- Chimera-users - RBVI Mailing Lists

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

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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 >> > >

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I figured it out
by Arthur Szabo 03 Apr '17

03 Apr '17

Thanks A G Szabo

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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

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UCSF Chimera installation - library ubuntu 16.04
by Vasileios Kargas 01 Apr '17

01 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

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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

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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

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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>

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Get side-view model? Or, height of clipping planes?
by Abba E Leffler 30 Mar '17

30 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

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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

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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

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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

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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

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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

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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

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Create an entire virus from Octant
by Li, Zongli 27 Mar '17

27 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

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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

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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

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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

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

17 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

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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

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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 >

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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

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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

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possible Chimera bug - saving bonds in MOL2 format
by Marek Maly 13 Mar '17

13 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/

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