done with Chimera? Is there any tutorials or manual for these calculation, visualization and drawing? If you could recommend some ways by which I can learn to do these, I would be greatly grateful. Best regards

2 1

APBS electrostatic potential map not visible
by Ahmad Khalifa 10 Sep '19

10 Sep '19

Hello, After PDB2PQR and APBS calculation, I get an .dx that I can't view (doesn't appear when I click show), let alone color. I tried to launch volume viewer, it does display a surface. What am I doing wrong? Regards.

2 1

Modeller from a Python script
by Samo Lešnik 10 Sep '19

10 Sep '19

Dear Madam/Sir, I would like to run the Modeller missing loop function implemented in Chimera by using a Python script, as I want to go through a number of protein structures. Is this possible? I do not find the appropriate commands in the comand list. I would use a local instalation of Modeller. Thank you for your help. Best regards, Samo

2 1

DNA drawing inquiry
by Woorim Choi 09 Sep '19

09 Sep '19

2 1

Way to compute residue wise RMSD using python script in chimera:
by Kamalesh Damodaran 09 Sep '19

09 Sep '19

Dear sir/madam, I would like to superimpose the two structures and compute the residue wise RMSD values. With Gui support in chimera, I opened the two structures and used Matchmaker to superimpose two structures. In Matchmaker, I checked the box 'Show pairwise alignment(s)' and click Apply, subsequently it displays MultAlignViewer dialogue box, where --> Headers --> RMSD : backbone --> Save --> filenamegiven. This process would give me residue wise RMSD score only for backbone atoms in .hdr format. I wants to write python script to do the same, so that I will compare large number of structures, and my script is able to perform till the procedure of superimposition using matchmaker and display MultAlignViewer dialogue box. I don't know the way to store the RMSD : backbone and RMSD : calpha in .hdr format using python script through chimera. Can some one please help me in this. The reason why I specifically want to do in this approach is, because among the two structures, some residues of one structure is missing. Since this approach will compute RMSD only for the matching residues, I am interested in this. Hope my question is not confusing. Thanks in advance. Best regards, Kamalesh D.

2 3

cage builder
by Artur Biela 06 Sep '19

06 Sep '19

Hi all, I would like to build a cage model using cage builder, but the problem is that I need to use different polygons than available in the pop-up window of cage builder. My question is: is there any option to use for example octagons, decagons or even more-gons? Thank in advance Artur =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Artur BIELA, PhD Scientific Assistant Bionanoscience and Biochemistry Laboratory Malopolska Centre of Biotechnology Jagiellonian University 7A, Gronostajowa Street 30-387 Krakow Poland Department of Cell Biology and Imaging Institute of Zoology and Biomedical Research Jagiellonian University Gronostajowa 9 30-387 Krakow artur.biela(a)uj.edu.pl http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory publons<https://publons.com/mashlets?el=badgeCont570&rid=M-3954-2019> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

3 3

How could I know the segment label
by Huiya Zhou 03 Sep '19

03 Sep '19

Hi, I use the “Segment Map” for the volume data to divide the density map into parts. How could I know the information of each region? For example, the label, the average value of each region. I also would like to know the regions which are connected with one specific region. How could I obtain information in python script? Thanks, Huiya

2 1

Support chimera
by Jose Alirio Mendoza Mesa 03 Sep '19

03 Sep '19

Hi there, my name is Jose Alirio Mendoza. Currently, I am carrying out my PHD thesis in which I am using the chimera program to show the tomography results. Nevertheless, I am being presented some problems when trying to measure my particle in Chimera. The file of my product is “mrc” and I have been investigating about chimera usage where I have realized that the file must be “pdb” for the program to recognize it. I do not really know how to convert my molecule to the required file, and I guess that is the problem by which I cannot measure the distance of my particle. When I click “tools – structure analysis – distance” it does not appear the code of my molecule as in picture below [image: imagen.png] This is my particle and what I get when using the tool for measuring. I have other three tomography for one publication. [image: imagen.png] There is not any code in the tool square and that is why I guess to no be able to measure the particle. Other tool I tried to use is the scale bar, however the value of it is not according to my calibration. [image: imagen.png] How may I change that calibration? In our research group we want the publish the articles citing chimera as visualization tool so we would really appreciate your help. Here is attached the file we have worked in chimera. pollo 13.mrc <https://drive.google.com/a/unal.edu.co/file/d/1cAs2g1kP88o8im65xuTbOz11o9pk…> -- *Qco. JOSE ALIRIO MENDOZA MESA* Candidato a Doctor en ciencias Universidad Nacional de Colombia. 3165000 Ext. 14475 *LABORATORIO DE CATALISIS HETEREOGENEA*

2 1

Re: [Chimera-users] code 256
by Greg Couch 30 Aug '19

30 Aug '19

Like I said before in http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-August/016113.html, you need to use the daily build of Chimera. Go the Chimera download web page, http://www.cgl.ucsf.edu/chimera/download.html. Scroll down past the 1.13.1 downloads, and pick the 64-bit Linux daily build version to download. Then install it. When 1.14 comes out, it will not have this problem. -- Greg On 8/29/2019 11:22 PM, Aleksandra Jarmołowicz wrote: > > I am using Ubuntu 19.04. So what can I do to use Chimera with this > version? Before update of the system programme runs well. > > Aleksandra Jarmołowicz > Ph.D. Student > > Department of RNA Structural Genomics > Institute of Bioorganic Chemistry > Polish Academy of Sciences > Z. Noskowskiego str. 12/14 > 61-704 Poznań > Phone: +48 61 852 8503 ext 143 > ajarmolowicz(a)ibch.poznan.pl <mailto:ajarmolowicz@ibch.poznan.pl>

1 0

Buried_area python function
by Kevin Wang 29 Aug '19

29 Aug '19

Hi, I am trying to use the buried_area function below. What are the arguments that I need to pass in? def buried_area(operation, atoms1, atoms2, probeRadius = 1.4, vertexDensity = 2.0): My current code is as follows: #calculate buried area import os import chimera import xlsxwriter from Measure import measure from chimera import * workbook = xlsxwriter.Workbook('contactArea.xlsx') worksheet = workbook.add_worksheet() Path = "/Users/kevinwang/desktop/VEGFR_NO_LIGAND/results/clustering/pdbfit/split" i = 0 filelist = os.listdir(Path) for x in filelist: if x.startswith("trp.pdb."): #if (x == "trp.pdb.00001"): opened = chimera.openModels.open(x, type ="PDB") chimera.update.checkForChanges() try: runCommand('surface :286-596') runCommand('surface :899-1230') y = measure.buried_area() worksheet.write(i,0,x) worksheet.write(i,1,y) except: worksheet.write(i,0,x) worksheet.write(i,1,"ERROR") i = i + 1 print("Processed: " + x) print("Total #: " + str(i)) runCommand('close all') chimera.update.checkForChanges() workbook.close() Best, Kevin

2 1

copy transformation between volumes
by Oleksiy Kovtun 29 Aug '19

29 Aug '19

Dear community, I need your advice on the following problem. I align map #1 to the reference volume using fit command, and then need to confer this transformation to map #2. This could be done by using matrixcopy command. However in this particular case #1 has twice larger voxel size than #2. It is understod, that since transformation matrix describes shifts in non-scaled pixels, I can not use matrixcopy command. Is it correct to scale translations (column 4) in the fit matrix for #1 and apply it to #2 with matrixset command? Thank you and best regards, Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

2 1

Python Script to Find Contact Area Between 2 Proteins
by Kevin Wang 29 Aug '19

29 Aug '19

Hi, I am writing a python script to find the area between 2 proteins using the contact_area python command below. def contact_area(p1, p2, d, color = None, offset = None, slab = None, smooth = False, optimize = True): Is there a specific object for p1 and p2 and if so how do I get it? My current code is as follows: import os import chimera from Measure import contactarea from chimera import * Path = "/Users/kevinwang/desktop/VEGFR_NO_LIGAND/results/clustering/pdbfit/split" filelist = os.listdir(Path) for x in filelist: #if x.startswith("trp.pdb."): if (x == "trp.pdb.00001"): print x opened = chimera.openModels.open(x, type ="PDB") runCommand('surface') y = contactarea.contact_area('0.1', '0.2', 2.5) text_file = open("buriedArea.txt", "w") text_file.write(y) text_file.close() The error message I am getting is as follows: AttributeError: 'str' object has no attribute 'geometry' File "/Applications/Chimera.app/Contents/Resources/share/Measure/contactarea.py", line 8, in contact_area v1, t1 = p1.geometry How should I be passing in my arguments? Best, Kevin

2 3

code 256
by Aleksandra Jarmołowicz 29 Aug '19

29 Aug '19

Dear Sir or Madame, During chimera-1.13.1-linux_x86_64 installation process I have found some difficulties. I have not found any solutions on your website. After running instalation an error appears : ERROR in chimera_final_install: unable to install deskop icon: result code from installer: 256 I would be very greatful for any help. Kind regards, Aleksandra Jarmołowicz -- Aleksandra Jarmołowicz Ph.D. Student Department of RNA Structural Genomics Institute of Bioorganic Chemistry Polish Academy of Sciences Z. Noskowskiego str. 12/14 61-704 Poznań Phone: +48 61 852 8503 ext 143 ajarmolowicz(a)ibch.poznan.pl

2 1

Can multiple marker sets be batch-saved into individual .cmm files?
by Jun Ha Song 28 Aug '19

28 Aug '19

Dear RBVI, I need to save around 340 market sets into individual .cmm files, 1 .cmm for each marker set I have in my Chimera session. I have been looking at UCSF Chimera documentation for some time ( https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/…) and I wanted to ask if multiple marker sets (each with its own unique model ID) can be saved in single batch command line. Is there a possibility of specifying commands like *save* or *write* or *export* with atom specification of all the model that I want to save to make Chimera save all my 340 marker sets as their individual .cmm files? I was hoping that I could simply use something like *save #1-340 individual UseModelIDasFilename format .cmm directory E:\LBNL\Individual_Models* to make it happen, but all the commands that I thought of as potential candidate for batch-save command doesn't mention whether it can work with volume tracer's "Save current marker set as...". or, if I can use Volume Tracer's "Save current marker set as..." using a script, I could handle this by making myself very simple macro, but I don't know whether volume tracer's codes would allow some quick script to substitute its "Save current marker set as..." function. So, in summary, I wanted to know if... Q1 : Is there a command in UCSF Chimera that allows batch saving multiple market sets as individual .cmm files? Q2 : Can Volume Tracer's "Save current marker set as..." function be used by using some kind of script? Sincerely, Junha Song.

2 1

Get map contour level with python script or command
by Kyle Morris 28 Aug '19

28 Aug '19

Dear chimera users and dev, Is there a chimera or python command that can report the current contour level of a volume that is in model number #n back to the reply log or equivalent? I want to do this after executing 'volume #n sdLevel 3’ such that I can programmatically retrieve the contour level associated with a particular sigma level of a currently loaded volume. Apologies if in my searching I have missed this on the boards, I think this is a novel question though. Thanks as always for your help. Best wishes, Kyle

3 2

How to read a volume in python script
by Huiya Zhou 28 Aug '19

28 Aug '19

Hello, I am trying to use UCSF Chimera to analysis cry-EM density maps. I would like to read a density map (for example: a .mrc file) in python script and get the array (or a three dimensional matrix) of all voxels of this density map. How could I realize this? By the way, I tried to learn some basic chimera functions which can be used in python on this website: https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html> However, it seems this website can’t be opened and it shows me a blank page. Best, Huiya

3 2

Chimera Error
by Ryan Harlich 27 Aug '19

27 Aug '19

Hi Chimera, I am having trouble opening a pdb file. I get the following error: ValueError: can’t normalize zero length array File \Chimera1.13.1\share\chimera\tkgui.py, line 3030, In showLabelBalloon Objs = self.viewer.pick(event.x, event.y) All other PDBs are opening so I am not sure why this one won’t open. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

2 1

Subtracting the difference in EM volumes
by Y. Mutum 27 Aug '19

27 Aug '19

Hi Is there a way to subtract the non-overlapping bits and retain only the overlapping volumes between 2 EM density maps in Chimera? I have tried the vop subtract command, but it only seems to subtract the overlapping bits and not the inverse of it (non-overlapping bits)? Sorry, if I have missed it. Thanks Yilog

2 1

Divided the Volume Data into two parts
by Huiya Zhou 23 Aug '19

23 Aug '19

Hello, I would like to divided a density map (volume data) into two parts. For example, the size of the whole density map is 320*320*320. I want to get one part which covers the region from (i,j,k) to (x,y,z), e.g. from (0,0,0) to (100,100,100). The rest is the other part. The transparency for the first part is 0 and for the second part is 0.5. And I still want to get the histogram of the first part. How could I achieve this in a python script? Actually, I want to get the histogram of different regions. I plan to run a loop for different regions (Change the (i,i,k) and (x,y,z) for the first part). Could I save all of the histograms in one file which is not a window of the Chimera but a picture. Best, Huiya

2 1

Selecting bonds/pseudobonds with a cutt-off distance
by Yasser Almeida Hernández 23 Aug '19

23 Aug '19

Hi all, how can I select bonds/pseudobonds with a cutt-off distance, say bonds/pseudobonds with more than/less than X? Thanks in advance, Yasser

2 2

回复： scipy problem
by William 22 Aug '19

22 Aug '19

Dear Eric, I have tried the instructions following the FAQ, but there is another problem. The scipy installed successfully. However, it installed a higher version of the numpy when installing scipy. And the older version of numpy is still in. The chimera can not work. Anyway, thanks a lot. ------------------ 原始邮件 ------------------ 发件人: "Eric Pettersen"<pett(a)cgl.ucsf.edu>; 发送时间: 2019年8月20日(星期二) 凌晨1:46 收件人: "William"<3121437640(a)qq.com>; 抄送: "chimera-users"<chimera-users(a)cgl.ucsf.edu>; 主题: Re: [Chimera-users] scipy problem Hi William, I don’t know why Jaime’s instructions don’t work. Maybe he can follow up. Regardless, we have our own instructions for installing pip (and pip-able packages like scipy). It’s in the Chimera Programming FAQ. Question 3b. If those instructions don’t work, please let us know. —Eric Eric Pettersen UCSF Computer Graphics Lab

2 1

How to read a volume in python script
by Huiya Zhou 22 Aug '19

22 Aug '19

Hello, I am trying to use UCSF Chimera to analysis cry-EM density maps. I would like to read a density map (for example: a .mrc file) in python script and get the array (or a three dimensional matrix) of all voxels of this density map. How could I realize this? By the way, I tried to learn some basic chimera functions which can be used in python on this website: https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html> However, it seems this website can’t be opened and it shows me a blank page. Best, Huiya

2 1

copy/combine molecular models
by Rui Chen 22 Aug '19

22 Aug '19

Hello, I am working on a homodimer. I modelled loops of each chain one by one. I chose the best loops for each chain. Now I want to save them as a pub file. Please see the following screenshot. How to decide the new model's ID? I know the coordinate system is the reference coordinate, how do I decide which chain to use as the reference chain? Should I choose rename them uniquely? Looking forward to hearing from you. Thank you. [image: Screen Shot 2019-08-22 at 12.01.28 AM.png] Best regards, Rui

2 2

how to guess ligand's net charge?
by Thomas Evangelidis 21 Aug '19

21 Aug '19

Greetings, How does Chimera guess the net charge of a ligand when prompted to select the charge type (AM1-bcc or Gasteiger)? I am doing high throughput protein-ligand MD simulations and would like to know which open source library Chimera uses for this task. Thanks in advance. Thomas -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: tevang3(a)gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/

2 1

color by zone in chimeraX
by Pranav Shah 20 Aug '19

20 Aug '19

Hi Elaine and Co., I am trying to color a virus map with the relevant pdb file, the series of commands I am running are as follows, open virus.mrc open virus.pdb color /A plum target c color /B lightgreen target c color /C dodger blue target c color zone #1 near #2 dist 3 However, the resultant surface is rendered in splotches of red and blue, which leads me to think the it is coloring the surface using atom type. Could you tell me how I can get Chimera X to color the surface using the colors of the chains only? FYI, color by zone works flawlessly in chimera. Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

2 2

scipy problem
by William 19 Aug '19

19 Aug '19

Hello, I tried to install scipy in chimera python following the steps below: When I tried the third step, it raised midaserror. The error is as follows： Is there anything wrong with my path? Thanks.

3 2

Match showmatrix true motion in original coordinates
by Ahmad Khalifa 13 Aug '19

13 Aug '19

Hi, Running match showmatrix true, gives two matrices. What's the difference between the two? I already saved the file after fitting it so it should have only one set of coordinates, its original coordinates?! Regards Motion of #76 in #2 coordinate system Matrix rotation and translation 0.99998889 -0.00169318 0.00440013 -1.57825672 0.00165962 0.99996960 0.00761849 -4.96792547 -0.00441290 -0.00761111 0.99996130 169.74075587 Axis -0.85023004 0.49200930 0.18717833 Axis point 0.00000000 21533.64775327 2718.66675667 Rotation angle (degrees) 0.51315730 Shift along axis 30.66940614 Motion of #76 original coordinates in #2 coordinate system Matrix rotation and translation 0.78916125 0.61416829 0.00467203 -143.02960322 -0.61417583 0.78916918 0.00023085 242.10381668 -0.00354524 -0.00305162 0.99998906 98.04867640 Axis -0.00267220 0.00668954 -0.99997405 Axis point 281.92931592 330.08522286 0.00000000 Rotation angle (degrees) 37.89294229 Shift along axis -96.04436567

2 1

Chimera bug report submission
by Tanara Arenhart 12 Aug '19

12 Aug '19

The following bug report has been submitted: Platform: Windows64 (WGL) Microsoft Windows Unknown 10.0 (Build 17134) x64 Chimera Version: 1.13.1_b41965 Description Hi! I'm trying to dock my protein with a ligand, but everytime appears this message: "receptor and ligand cannot be the same model". I don't know why, because i'm doing the same things I always do. What could be happening? Thank you! Open models #0 3dbs.pdb #1 smiles:CC1CCC2C3(CCC(... #2 AutoDock Vina Search Volume Reply log: Failed to translate SMILES to 3D structure via NCI web service (SMILES: receptor and ligand cannot be the same model) Failed to translate SMILES to 3D structure via Indiana University web service (SMILES: receptor and ligand cannot be the same model) Web services failed to translate SMILES string to 3D structure. Translated SMILES to 3D structure via NCI web service (SMILES: CC1CCC2C3(CCC(C(C3CCC2(C14CC5=C(O4)C(=CC(=O)C5=O)C)C)(C)C)O)C) No incomplete side chains Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: 0 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Assigning partial charges to residue STP (net charge +0) with gasteiger method Running ANTECHAMBER command: C:/Program Files/Chimera 1.13.1/bin/amber16/bin\antechamber -i c:\users\nara_\appdata\local\temp\tmpi9opye\ante.in.mol2 -fi mol2 -o c:\users\nara_\appdata\local\temp\tmpi9opye\ante.out.mol2 -fo mol2 -c gas -nc 0 -j 5 -s 2 -dr n (STP) (STP) Welcome to antechamber 17.3: molecular input file processor. (STP) (STP) Info: Finished reading file (c:\users\nara_\appdata\local\temp\tmpi9opye\ante.in.mol2). (STP) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (STP) (STP) (STP) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (STP) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d "C:/Program Files/Chimera 1.13.1/bin/amber16/dat/antechamber/ATOMTYPE_GAS.DEF" (STP) Charges for residue STP determined Total charge for #0: 0.000 #0, chain A: phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit γ isoform Traceback (most recent call last): File "C:\Program Files\Chimera 1.13.1\share\chimera\preferences\base.py", line 447, in save WindowsError: [Error 32] O arquivo j� est� sendo usado por outro processo Cannot replace previous preferences file: C:\Users\nara_\AppData\Roaming\.chimera\preferences: WindowsError: [Error 32] O arquivo j� est� sendo usado por outro processo File "C:\Program Files\Chimera 1.13.1\share\chimera\preferences\base.py", line 447, in save See reply log for Python traceback. Residues with incomplete side chains: MET 143.A GLU 322.A Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' MET 143.A: phi none, psi -122.2 trans Chi angles for MET 143.A: GLU 322.A: phi -130.9, psi 172.4 trans Chi angles for GLU 322.A: Applying GLU rotamer (chi angles: -62.4 -179.4 -3.8) to GLU 322.A Applying MET rotamer (chi angles: -65.8 -61.8 -69.4) to MET 143.A Terminii for 3dbs.pdb (#0) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: MET 143.A Chain-initial residues that are not actual N terminii: GLU 267.A, CYS 357.A, LEU 460.A, PHE 497.A, HIS 525.A, ARG 544.A, GLU 981.A Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: ALA 253.A, GLU 322.A, CYS 435.A, GLY 489.A, ASN 522.A, ALA 528.A, HIS 967.A, VAL 1091.A 718 hydrogen bonds Adding 'H' to GLU 267.A Adding 'H' to CYS 357.A Adding 'H' to LEU 460.A Adding 'H' to PHE 497.A Adding 'H' to HIS 525.A Adding 'H' to ARG 544.A Adding 'H' to GLU 981.A Removing spurious proton from 'C' of VAL 1091.A Hydrogens added Charge model: AMBER ff14SB Total charge for #0: -8.000 receptor and ligand cannot be the same model receptor and ligand cannot be the same model OpenGL Vendor: Intel OpenGL Renderer: Intel(R) HD Graphics OpenGL Version: 4.4.0 - Build 20.19.15.4835 Manufacturer: Dell Inc. Model: Inspiron 5452 TotalPhysicalMemory: 4203823104 ―――――――――――――――――――― Multisampling: False Shadows: False Shadow texture size: 2048 Silhouettes: False Depth cue: True Subdivision quality: 1.50 Single-layer transparency: True Transparent background: False Shaders supported: True Using shader: True Window size: 1366 663 Camera mode: mono Orthographic projection: False Center of rotation: front center Near/far clipping: False Key light: True Fill light: True Back light: False Ambient light: 0.20 Specular sharpness: 30.00 Specular reflectivity: 1.00 ―――――――――――――――――――― AntialiasLines: native AntialiasPoints: native BlendEquation: native BlendFuncSeparate: native BrokenAttribLocation: native, disabled ChoosePixelFormat: extension ColorTable: not supported CompileAndExecute: native CompiledVertexArray: extension CubeMap: native CullVertex: not supported DrawElementsInstanced: native, disabled DrawRangeElements: native FBConfig: not supported FBOShadows: native FastMultisampling: native, disabled FramebufferMultisample: native FramebufferObject: native LimitVertexAttribDivisor: native, disabled Multisample: native Multitexture: native PackedDepthStencil: native PalettedTexture: not supported PointParameters: native SeamlessCubeMap: native SeparateSpecularColor: native Shading: native Shadows: native StereoMultisample: native StereoRubberBanding: native Texture3D: native TextureColorTable: not supported TextureEdgeClamp: native TrustColorLogicBlend: native TrustNormals: native VertexArray: native VertexAttrib: native VertexAttribDivisor: native VertexBufferObject: native, disabled WindowPos: not supported

2 1

A question about the Volume Viewer
by Grosman, Claudio F 09 Aug '19

09 Aug '19

Hello everyone, I have (what I think is) a very simple question: what is the particular value of "level" (that is, the threshold) that appears automatically when one opens a 3D density map? After playing around with the threshold, I always feel like the initial value is the best one, but I wonder what exactly this value is. In the online documentation of Chimera, this issue is addressed. The text reads that the initial value of this threshold is such that 1% of the voxels have density values above it. Is this really the case? Only voxels with intensities above the threshold are displayed. Am I seeing only 1% of the voxels, then? I am afraid, I am confused. Thank you very much, in advance. Claudio

2 2

Selecting one ID 0 when two ID 0s are present
by Ryan Harlich 09 Aug '19

09 Aug '19

Hi Chimera, I have a problem where there are two ID 0. One is the normal density map the other is a solid (or what seems to be a movie of the protein). I want to select the density map. In the GUI interface I would open volume viewer and select radio button surface for category Style. Then a little below select All instead of One. I was wondering how to do this with command line? What I am trying to do is get a chain of the pdb structure and zone the density map. However the files are really big so I am trying to do it via ssh on another computer so I will be doing it with the –nogui flag. So if I can do everything via command line that would be great. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

2 5

Double chain IDs
by Albert WEIXLBAUMER 08 Aug '19

08 Aug '19

Dear Chimera developers, My apologies if this question has been asked before but I was not able to find an answer so far. I am dealing with PDB files that contain too many individual chains and as such need two-character chain IDs. Ideally I do not want to split the PDB-files (to be able and work with single-character chain IDs). In addition, the PDB-file also contains more than 100,000 atoms and thus uses alphanumeric atom numbers. It seems Chimera is not aware of the two-character chain IDs because selecting a certain chain in the GUI shows only single character chain IDs and it leads to the selection of the two distinct chains (e.g. chain AA and chain BA are both treated as chain A). Is there a workaround? I’ve also noticed that saving such a PDB-file in Chimera changes all ATOM records to HETATM - I don’t know if this is related to the double-character chain IDs or alphanumeric atom numbers but this causes problems downstream because it’s very difficult to change this back to ATOM records without also affecting true HETATM entries. Thank you for your help! Best regards, Albert -- Albert Weixlbaumer Centre for Integrative Biology Department of Integrated Structural Biology Institute of Genetics and Molecular and Cellular Biology IGBMC - UMR 7104 - U 1258 1, rue Laurent Fries BP 10142 67404 ILLKIRCH CEDEX FRANCE Phone: +33 3 6948 5103 Email: Albert.Weixlbaumer(a)igbmc.fr<mailto:Albert.Weixlbaumer@igbmc.fr> OpenPGP KeyID: 0x7F644168

2 1