March 2020 - Chimera-users - RBVI Mailing Lists

problems in opening PDB file
by Laura Rotilio 24 Mar '20

24 Mar '20

Goodmorning, I'm writing because I'm trying to open my pdb file but this error came out "Attempt to form loop bond". I tried to have a look at the _init_.py file in the line 1109 and I found this message: molList = pdbio.readPDBfile(file, errOut=errLog) I can't understand this message and I don't know how to eventually modify my pdb file in order to be able to open it. Thanks in advance for helping me, Laura Rotilio -- Laura Rotilio, Ph.D. Student *Structural Biology Lab., Prof. A. Mattevi* Dept. Biology and Biotechnology "L. Spallanzani" University of Pavia Via Ferrata 9, 27100 Pavia Italy Tel. +39-0382-985525/985534 Fax +39-0382-528496 Web www.unipv.it/biocry

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automating a task
by Dieter Blaas 24 Mar '20

24 Mar '20

Dear Elaine and all, I need to run the following repeatedly on five loaded volumes (x1.mrc, x2.mrc, x3.mrc, x4.mrc, and x5.mrc) each time with a different x: Tools > Volume Data > Surface Color > Color Surface x1.mrc by volume data gradient norm volume file x1.mrc > options set > color The colors and palette settings remain the same for all runs. Is there a way of automating this with a script? I have tried to save the session, change all occurrences of x for the different x but on evoking the modified python script all volumes are shown in the correct arrangement and level but not coloured and I get the Chimera Warning: Could not restore surface color on surface model with id 0.0 because volume used in colouring was not restored Thank you very much, stay healthy! Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Unstructured residues disappear from sequence after save and reopen
by Rob Blakemore 23 Mar '20

23 Mar '20

Hi, I'm encountering a problem wherein unstructured residues are present in the sequence the first time I fetch it from PDB, but are omitted after I save the file locally and reopen it. Has anyone else encountered this and would you happen to know a workaround? Details I'm running Chimera 1.14 (build 42094) on MacOS Mojave V10.14.6 I'm using 6VXX as the PDB file. When I fetch a structure by ID: (PDB mmCIF) and open a sequence (Tools --> Sequence --> Sequence), it shows me a complete sequence containing both residues present in the structure, as well as unresolved/unstructured residues. The unresolved residues are outlined by a red border. However, if I save this session to a file or save the structure to PDB and then reopen it; if I then open the sequence, it only shows me the sequence of residues present in the structure, and omits all of the unresolved / unstructured residues. (All the red outlined residues are now gone) Is there any way to preserve the unstructured residues when saving these files? Thank you, Rob Blakemore robert.blakemore(a)tufts.edu

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mailing list glitch
by Greg Couch 19 Mar '20

19 Mar '20

FYI, if you tried to send email to chimera-users(a)cgl.ucsf.edu in the last 6 hours and it was rejected, try again. It should be fixed now.

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Re: [Chimera-users] [EXT] Re: spheres chimera
by Elaine Meng 19 Mar '20

19 Mar '20

> On Mar 19, 2020, at 8:46 AM, Galotto, Giulia <ggalotto(a)wpi.edu> wrote: > > Elaine, > I tried emailing the address you gave me and it gives me an error, it says that email does not exists. > I am sorry to bother you again, I would be happy to email the right address next time 🙂 > > In the mean time I will write here the problem I was having, feel free to forward it to the chimera address: > > I clip the protein I am trying to visualize and I can actually see it sliced. > When I write conic in the command line it creates a file not clipped of my protein, it basically recreates the original image unclipped. > I tried from both mac and pc. Do you have any idea why that might be? > > Thank you so much for being so responsive to these emails! This is very helpful. The email address chimera-users(a)cgl.ucsf.edu definitely exists. I cc'd it on this message and on the previous message. It may say that you have to wait for the moderator to approve your message, but that usually happens in a day or two. This is the best way to ensure you get an answer. I cannot reproduce this problem. When I clip the protein shown as spheres, for example using the Side View tool, the conic result shows the same clipping except with solid spheres. See attached screenshot. Elaine > > > From: Galotto, Giulia <ggalotto(a)wpi.edu> > Sent: Thursday, March 19, 2020 11:41 AM > To: Chimera <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [EXT] Re: spheres chimera > > Hi all, > I have a question about the conic function. > I clip the protein I am trying to visualize and I can actually see it sliced. > When I write conic in the command line it creates a file not clipped of my protein, it basically recreates the original image unclipped. > I tried from both mac and pc. Do you have any idea why that might be? > > Thank you so much for being so responsive to these emails! This is very helpful. > > Best, > Giulia > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Wednesday, March 18, 2020 6:39 PM > To: Galotto, Giulia <ggalotto(a)wpi.edu> > Cc: Chimera <chimera-users(a)cgl.ucsf.edu> > Subject: [EXT] Re: spheres chimera > > Hi Giulia, > (For next time), please send questions to chimera-users(a)cgl.ucsf.edu instead of me individually. I CC'd that address here. > > There is no option like that for the interactive spheres display, sorry. It is only available for molecular surfaces. > > However, for a non-movable display that is like that, you can try using the "conic" command for rendering to show spheres as solid when they are clipped. You have to first move the structure, then use conic; for example, a Chimera command that works for me on a Mac is: > > conic -o ~/Desktop/myfile.png -s > > ... which will then draw a non-movable image of the current position and create the specified output file. There are other options to this command, see these pages for details: > <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…> > <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Mar 18, 2020, at 3:03 PM, Galotto, Giulia <ggalotto(a)wpi.edu> wrote: > > > > Hi, > > I am writing to ask a question about a chimera representation. I am representing the protein as VDW spheres, but I would like the spheres to be filled, not hollow. This is because I am going to do per model clipping and slice the protein in two. When I slice it I see the empty spheres, and I would like the see them filled instead. > > Is there a way to do this? > > Thank you so much! > > Best, > > Giulia Galotto > > Worcester Polytechnic Institute

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Re: [Chimera-users] spheres chimera
by Elaine Meng 18 Mar '20

18 Mar '20

Hi Giulia, (For next time), please send questions to chimera-users(a)cgl.ucsf.edu instead of me individually. I CC'd that address here. There is no option like that for the interactive spheres display, sorry. It is only available for molecular surfaces. However, for a non-movable display that is like that, you can try using the "conic" command for rendering to show spheres as solid when they are clipped. You have to first move the structure, then use conic; for example, a Chimera command that works for me on a Mac is: conic -o ~/Desktop/myfile.png -s ... which will then draw a non-movable image of the current position and create the specified output file. There are other options to this command, see these pages for details: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/conic.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/conic1.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 18, 2020, at 3:03 PM, Galotto, Giulia <ggalotto(a)wpi.edu> wrote: > > Hi, > I am writing to ask a question about a chimera representation. I am representing the protein as VDW spheres, but I would like the spheres to be filled, not hollow. This is because I am going to do per model clipping and slice the protein in two. When I slice it I see the empty spheres, and I would like the see them filled instead. > Is there a way to do this? > Thank you so much! > Best, > Giulia Galotto > Worcester Polytechnic Institute

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Truncate crystals in Chimera
by Divita Mathur 18 Mar '20

18 Mar '20

Hello I am a novice in molecular modeling. I have created a gold nanoparticle cube using “make copies” in the Unit Cell option. But it is a cube, and usually gold particles are considered “spherical”. How can I “trim” or truncate a crystal generated via a unit cell? Best, Divita Mathur

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Chimera installation and working issue
by MUNMUN BHASIN 18 Mar '20

18 Mar '20

Dear Sir/Madam, I have been using Chimera for quite long time but recently since the new mcOS update to Catalina, there is problem in its installation. For installing the same a message pops up "Chimera can’t be opened because Apple cannot check it for malicious software". After allowing the installation of the same, this same problem arises after the system restart. It starts off with the verification again and the same steps have to be repeated all over again. Please suggest a fix for the aforementioned problem so that the issue of allowing chimera's installation all the time is resolved. Thank you -- Munmun Bhasin Prof. Raghavan Varadarajan's Lab Molecular Biophysics Unit Indian Institute of Science Bangalore- 560012 Karnataka, India

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Re: [Chimera-users] Frame rate drop with viewing panel open
by Tom Goddard 17 Mar '20

17 Mar '20

Hi Dan, If you see reduced rendering speed even after Side View is closed that sounds like a bug. I do not observe that in Chimera 1.14 on macOS Catalina. If you like you can use Help / Report a Bug.... If I understand your description (100 x 300-residue proteins) you have 100 models opened. It is quite possible rendering will not utilize the GPU or CPU fully in that situation with so many models opened because of the design of the Chimera graphics code. For each model it is issuing tens to hundreds of separate OpenGL graphics calls and using several different buffers to hold the data for each model. The overhead of thousands of graphics calls on small data could easily fail to saturate the CPU or GPU. What can happen is the graphics driver gets a heavy CPU load just marshalling all those calls and sending them to the graphics card, and that heavy CPU use many not be assigned to the Chimera application, instead it is operating system kernel time. So your situation of 100 models may be CPU bound but you are not seeing the CPU load because it is the operating system graphics driver. When you open the Side View the number of graphics calls doubles. But when you close it it should return to half the calls and render at the same speed as before you started side view. The Nvidia GTX 780 is from 2013 and the graphics driver support for such old cards may not be too good. Tom > On Mar 17, 2020, at 3:26 PM, Daniel P Farrell <danpf(a)uw.edu> wrote: > > Hi Tom, > > Thanks for your response. > > I have a modest GPU, GTX780. ( i will attach the requested information below) > However, this should be more than enough to handle the workloads I am running with. > > some points I should mention: > 1. For me - the biggest problem is the reduction in FPS persists even after closing the side-view panel, and doesn't go away until a new session is started. This appears to happen on both a desktop, and a lesser, (linux) integrated-graphics laptop. > 2. When monitoring the GPU usage, I see that even though view panel is away, gpu utilization still comes to a rest a 0%, and the framerate is still significantly decreased. > 3. The only way to get my GPU usage above 50% given an intense scenario (large density map, 100x300-residue proteins) is if I turn on the publication 1 preset (easily maxes at 100% usage). > 4. With the default viewing setting, I max out at ~30% usage if I run "turn x -100 1000" and randomly rotate the screen with my cursor. > 5. With the default viewing setting and the side-view open, I max out at ~50% usage if I run "turn x -100 1000" and randomly rotate the screen with my cursor. however, the frame display is significantly more choppy > > I think something definitely funky is going on with the side view panel.... > > > OpenGL Vendor: NVIDIA Corporation > OpenGL Renderer: GeForce GTX 780/PCIe/SSE2 > OpenGL Version: 4.6.0 NVIDIA 430.26 > /etc/debian_version: > buster/sid > /etc/os-release: > NAME="Ubuntu" > VERSION="18.10 (Cosmic Cuttlefish)" > ID=ubuntu > ID_LIKE=debian > PRETTY_NAME="Ubuntu 18.10" > VERSION_ID="18.10" > HOME_URL="https://www.ubuntu.com/ <https://www.ubuntu.com/>" > SUPPORT_URL="https://help.ubuntu.com/ <https://help.ubuntu.com/>" > BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/ <https://bugs.launchpad.net/ubuntu/>" > PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy <https://www.ubuntu.com/legal/terms-and-policies/privacy-policy>" > VERSION_CODENAME=cosmic > UBUNTU_CODENAME=cosmic > /etc/lsb-release: > DISTRIB_ID=Ubuntu > DISTRIB_RELEASE=18.10 > DISTRIB_CODENAME=cosmic > DISTRIB_DESCRIPTION="Ubuntu 18.10" > /proc/cpuinfo: > cpu: 8 GenuineIntel Intel(R) Core(TM) i7-4770K CPU @ 3.50GHz (x86_64) > cpu MHz: 3595.237 > cache: 8192 KB > /proc/meminfo: > MemTotal: 24632820 kB > Graphics: > 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK110 [GeForce GTX 780] [10de:1004] (rev a1) > Subsystem: eVga.com. Corp. GK110B [GeForce GTX 780 SC w/ ACX Cooler] [3842:0784] > Kernel driver in use: nvidia > > ―――――――――――――――――――― > Multisampling: False > Shadows: False > > On Tue, Mar 17, 2020 at 12:40 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Daniel, > > Rendering the Side View takes about the same amount of GPU processing as rendering the main window, so when you show the Side View you are using twice as much GPU and it will slow down if you have enough models open so your GPU can only render 60 times a second then adding the Side View will drop it to 30 frames per second. But the 60 frames per second you see is because Chimera targets 60 since that what typical desktop displays refresh at. Maybe you have large molecules or slow graphics, or don't have a good graphics driver installed. On a 2019 MacBook Pro with Radeon Vega 20 graphics and Chimera 1.14 the 60000 atom PDB 1aon with initial ribbon display rotates at 60 frames per second but if I show Side View rotation drops to about 40 frames per second. With a nice graphics card like an Nvidia RTX 2070 I expect it would easily maintain 60 frames per second with hundreds of thousands of atoms. > > To see what graphics driver Chimera is using use Help / Report a Bug. > > Tom > > > > On Mar 16, 2020, at 7:40 PM, Daniel P Farrell <danpf(a)uw.edu <mailto:danpf@uw.edu>> wrote: > > > > Hello, > > > > I've been using chimera for a long time now, and I always thought there was some sort of memory leak because it was so slow after 30+ minutes of usage. > > > > Today I started a new session and somehow discovered it wasn't a memory leak, but the viewing panel! > > > > This is on Ubuntu 18.10 > > > > I'm 'guessing' it's the side view sapping some computational power? but my CPUs aren't maxed out, and my GPU is also showing low usage so it must be some strange bug. > > > > Here i load the benchmark window and set it to continuously measure frame rate: > > >>> happily twirling large structure + lots of molecules > > Frame rate: 61.6 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 59.9 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 59.9 > > Frame rate: 60.0 > > Frame rate: 59.8 > > >>> open viewing panel by clicking 'side view' icon on sidebar + continue twirling > > Frame rate: 29.6 > > Frame rate: 27.1 > > Frame rate: 11.8 > > Frame rate: 19.4 > > Frame rate: 19.7 > > Frame rate: 19.7 > > Frame rate: 24.0 > > Frame rate: 30.0 > > > > Even though I know ChimeraX is the main focus now, I would love this to get fixed! > > > > ~Dan > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

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Frame rate drop with viewing panel open
by Daniel P Farrell 17 Mar '20

17 Mar '20

Hello, I've been using chimera for a long time now, and I always thought there was some sort of memory leak because it was so slow after 30+ minutes of usage. Today I started a new session and somehow discovered it wasn't a memory leak, but the viewing panel! This is on Ubuntu 18.10 I'm 'guessing' it's the side view sapping some computational power? but my CPUs aren't maxed out, and my GPU is also showing low usage so it must be some strange bug. Here i load the benchmark window and set it to continuously measure frame rate: >>> happily twirling large structure + lots of molecules Frame rate: 61.6 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 59.9 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 59.9 Frame rate: 60.0 Frame rate: 59.8 >>> open viewing panel by clicking 'side view' icon on sidebar + continue twirling Frame rate: 29.6 Frame rate: 27.1 Frame rate: 11.8 Frame rate: 19.4 Frame rate: 19.7 Frame rate: 19.7 Frame rate: 24.0 Frame rate: 30.0 Even though I know ChimeraX is the main focus now, I would love this to get fixed! ~Dan

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Chimera-users March 2020