- Chimera-users - RBVI Mailing Lists

building modeller loops refinement
by ARMIN HODAEI 06 Apr '17

06 Apr '17

Dear Chimera Users, I want to use refining loop option to build missing residues for my target protein. First I get the FASTA file structure of protein then I load it into Chimera, after that in the Structure tab I select load structure, then I see the protein. After that Again in the "Structure" tab I select Modeller(loops/refinement). The rest is easy for creating the new structure PDB. But the problem is that I want whole protein to be treated in this refinement, but it only chose one chain, How can I do this for both chains at once? Sincrely, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

2 3

(no subject)
by Kavya Shankar 05 Apr '17

05 Apr '17

Hi, I would like to know how the axis of symmetry is calculated in a dimer as in the precise algorithm that is used to do this. Thank you. Regards, Kavya Shankar

2 1

Defining glycosidic bond of nucleotide objects
by Charles-Alexandre Mattelaer 04 Apr '17

04 Apr '17

Dear Chimera-users I'm currently doing modeling on hexitol nucleic acids and using Chimera to visualize the trajectories. Since the atoms in the hexitol-ring are numbered differently than in the standard ribose, Chimera has some difficulties displaying the correct ribbon (backbone) and slab (bases). I've been able to define my own ribbon style using the Ribbon Style Editor and creating a new ribbon style based on the standard 'nuleic acid' trace and replacing the existing backbone atoms with the corresponding atom names for the non-standard hexitol residues. The main problem is setting a slab object to replace the base atoms. The 'nucleotide objects' settings are based on a glycosidic bond on the C1' of ribose. In HNA the glycosidic bonds are found on C2' of hexitol. I believe this is causing the problem. Additionally, I can add that using the 'ladder'-like objects, a gap between the 'steps' and the backbone occurs. (I've tried setting the base as anchor but to no avail.) I was wondering if there would be a way to redefine the anchor atom of the nucleotide objects? (I searched in the manual but haven't found any ways to redefine the anchor itself.) This would greatly improve visibility of larger oligonucleotides and would help me a lot. Kind regards and thank you in advance Charles-Alexandre Mattelaer

3 2

attributes
by John Mercer, Ph.D. 04 Apr '17

04 Apr '17

Hi, If you have a structure file so large that it needs loaded as two separate files, e. g. a ribosome, is it still the case that a designer attribute file for individual subunits across the whole structure would still be handled by the usual single file attribute mechanism or is something else necessary? Does ChimeraX have an attribute mechanism that is the same as Chimera? Best, -John Mercer Duke University

2 2

another question
by Arthur Szabo 04 Apr '17

04 Apr '17

In the menu used to save images there are two boxes, one for the image width and the other for the image height In the part of the menu below I have set the pixel units for the image width to 5000, with the height being automatically set. These are not the default settings. How can I make them the default settings? In the version of Chimera that I recently downloaded the default settings were 1600 and 796, respectively. The default settings of the former chimera download (my computer had been corrupted so downloaded Chimera again). I can't find anywhere in this image saving menu to change the default settings. Thank you Arthur G. Szabo [cid:image001.png@01D2AD56.F614B2B0]

2 1

[summovie]
by Edoardo D'Imprima 04 Apr '17

04 Apr '17

Hi Oli, one quick question: I noticed the interesting question you posted on the Unblur forum regarding the use of summovie. Did actually worked out the “corrected” version by Tim that should allow you to perform dose weighting and saving the aligned movies? Cheers, Edoardo --------------------------------------------------- Edoardo D'Imprima PhD Student Max Planck Institute of Biophysics Structural Biology Department Max-von-Laue Straße 3 60438 Frankfurt am Main Germany Tel: +49 (0) 69 6303 3015

1 0

(no subject)
by Kavya Shankar 03 Apr '17

03 Apr '17

Hi, I learnt that a dimer axis of symmetry is got by using matchmaker and then the rotation is measured from it. I would like to know the algorithm that is used to calculate the axis of symmetry and how exactly it is done if possible. Thank you. Regards, Kavya Shankar

2 2

active questions
by Arthur Szabo 03 Apr '17

03 Apr '17

I am working with a structure that is largely a protein, and there is a short oligonucleotide associated with it. In the tools menu the sequence of the protein is Chain A and the short oligonucleotide is Chain C. I have shown their respective sequences. I also know how to highlight components of each chain etc. However, there is a short dinucleotide with two thymine residues that are also part of the structure. I was able to select these residues and the two thymine residues in the oligonucleotide by using the SELECT menu: residues: dT. So in total four thymine residues are selected and with the ACTIONS menu I can visualize them. Going to Chain C I can hide the two thymine residues on the longer oligo. How can I select the other two thymine residues that make up the short dinucleotide? One of these thymines is covalently bound to a tyrosine residue through a phosphodiester bond. I can visualize the tyrosine monophosphate through Chain A, and one can see it connected to the relevant thymine residue. But I would like to color the two thymine residues. But I cannot select them or at least I do not know how to select them. I am not an expert at using the command line. Likely there is something there. Again your assistance is sincerely appreciated. Arthur G. Szabo

2 2

Stereo
by Arthur Szabo 03 Apr '17

03 Apr '17

Is it possible to create a stereo view image from a single pdf image. I have colored different segments of the original pdf image. Thanks A G Szabo agszabo(a)outlook.com<mailto:agszabo@outlook.com>

2 3

Residue information failed
by Kunrong Mei 03 Apr '17

03 Apr '17

Hi all, I have met a problem as I used the mouse pointer to show the residue information. Normally, Chimera automatically displays the residue information (residue name, model ID, chain ID, and residue number...) by default when the mouse pointer is placed at a special position. This is ultra helpful when analyzing structures. My problem is that, after I registered to Chimera today, this function lost and it doesn't show the residue information any more. Has anyone met this kind of problem before? Or does anyone know how to fix it? Thanks, Kunrong

3 2

Re: [Chimera-users] Chimera comparing homodimer with flipped homodimer
by Elaine Meng 03 Apr '17

03 Apr '17

Hi Kavya, The “mm” command used to align the structures and “measure rotation” used to report the resulting rotation are fully described in the documentation, see <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> Regards, Elaine > On Apr 3, 2017, at 8:15 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > Hi Elaine, > > I want to know exactly how the axis of symmetry has been calculated for the dimer. What coordinates are used to perform the alignment of the chains? This will really help me out with my research. > > Thank you. > > Regards, > Kavya Shankar > > On Thu, Mar 30, 2017 at 11:25 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Kavya, > I didn’t have a good example handy yesterday, but here is a more specific example, in commands: > > open 5hvp > open 5hvp > mm #0:.a:.b #1:.b:.a pair ss > show :241.b > measure rotation #0 #1 > > This opens PDB 5HVP twice, matches it to itself except pairing A in one with B in the other and vice versa, shows only residue 241 in chain B so that you can see pairing is A-B, and measures axis of rotation between the two copies of 5HVP. The measurement is also reported in the Reply Log (open from Favorites menu): > > Position of 5hvp (#1) relative to 5hvp (#0) coordinates: > Matrix rotation and translation > -0.32555997 0.82635225 -0.45951350 0.78339640 > 0.82635225 0.01248149 -0.56301524 15.06413576 > -0.45951350 -0.56301524 -0.68692152 28.23994571 > Axis 0.58070648 0.71150597 -0.39565040 > Axis point -5.75571422 -0.00000000 18.30836454 > Rotation angle (degrees) 180.00000000 > Shift along axis 0.00000000 > > I also attach an image below. > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > <flip-axis.png> > >> On Mar 29, 2017, at 10:10 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Kavya, >> I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with “measure rotation.” >> Elaine >> >>> On Mar 29, 2017, at 10:05 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: >>> >>> Hi, >>> >>> To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged. >>> >>> Thank you. >>> >>> Regards, >>> Kavya Shankar >>> >>> On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>>> On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: >>>> >>>> Hi, >>>> Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. >>>> Thank you. >>>> Regards, >>>> Kavya Shankar >>> >>> Hi Kavya, >>> Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> >>> >>> After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> >>> >>> I hope this helps, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues >>> >>> >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> > >

1 0

I figured it out
by Arthur Szabo 03 Apr '17

03 Apr '17

Thanks A G Szabo

1 0

question
by Arthur Szabo 03 Apr '17

03 Apr '17

Previously I had stumbled on how to change the shading on ribbon structures. The default has shading, but with the default setting the colors of the ribbons are shaded and this shading changes when one rotates the structure. Kindly remind me how I can alter the shading of the ribbons. Presumably the settings are through the Tools section. Thank you Arthur G. Szabo

1 0

UCSF Chimera installation - library ubuntu 16.04
by Vasileios Kargas 02 Apr '17

02 Apr '17

Dear Chimera developer, I am trying to install UCSF-Chimera and I have an issue with the libXext.so.6 library I 've installed the library package that contains this and I can locate it at: /usr/lib/x86_64-linux-gnu However I get this error: vk335@hunter:~$ ./chimera-1.11.2-linux.bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/home/vk335' inflating: chimera_install_L6RcLz/installer inflating: chimera_install_L6RcLz/chimera.bin Enter install location: ~/UCSF-Chimera-1.11.2 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /home/vk335/UCSF-Chimera-1.11.2' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org) Install desktop menu and icon? yes Traceback (most recent call last): File "/home/vk335/UCSF-Chimera-1.11.2/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/home/vk335/UCSF-Chimera-1.11.2/share/chimeraInit.py", line 603, in init import chimera File "/home/vk335/UCSF-Chimera-1.11.2/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: libXext.so.6: wrong ELF class: ELFCLASS64 ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_L6RcLz' Installation is done; press return. If I install it in the default Chimera directory without desktop icon it proceeds to the installation but I can not run chimera - taking the same error: ImportError: libXext.so.6: cannot open shared object file: No such file or directory Any suggestions how to solve it? Should this be linked to somewhere else in order the Chimera to find it? Thank you very much in advance. Best regards, Vas

2 1

Residue information failed
by Kunrong Mei 31 Mar '17

31 Mar '17

Hi all, I have met a problem as I used the mouse pointer to show the residue information. Normally, Chimera automatically displays the residue information (residue name, model ID, chain ID, and residue number...) by default when the mouse pointer is placed at a special position. This is ultra helpful when analyzing structures. My problem is that, after I registered to Chimera today, this function lost and it doesn't show the residue information any more. Has anyone met this kind of problem before? Or does anyone know how to fix it? Thanks, Kunrong

1 0

Add secondary structure or symbols to headers of multalign viewer (sequence）
by 陈柳青 31 Mar '17

31 Mar '17

Dear all ! Is it possible to add secondary structure or symbols to multalign viewer headers? I know can use "alignment header definition files" do this , but i don't know how to make the definition files, anyone can give me these files or tell me how to do it? thanks! Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

2 1

Re: [Chimera-users] Chimera comparing homodimer with flipped homodimer
by Elaine Meng 31 Mar '17

31 Mar '17

Hi Kavya, Your “mm” command matched A to A and B to B, so there was no rotation between the two copies. It was hard to see if you entered exactly the same “mm” command as in my example (needs to be exactly the same, with colon : dot . and no extra spaces), but it you did, maybe you are using an old version of Chimera that interpreted the command differently. I only started Chimera and entered those 5 exact commands to get the result I showed. Tested in Chimera version 1.11.2 and recent 1.12 daily build. Elaine > On Mar 31, 2017, at 6:55 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > I have attached the screenshots. I have opened the same pdb file. > > Thank you. > > Regards, > Kavya Shankar > > On Fri, Mar 31, 2017 at 9:37 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > Thank you so much. When I do this I get a rotation angle of 0 degrees. Am I doing something wrong? > > Thank you. > > Regards, > Kavya Shankar > > On Thu, Mar 30, 2017 at 11:25 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Kavya, > I didn’t have a good example handy yesterday, but here is a more specific example, in commands: > > open 5hvp > open 5hvp > mm #0:.a:.b #1:.b:.a pair ss > show :241.b > measure rotation #0 #1 > > This opens PDB 5HVP twice, matches it to itself except pairing A in one with B in the other and vice versa, shows only residue 241 in chain B so that you can see pairing is A-B, and measures axis of rotation between the two copies of 5HVP. The measurement is also reported in the Reply Log (open from Favorites menu): > > Position of 5hvp (#1) relative to 5hvp (#0) coordinates: > Matrix rotation and translation > -0.32555997 0.82635225 -0.45951350 0.78339640 > 0.82635225 0.01248149 -0.56301524 15.06413576 > -0.45951350 -0.56301524 -0.68692152 28.23994571 > Axis 0.58070648 0.71150597 -0.39565040 > Axis point -5.75571422 -0.00000000 18.30836454 > Rotation angle (degrees) 180.00000000 > Shift along axis 0.00000000 > > I also attach an image below. > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > <flip-axis.png> > >> On Mar 29, 2017, at 10:10 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Kavya, >> I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with “measure rotation.” >> Elaine >> >>> On Mar 29, 2017, at 10:05 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: >>> >>> Hi, >>> >>> To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged. >>> >>> Thank you. >>> >>> Regards, >>> Kavya Shankar >>> >>> On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>>> On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: >>>> >>>> Hi, >>>> Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. >>>> Thank you. >>>> Regards, >>>> Kavya Shankar >>> >>> Hi Kavya, >>> Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> >>> >>> After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> >>> >>> I hope this helps, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues >>> >>> >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> > > > > <step1.png><step3.png><step4.png><Step2.png>

1 0

Get side-view model? Or, height of clipping planes?
by Abba E Leffler 31 Mar '17

31 Mar '17

Dear All: I'm making a figure showing a ligand bound deeply in a cryptic pocket of a protein. To show it best, I've oriented the complex so that I am looking down directly on to it. Then, I adjust the hither and yon clipping planes to bracket the ligand so you get a cross-section through the protein containing the ligand and binding site. Is there a way to get the heights of the clipping planes, and then draw planes representing them? Better yet, can the image in the side view planning somehow be saved to high resolution with the yellow clipping planes indicated, but perhaps without the red field of view lines? Basically, for the figure I need some way of showing the viewer where the clipping planes are on the protein. This is critical because viewers need to know in a broad sense where the ligand is located. Thank you for your help

2 2

Collaboratory
by Theodor Emil Gescher 30 Mar '17

30 Mar '17

Dear Chimeramasters and mistresses, I'm having some serious difficulty starting a collaboratory session in UCSF Chimera on Mac. I have tried both an outdated version (build 40427) and the latest (build 41367). I can't find any mention within the program of collaboratory, and because of the Mac OS I don't think it's possible to start a hub from outside Chimera. Is there an additional extension that needs to be downloaded and installed seperately? Yours studiously, Theo

2 1

Re: [Chimera-users] [chimera-dev] (no subject)
by Elaine Meng 30 Mar '17

30 Mar '17

Hi Kavya, I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with “measure rotation.” Elaine > On Mar 29, 2017, at 10:05 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > Hi, > > To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged. > > Thank you. > > Regards, > Kavya Shankar > > On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > > > Hi, > > Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. > > Thank you. > > Regards, > > Kavya Shankar > > Hi Kavya, > Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> > > After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

1 1

Scripting commands for existing morph
by Cristina Paulino 29 Mar '17

29 Mar '17

Dear all, I would like to create a movie from an existing morph between two pdb coordinates. I was able to create a movie via the GUI as described in the manual. However I prefer to use scripts as it allows me to control every single step. I would like to be able to define exactly which frames should be shown when. For example, I would like to define in a script that it should wait at endpoint one (first structure) for x number of movie frames. Then interpolate (morph) to the other endpoint (second structure) for x number of movie frames and then wait again for a specified number of movie frames. Or even more complicated rotate the molecule or superimpose something else while it is interpolating/morphing between the pdb coordinates. Can anyone help me out? I couldn't find any good description for this. Many thanks in advance Cristina

2 5

Re: [Chimera-users] [chimera-dev] (no subject)
by Elaine Meng 29 Mar '17

29 Mar '17

> On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank(a)umail.iu.edu> wrote: > > Hi, > Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. > Thank you. > Regards, > Kavya Shankar Hi Kavya, Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> After two models are superimposed, you can get the axis and rotation amount with command “measure rotation” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues

1 0

ChimeraX Alpha release
by Eric Pettersen 28 Mar '17

28 Mar '17

Hi all, We have released an alpha version of ChimeraX. While it still lacks many features, it has enough useful new and fun features that you might want to take it out for a spin even if it doesn’t prove ready to be your day-to-day workhorse yet. Hope you like it! Home page: http://www.cgl.ucsf.edu/chimerax/ <http://www.cgl.ucsf.edu/chimerax/> Download page: http://www.cgl.ucsf.edu/chimerax/download.html <http://www.cgl.ucsf.edu/chimerax/download.html> —Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

来自"高振飞" <16110440015@fudan.edu.cn>的邮件
by 高振飞 28 Mar '17

28 Mar '17

Dear professor: I'm a student from Fudan University, I want use the software -- chimera. But I can't download it, can you send it to me by using E-mail? thank you very much. with my best regards yours sincerely Zhenfei Gao -- Zhenfei Gao(高振飞) Department of Macromolecular Science Fudan University 310 Yuejin Hall 220 Handan Rd. Shanghai, China 200433 M: +86-18516637266 QQ: 7693692

2 1

Create an entire virus from Octant
by Li, Zongli 28 Mar '17

28 Mar '17

Hello, I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map? Thanks, Zongli

3 4

MD analysis outputting to file
by Neha Gandhi 23 Mar '17

23 Mar '17

Dear Chimera support, I want to calculate the centroid of the sugar ring and the distance from the centroid to another atom of amino-acid. I know this can be done using the Structure analysis tools in Chimera. I want to use distance command in the MD ensemble analysis and output it to the analysis to the text file. How can I write output per frame to a text file in Chimera? Your insight is appreciated. -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate

2 1

Ensemble models
by Mohamed Noor 20 Mar '17

20 Mar '17

Hello. I have an ensemble of models from phenix.ensemble_refinement. I notice that Chimera automatically loads the models and displays only a subset of atoms as "atoms/bonds". Can I save this as a preset while changing other settings manually so that I can go back to the automatic preset if I make a mistake somewhere? Secondly, is it possible for Chimera to calculate rmsf of each residue and output the values to a CSV file? I would like to replot them in Excel. Thanks. Mohamed

2 1

Looking at docked data with the receptor shows as surface
by Jonathan Y Wang 20 Mar '17

20 Mar '17

To whom it may concern, Hi! I recently docked a ligand onto a receptor using the AutodockVina tool and when I opened the data the ligand seemed to be placed in the middle of the trimer. I showed the receptor as surface and it seems as if the ligand is too big to fit inside any of the holes surrounding the trimer, but somehow it has placed itself inside. I additionally opened it using PyMol to double check the file, but it also seems too small to fit inside any of the holes. My inquiry is this: Does AutodockVina take into account surface projections when performing docking? Thank you so much for your time, Jonathan Wang

2 3

Getting names of selected atoms and renaming
by Vladyslav Dziuba 18 Mar '17

18 Mar '17

Dear Sir or Madam, I have some difficulties with using ORCA and UCSF Chimera together. Let me describe my problem first. I need to freeze some atoms (actually, a lot of atoms) in my calculations (geometry optimization), e.g. make their coordinates constant. To do that I need to specify numbers of atoms from xyz file, which is obtained from pdb-file. The problem is that for every atom in pdb-file OpenBabel generates a new number (for example H27 may become 100th atom in xyz file), so that specifying atoms that must be frozen becomes much more complicated. Given that, I'd like to ask to help me find answer on some questions: 1. How can I rename atoms? It would greatly help me identificate atoms that must be frozen. Can I rename only all selected atoms? 2.Can I modify names of selected atoms? 3. How can I get list of numbers of selected atoms? For instance I've chosen some aminoacids residues and I want to get names or numbers of all atoms chosen. Because if I one wants to get a list of atoms in xyz file, he needs names or numbers of atoms in pdb file, but the last ones are disordered. Manual atom picking and comparison in pdb- and xyz-files is very time-consuming. UCSF Chimera is a truly powerful program so I believe there must exist an elegant solution to my problem. Hope to receive a letter from you soon. Thanks in advance! Best regards, Vladislav Dziuba

3 4

Re: [Chimera-users] Smoothing and binning volume data
by Tom Goddard 16 Mar '17

16 Mar '17

Set "step 1” above the histogram in the Volume Viewer window to display the full resolution of the data. If step is 2 that means only every other density map grid point is shown along each axis. The step gets set automatically to values greater than 1 when the map is large to avoid slowing down the graphics (rotating, zooming…). The initial step it chooses is controlled by the volume viewer menu Features / Data Display Options… , “Adjust step to show at most [N] Mvoxels”. Tom > On Mar 16, 2017, at 11:41 AM, Andrea Fera <andrea.fera(a)gmail.com> wrote: > > Hi Tom! > > Tank you for your information. > Let me try to explain better what I asked. > > What I seem to have revised is that the virtual sections of my maps have a much higher resolution than the rendered images by Chimera. > This should be because, evidently, I didn't understand yet how to control the default smoothing and/or binning in the volume viewer, of which I used until now the default value. > Can you tell me how to do, or what to vary? > > Thank you for the tip about using two colors in the rendering. Going to try immediately. > Thanks, > Andrea > > > > > > > > > > -- > Andrea Fera, PhD – [Senior Research Scientist] > Advanced Molecular Imaging ; DUNS 824-XXX-XXX > Unit for Cytoskeletal Dynamics , NICHD, National Institute of Health > Email: andrea.fera(a)gmail.com <mailto:andrea.fera@gmail.com> > > > On 16 March 2017 at 14:28, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Not sure what you are asking. You can do Gaussian filtering to smooth a map, or binning to average 2x2x2 voxels together producing a smaller smoother map using the Volume Filter tool. > > To color “solid” style map rendering different colors at different data values click the nodes on the yellow line on the volume viewer histogram and then click the color button below the histogram to change the colors. > > Tom > > >> On Mar 15, 2017, at 7:49 PM, Andrea Fera wrote: >> >> Dear Tom, >> >> How are you? >> I am using Chimera more and more recently, and I have come to the point where I need to be able to control the amount of smoothing and/or binning that it inserts passing from the virtual sections to the rendering. >> >> Could you please send me some information on where I could look for this information? >> >> Another, related, thing. Is there a way that I can color in red or brighter color the part of the rendering including voxels below (or above) a certain threshold value? >> >> I hope that I am not asking anything too strange. >> Especially the first thing would help me greatly. >> >> Thank you, >> Andrea >> >> -- >> Andrea Fera, PhD – [Senior Research Scientist] >> Advanced Molecular Imaging ; DUNS 824-XXX-XXX >> Unit for Cytoskeletal Dynamics , NICHD, National Institute of Health

1 0

Smoothing and binning volume data
by Tom Goddard 16 Mar '17

16 Mar '17

Not sure what you are asking. You can do Gaussian filtering to smooth a map, or binning to average 2x2x2 voxels together producing a smaller smoother map using the Volume Filter tool. To color “solid” style map rendering different colors at different data values click the nodes on the yellow line on the volume viewer histogram and then click the color button below the histogram to change the colors. Tom > On Mar 15, 2017, at 7:49 PM, Andrea Fera wrote: > > Dear Tom, > > How are you? > I am using Chimera more and more recently, and I have come to the point where I need to be able to control the amount of smoothing and/or binning that it inserts passing from the virtual sections to the rendering. > > Could you please send me some information on where I could look for this information? > > Another, related, thing. Is there a way that I can color in red or brighter color the part of the rendering including voxels below (or above) a certain threshold value? > > I hope that I am not asking anything too strange. > Especially the first thing would help me greatly. > > Thank you, > Andrea > > -- > Andrea Fera, PhD – [Senior Research Scientist] > Advanced Molecular Imaging ; DUNS 824-XXX-XXX > Unit for Cytoskeletal Dynamics , NICHD, National Institute of Health >

1 0

VPAT (Voluntary Product Accessibility Template)
by Ashdale, Martin 16 Mar '17

16 Mar '17

Good Morning, I am looking into using your product with my AP Biology classes and I need to get approval to download your software. The IT Department would like the VPAT (Voluntary Product Accessibility Template) so that I can submit it for approval. If you have it available could you please send it to me. I appreciate your time and look forward to teaching with your product. Thanks, Martin Ashdale Biology Teacher Harford Technical High School 200 Thomas Run Road Bel Air, MD 21015 (410) 638-3804

2 1

Selecting certain atoms with exception
by Kelvin Lau 14 Mar '17

14 Mar '17

Dear Chimera users, I'm trying to do the following: -select all the atoms of a single residue (trp) -except for one (residue number 285) I am not sure how to use a negation command to leave out only 285. Any ideas? Cheers Kelvin -- Kelvin Lau Structural Plant Biology Laboratory Department of Botany and Plant Biology Science III University of Geneva 30 Quai E. Ansermet 1211 Geneva Switzerland Email: kelvin.lau(a)unige.ch Phone: +41 22 379 3026

3 2

possible Chimera bug - saving bonds in MOL2 format
by Marek Maly 14 Mar '17

14 Mar '17

Hello, it seems that Chimera (1.11.2) has problem to save some bonds in MOL2 format. If you open attached file "source.mol2" , Chimera reads/show perfectly all the bonds including those where is "Ru" atom present, but when you save it in MOL2 format in Chimera (see attached file "Chimera_MOL2.mol2"), then all the "Ru-x" bonds are omitted and naturally if you open this "Chimera MOL2" file in Chimera no "Ru-x" bonds are shown. Interestingly, if the original MOL2 file "source.mol2" is opened in Chimera and then saved in PDB format ("Chimera_PDB.pdb"), all bonds are written and so if this PDB file is opened in Chimera all bonds are visualized. Would be nice if the perfect bond preservation which works in MOL2->PDB case worked also in MOL2->MOL2 case. Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

2 2

chimera 1.11.2 interlaced stereo
by Jean-Marie WURTZ 13 Mar '17

13 Mar '17

Hi, I am a long time user of chimera and had never such a problem. I would like to use the interlaced stereo with a zalman monitor but I get the following error : Unable to turn on stereo viewing (Unable to find hardware stereo support (couldn't choose pixel format Couldn't configure togl widget)). I must say that VMD stereo is working. But I understood also that both programs work differently with regard to steero. My configuration: Dell M4500 precision Windows 10 Quadro FX 1800M driver 342.01 What can I do to get it working? Thanks for your help. Best regards -- Jean-Marie Wurtz Professeur de Bioinformatique Tél : +33 (0)3 69 48 51 04 Fax : +33 (0)3 88 65 32 76 jm.wurtz(a)unistra.fr<mailto:jm.wurtz@unistra.fr> wurtz(a)igbmc.fr<mailto:wurtz@igbmc.fr> IGBMC-CEBGS Département de Biologie et de Génomique Structurales Equipe de Biologie Structurales de Cibles Epigénétiques Parc d'Innovation, 1 rue Laurent Fries BP 10142 F - 67404 ILLKIRCH CEDEX http://archive.igbmc.fr/recherche/Prog_ISB/Eq_JCava/index.html [UniversitÃ© de Strasbourg]<http://www.unistra.fr>

3 2

Re: [Chimera-users] [chimerax-users] animations
by Elaine Meng 12 Mar '17

12 Mar '17

Hi Giorgio, You would still have to use the “export” command that exports one file at a time, but it can be run at every frame by combining it with the “perframe” command. For example, in Chimera the following (should be all one line even though the Mail app may break it up): perframe "export ~/temp/$1.x3d" zero 2; play wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 50; wait 50; ~perframe …where ~/temp is a directory that already exists, will make files 01.x3d …. 50.x3d in that directory. In ChimeraX, there is a “perframe” command and “save” to export X3D, but no “play wiggle” command. <http://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 9, 2017, at 11:44 AM, Giorgio Luciano <giorgio.luciano(a)gmail.com> wrote: > > Thanks for the info and sorry for my late reply. I generally export using x3d what I was thinking about is, how can someone export the single model for an animation ? As an example if I make wiggle a molecule play (wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 200 ) may I export in batch the molecules for the single frame ? > Any help will be greatly appreciated :) >

2 1

Re: [Chimera-users] question on MAV
by Elaine Meng 10 Mar '17

10 Mar '17

> On Mar 10, 2017, at 12:59 AM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Elaine, > I would appreciate it if you could let me know how to make specific residues bold in MAV. Not all of them but only specific residues. > Thank you so much for your help. > Jackie Vitali Hi Jackie, Sorry, MAV (Multalign Viewer) does not have the option to use different fonts for different residues… as you probably saw, the Preferences… Appearance options only change the font of all the residues. To highlight specific residues in MAV, you could draw a box around them to make a region, and then using the Region Browser, change region background color and/or outline color, <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> ...or you could create a custom header to put a symbol above the column. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

replay morph created with vop morph?
by Oliver Clarke 10 Mar '17

10 Mar '17

Hi all, Is there any way to replay a morph created using vop morph? Or to change the representation of the map prior to playing? I have a sequential morph of multiple different conformations (which I can’t make with the morph map GUI tool), but I would like to change the display of the map before creating a movie (which vop morph does not seem to allow). Example command: vop morph #1,2,3,4,5 interpolateColors false constantVolume true Cheers Oli

2 3

Can you delete a residue attribute?
by Mungo Carstairs (Staff) 08 Mar '17

08 Mar '17

Hi, I would like to be able to set and remove residue attributes (using Chimera commands over the REST service). Setting is fine, but removing seems to be limited to changing the value to either an empty string or None. https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html Is there any way to actually remove attributes after they have been set on residues? Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

2 2

running DockPrep and Vina from python
by Lee A.G. 06 Mar '17

06 Mar '17

Hello I have been trying to run DockPrep and Vina from a python script to generate a pdbqt file to be used in subsequent Vina docking studies (with a config file). What I have at present is the following (I have edited DockPrep\_init_.py to make nogui=True ; the receptor has been loaded as model #0, and the ligand as model #1) from DockPrep import prep model=Midas.open('4iaq.pdb') prep(model) modelname='4iaq.mol2' from WriteMol2 import writeMol2 writeMol2(model, modelname) #VinaRun OutFileName='C:/Autodock/5HT/4iaq/Test2/4iaq' rc("vina docking receptor #0 ligand #1 output " + OutFileName + " prep true wait true") The generated 4iaq.receptor.pdb file contains the protein as modified by DockPrep, without the charges etc, and with the original PDB residue numbering. The 4iaq.receptor.pdbqt file contains the unmodified protein with charges etc, and with the original PDB residue numbering. The 4iaq.mol2 file contains the modified protein, with charges etc, but with residue numbering modified to start at 1. What I hoped to produce was a 4iaq.receptor.pdbqt file containing the modified protein with charges etc, and with the original PDB residue numbering, and this is just about the only thing I don't have. Any help would be very gratefully received. Anthony

2 2

Re: [Chimera-users] Moving icosahedron to model
by Tom Goddard 03 Mar '17

03 Mar '17

Hi David, I could not tell from the image if the surface was from a PDB or a density map. If it is from a PDB then the coordinate system is based on the crystal packing. That means the origin could be anywhere and the rotation can be arbitrary. So then getting an icosahedron outline aligned can be a real pain, although sometimes the crystal packing has a virus centered at 0,0,0 and a standard orientation like 2-fold symmetry axes along x,y,z (e.g. 2bbv). In the hard cases there are various tricks. For instance use the shape command to center the icosahedron on the atomic model (e.g. "shape icos radius 200 center #0 mesh true div 1") Tom > On Mar 3, 2017, at 11:12 AM, David Bhella wrote: > > Hi Tom > I think Kok Lian's structure is a surface from a PDB file created using multiscale models. I feel the origin and symmetry should be available from the PDB file in some way, but I too have struggled with getting icosahedral structures from PDB into a sensible orientation. > > Sent from my iPhone > >> On 3 Mar 2017, at 18:38, Tom Goddard wrote: >> >> Is your virus surface from a density map? If so it probably has the origin set in such a way that the center of the virus is not 0,0,0 while the center of your icosahedron outline is 0,0,0. To remedy that you would change the origin of the map in Volume Viewer, menu Features / Coordinates set origin index to for example 128 if the map size is 256 grid points. That is likely to put the map origin at the center of the virus particle. >> >> Tom >> >>> On Mar 3, 2017, at 1:18 AM, KL Ho wrote: >>> >>> Dear All, >>> I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you. >>> >>> Best wishes, >>> KokLian >>> <image1.png>_______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

1 0

Moving icosahedron to model
by KL Ho 03 Mar '17

03 Mar '17

Dear All, I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you. Best wishes, KokLian

3 2

move icosahedron surface to a model
by Ho Kok Lian 03 Mar '17

03 Mar '17

Hi All, I am a beginner of chimera. Sorry for the simple question. May I know how to move the icosahedron surface (see attached figure) to the model according to its symmetry? Many thanks. Kok-Lian

1 0

Segmentation fault when issuing chimera command
by Hui Shi 01 Mar '17

01 Mar '17

Hi there, Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here. I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed. But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version. I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work. Any suggestions on how to deal with problem? Thanks a lot in advance! Hui

3 8

Re: [Chimera-users] Error opening larger proteins
by Eric Pettersen 01 Mar '17

01 Mar '17

Hi Catherine, It turns out that the singular value decomposition function that Chimera uses to get the eigenvectors and eigenvalues for the plane computation uses a lot of memory if you use a large number of atoms to define the plane (or axis for that matter). There is a non-default setting for that svd function that I just discovered that uses much less memory and seems to produce identical results, so I have switched Chimera to using that setting. The switched version will be available as the next daily build. Look for daily builds dated March 1 or newer. Also, you may be able to get your current version to work if you simply use less atoms to compute the plane. The selection you were using — “sel :.A,.B,.C,.D” — will not only select all the protein but also all the waters, ligands, and ions. Perhaps just “sel protein” would be more appropriate (depending on what you want the plane for) and might work in your current build. —Eric Eric Pettersen UCSF Computer Graphics Lab > On Mar 1, 2017, at 9:09 AM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > Hello, > > When I try to open large protein in Chimera, and try to define plane for the protein, It is throwing me an error saying "Memory Error". Can you please help me with this error? > > Note: Attached a snapshot of the error. > > Thanks, > Catherine > <Screenshot.png>

1 0

MMTK/Chimera interface error
by ADIL AHIRI 27 Feb '17

27 Feb '17

hi everyone, I work on the modeling of the effect of phosphorylation on segment peptide. I had a problem when i use this interface MMTK/Chimera interface because when i use a doubly phosphorylated peptide i have this message: KeyError: 'No parameters for bond Atom 0.ARG_12__0_0_1_286__B.peptide.C (atom type C) - Atom 0.TPO_13__0_0_1_287__B.N (atom type n)' You will find attached a sample problem source file. Is there anyone who can help me solve this problem please. Codially

2 1

coloring a surface based on proximity to a point
by Hamish Todd 27 Feb '17

27 Feb '17

Hey everyone. So I have a coloration for a set of surfaces that is very close to what I want. I want to make a change to it though: I want parts of the surfaces close to certain points to change their color. And I want the rest of the surface to be unchanged from the current coloring. Is this possible? Would be much obliged if any advice could be offered! Hamish Todd -- @hamish_todd

2 1

starting pre-existing morph
by Elena Zehr 27 Feb '17

27 Feb '17

Hi, I have a chimera session with a morph between two structures. I wish to start playing the morph from the command line. What would be the argument for this? Many thanks, Elena

2 1

FW: Commercial Chimera
by Williams, Joanne 27 Feb '17

27 Feb '17

On 2/26/17, 10:29 PM, "Agnieszka Dobinska" <adobinska(a)okinawa-pt.com> wrote: >Dear Sir/Ma'am, > >I have a questions regarding commercial use of Chimera. > >Provided that we are commercial users of Chimera (subject to commercial >agreement), and we are creating files using Chimera, does our customers >need to >have the commercial Chimera to browse the files we have sent them, or >they can >use the free one. > >Best regards, >Agnieszka Dobinska > >~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~ >Agnieszka Dobinska >Sales & Marketing Manager >Okinawa Protein Tomography Ltd. >1919-1 Tancha, Onna Village, Kunigami, >Okinawa Prefecture 904-0411 Japan >Tel. +81-98-982-3359 　FAX +81-98-982-3361 >Skype: okpt.sales >http://www.okinawa-pt.com >~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~ > > >

2 1

models disappear after using "split"
by Leschziner, Andres 24 Feb '17

24 Feb '17

Hi, I used “split” to break a model into its 19 component chains. The chains appear in the Model Panel and are marked as “Shown" but are gone from the display. Everything else I have in the session works normally but nothing I have tried so far makes the split models show up. Any help solving this would be much appreciated! -Andres ______________________________________ Andres Leschziner Professor Department of Cellular and Molecular Medicine and Section of Molecular Biology, Division of Biological Sciences University of California, San Diego Leichtag 483 9500 Gilman Dr. La Jolla, CA 92093-0694 aleschziner(a)ucsd.edu<mailto:aleschziner@ucsd.edu> 858-246-1252 ______________________________________

2 1