- Chimera-users - RBVI Mailing Lists

Chimera 1.14 Crashes When Attempting to Use the ViewDock Function
by Michael Bielecki 03 Apr '20

03 Apr '20

Hi, Chimera started to crash when choosing a structure for ViewDock. This started to happen after installing ChemOffice (could it be related?). I will be grateful if you could help me troubleshoot this. System: Windows 10, 64bit, NVIDIA GeForce GTX 1650 Sincerely, Mike

2 1

Problems when using pdb2pqr and APBS calculation
by Chen Yinglu 03 Apr '20

03 Apr '20

Hi all, When running pdb2pqr and APBS in chimera, I got some problems. 1. When running PDB2PQR, it came in the ReplyLog at first with “Model 0 (dimer.pdb) appears to be a protein without secondary structure assignments”. I don’t know what does it mean. Is there anything I should do before running pdb2pqr? 2. I tried to calculate the electrostatic surface of my protein with APBS, but the execution ran for about half an hour and had no stop. So I cite the traceback as below. I want to know why it happened. Is there’s anything wrong in the settings? I didn’t change any parameters in the options. Thanks Yinglu Exception in thread Thread-47: Traceback (most recent call last): File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\threading.py", line 801, in __bootstrap_inner self.run() File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\threading.py", line 754, in run self.__target(*self.__args, **self.__kwargs) File "C:\Program Files (x86)\Chimera 1.13.1rc\share\WebServices\opal_client.py", line 205, in _queryStatusInThread status = self.sudsClient.service.queryStatus(jobID) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 521, in __call__ return client.invoke(args, kwargs) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 581, in invoke result = self.send(soapenv) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 613, in send reply = self.options.transport.send(request) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 66, in send return HttpTransport.send(self, request) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 82, in send fp = self.u2open(u2request) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 132, in u2open return url.open(u2request, timeout=tm) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 429, in open response = self._open(req, data) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 447, in _open '_open', req) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 407, in _call_chain result = func(*args) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 1228, in http_open return self.do_open(httplib.HTTPConnection, req) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 1201, in do_open r = h.getresponse(buffering=True) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 1121, in getresponse response.begin() File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 438, in begin version, status, reason = self._read_status() File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 394, in _read_status line = self.fp.readline(_MAXLINE + 1) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) timeout: timed out

2 1

modeling selected protein mutations to a sequence
by Teresa Brito-Robinson 02 Apr '20

02 Apr '20

Hi Chimera users, I am trying chimera for the first time and my question is: - How can I change (substitute) specific amino acids within an uploaded protein sequence to mimic a missense mutation? - Or how can I enter a whole new custom made protein sequence into chimera, so I can probe different variants of a protein sequence. I don't know how to make the file like pdb (protein database) so I can fetch my custom sequence? Thanks! Teresa

3 3

Command History
by Healey, Joseph 02 Apr '20

02 Apr '20

Hi Chimera team, I was wondering if the command history is stored as a (temp?) file somewhere? I presume it must need an on-disk record for the history between startups. Could you let me know where/how to find this on MacOS? It would be useful to do some searching of the file etc. Many thanks, Joe Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1(a)warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738

2 2

morphing
by Francesco Malatesta 30 Mar '20

30 Mar '20

Hello I am trying, for teaching purposes, to morph deoxy hemoglobin 1HBA and oxy hemoglobin 1BBB to show the O2-linked quaternary change. I get an obviously wrong morph, attached. Chimera is probably pairing different subunits? Do you think this morph can be done? Thank you Stay safe and well Francesco Francesco Malatesta Professor of Chemistry and Biochemistry FEBS Education Ambassador Department of Biochemical Sciences Sapienza University of Rome Tel: +39 06 49910944 Fax: +39 06 4440062 Cell: 338 6961519 Excellence in Learning and Teaching Biochemistry A FEBS Education Meeting Rome, September 16-17, 2019 www.sites.google.com/uniroma1.it/eltbiochemistry2019 -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system. -- * Emergenza Coronavirus: facciamoci contagiare dalla solidarietà aiutando i nostri ospedali universitari Le donazioni possono essere inviate alla Fondazione Roma Sapienza che devolverà il ricavato al Policlinico Umberto I e Ospedale Sant'Andrea. È possibile donare: – con bonifico bancario (iban: IT72P 01030 03213 000063 259373, bic: PASCITM1R13, beneficiario "Fondazione Roma Sapienza", causale "emergenza coronavirus") – con carta di credito, attraverso il PayPal della Fondazione Sapienza <https://www.fondazionesapienza.uniroma1.it/node/776>

2 1

Keyboard shortcuts for DockView?
by James Wagstaff 30 Mar '20

30 Mar '20

Hi all I am using the DockView extensions to inspect outputs of a virtual screen, and would like to use a keyboard shortcut to (re)assign the state of the currently selected compound. I am not familiar with the inner workings of Chimera so cannot easily see how to do this myself - I am hoping someone else has implemented this! Best James -- James Wagstaff +447910113349

2 4

NMWiz plugin
by George Tzotzos 27 Mar '20

27 Mar '20

Hi everybody, I downloaded the NMWiz Chimera plugin from github: https://github.com/prody/NMWiz-chimera <https://github.com/prody/NMWiz-chimera> From Chimera/Tools/Additional Tools/Add third-party plugin-location, I used the add button to point to the downloaded plugin folder. This doesn’t seem to work. Is there another way to add this plugin? Is it compatible with Chimera 1.14 Thank you in advance for any suggestions

2 1

box face capping
by Giulia Zanetti 27 Mar '20

27 Mar '20

HI all, is there a way to ‘cap high values at box faces’ through the command line? Thanks Giulia

2 1

Re: [Chimera-users] [EXT] Re: Problem with electrostatic surface
by Benedikt Moissl 26 Mar '20

26 Mar '20

Hi Elaine, thank you a lot for your fast response! Your suggestion helped and my problem is solved :-) Best regards Benedikt -----Ursprüngliche Nachricht----- Von: Elaine Meng <meng(a)cgl.ucsf.edu> Gesendet: Dienstag, 24. März 2020 18:27 An: Benedikt Moissl <benedikt.moissl(a)biologie.uni-regensburg.de> Cc: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> Betreff: [EXT] Re: [Chimera-users] Problem with electrostatic surface Hi Benedikt, You still need to show the surface of your molecule, e.g. with command "surface #0 & protein" (or "surface #1 & protein" since they are the same atomic coordinates). After you do that, it will be listed in the menu of choices of what surface to color in the Surface Color dialog. 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 23, 2020, at 11:35 PM, Benedikt Moissl <benedikt.moissl(a)biologie.uni-regensburg.de> wrote: > > Dear Chimera team, > > I am trying to display color the surface of my molecule according with Poisson-Boltzmann electrostatics using Chimera 1.14. I ran the PDB2PQR tool as described in the user guide and obtained a PDB2PQR file. With that, I ran the APBS tool and obtained a .dx file. As described, the Surface Color panel opens automatically, but here I am unable to choose my structure file for "color surface" (s. attachment 1). I can only choose the .dx file, which does not work. All three models obtained during this process are opened in the model panel though (s. attachment 2). > > Do you have any idea on how to fix this? > > Thank you very much in advance and keep up the great work! > Benedikt Moissl

1 0

Re: [Chimera-users] cobalt in Chimera
by Elaine Meng 25 Mar '20

25 Mar '20

On Mar 24, 2020, at 8:02 PM, Ke Shyue-Chu <ke(a)gms.ndhu.edu.tw> wrote: > Hi, Elaine, > I am trying to minimize an edited structure, Tools -> Structure Editing -> Minimize Structure --- using all default parameters, however, the cofactor B12 has a cobalt atom and that gives me an error message “Failure running ANTECHAMBER for residue B12[non-Co]. May I ask how to solve this problem? > Thank you. > Best regards, > Sc ke Hi Sc ke, It is not the cobalt ion causing the problem. That message says that ANTECHAMBER charge calculation failed on the non-Co part of residue B12, which means all the rest of the atoms besides Co, which is handled separately. That residue is large and complex and has a phosphate, all factors that are more likely to cause a failure of the AM1-BCC charge calculation method. You may have to use the simpler charge calculation method "Gasteiger" as specified in the Add Charge dialog. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addchar…> (For next time, to ensure you get an answer please send Chimera questions to chimera-users(a)cgl.ucsf.edu, CC-d here, rather than my individual address.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Problem with electrostatic surface
by Benedikt Moissl 24 Mar '20

24 Mar '20

Dear Chimera team, I am trying to display color the surface of my molecule according with Poisson-Boltzmann electrostatics using Chimera 1.14. I ran the PDB2PQR tool as described in the user guide and obtained a PDB2PQR file. With that, I ran the APBS tool and obtained a .dx file. As described, the Surface Color panel opens automatically, but here I am unable to choose my structure file for "color surface" (s. attachment 1). I can only choose the .dx file, which does not work. All three models obtained during this process are opened in the model panel though (s. attachment 2). Do you have any idea on how to fix this? Thank you very much in advance and keep up the great work! Benedikt Moissl ____________________________________________________________ Institute of Biochemistry, Genetics & Microbiology Department of Microbiology & Archaea Center Grohmann Lab – Single-molecule Biochemistry (Homepage <https://www.uni-regensburg.de/biologie-vorklinische-medizin/mikrobiologie/i…>) University of Regensburg | Universitätsstraße 31 | D-93053 Regensburg | Room: WN_E3._2.323 | Phone: +49 941 943 3184 | Fax: +49 941 943 2403 | Mail: benedikt.moissl(a)ur.de <mailto:benedikt.moissl@ur.de>

2 1

3. Problem with electrostatic surface (Benedikt Moissl)
by Boaz Shaanan 24 Mar '20

24 Mar '20

1 0

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

3 2

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 ------------------------------------------------------------------------

2 2

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

4 4

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.

1 0

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

2 1

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

1 0

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

2 1

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

2 1

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> >

1 0

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

2 1

Changing cryo-em density map x=voxel size in Chimera
by Ouadou, Anes (MU-Student) 16 Mar '20

16 Mar '20

Hello, I am using cryo-em density maps to create a deep learning model that detects C-alpha atoms. the model I trained uses maps with voxel size of 1x1x1 A. Experimental maps come in different voxel sizes. I found that I can change the voxel size using the option "model-spec". However, I looked everywhere in Chimera menu bar but could not find "model-spec". can you please show me where to find it. I am also open to any other suggestion to change voxel size. Regards Anes Ouadou CS PhD Student University of Missouri-Columbia aomqc(a)mail.missouri.edu Mobile: (573 )-289-9073

3 2

question about specific protein display
by Galotto, Giulia 13 Mar '20

13 Mar '20

Hi, I am using Chimera to display a protein domain in my paper. The domain has two mutations in the hydrophobic core: I would like to display the protein domain open in two parts, to show the buried residues exposed. Could you guide me on how to do this? Thank you so much for your help! Best, Giulia Galotto PhD Student Vidali Lab Worcester Polytechnic Institute

2 4

Re: [Chimera-users] Getting the analysis of the side chains that are not in the density map
by Dmitry A. Semchonok 13 Mar '20

13 Mar '20

2 1

Getting the analysis of the side chains that are not in the density map
by Dmitry Semchonok 13 Mar '20

13 Mar '20

Dear colleagues, I have a map with the fitted model inside. Some of the side chains are out for the density map. I want to have a get a file where the side chains that are not in the density map are listed. Does anyone know how to do that? Thank you! Sincerely, Dmitry

2 1

Help please
by Dr Musa Said 11 Mar '20

11 Mar '20

Dear there I am training myself in Chrimera software. The first example shows the ligand is on one side and 1HOM is on another side. Where did I g wrong, please. Please see the attachment. Regards Musa

3 4

Re: [Chimera-users] how to create a sphere in Chimera
by Elaine Meng 11 Mar '20

11 Mar '20

Hi Sc Ke, Chimera doesn't do that projection calculation; you would have to do it yourself. I think you could select all the nitrogens within the sphere and then write out their coordinates, but any other steps after that would require your own processing. You don't even need the sphere (it may just be for display purposes) since you already have an atom at the center of it to define the radius for finding nitrogens. I think you could select the nitrogens, for example, by just selecting the center atom (Ctrl-click on it, you may need to hide the sphere first if it's covering the atom), and then using a command something like: select N & sel za<8.5 ... where instead of 8.5 you would put the radius of the sphere. It means select element N and also within 8.5 angstroms of current selection, which is the center atom you selected first. You can hide the sphere by un-checking its S (Shown) checkbox in the Model Panel (show by choosing Model Panel from the Favorites menu). Then you could get the coordinates of the selected nitrogens, for example with command getcrd sel ... and then look in the Reply Log for the list of coordinates (show by choosing Reply Log from the Favorites menu). 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 10, 2020, at 6:05 PM, Ke Shyue-Chu <ke(a)gms.ndhu.edu.tw> wrote: > > Hi, Elaine, > Thank you for the detailed instruction. I got the sphere. > > May I ask one more question: > How do I define an equator plane of that sphere and project all nitrogen atoms within that sphere onto the equator plane; i.e. the polar coordinates of the nitrogen atoms within a sphere are what I would like to have? > Thank you very much. > sc > > -----Original Message----- > From: Elaine Meng [mailto:meng@cgl.ucsf.edu] > Sent: Thursday, March 05, 2020 12:46 AM > To: Ke Shyue-Chu <ke(a)gms.ndhu.edu.tw> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] how to create a sphere in Chimera > > Hi Sc Ke, > There is more than one way. Say you have already selected the single atom. Then, > > (A) to put a marker (essentially a fake atom) at that position, command “measure center”, for example: > > measure center sel mark true radius 4.0 color pink model #8 transparency 50 #8 > > see manual for command options > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html> > > (B) to put a spherical surface model at that position, command “shape sphere”, for example: > > shape sphere radius 8.5 center sel color orange modelid #8 transparency 60 #8 > > see command options > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#sphere> > > 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 4, 2020, at 2:40 AM, Ke Shyue-Chu <ke(a)gms.ndhu.edu.tw> wrote: >> >> Hi, >> I would like to know how to create a sphere of certain radius around a selected atom, for visualization purpose. >> Thank you. >> Sc Ke >> Professor >> Department of Physics >> National Dong Hua University >> Hualien, Taiwan > > > -- > 此電子郵件已由 AVG 檢查病毒。 > http://www.avg.com > >

2 1

Change default pseudobond color?
by Oliver Clarke 10 Mar '20

10 Mar '20

Hi, Is it possible to change the default pseudobond color? The current default is yellow, which is unreadable on a white background (but fine on a black background). Orange is readable on both black and white backgrounds - would it be possible to change the default color for distances to orange? Cheers Oli

2 2

Numbers(markers) inside/on the map
by Dmitry A. Semchonok 10 Mar '20

10 Mar '20

Dear colleagues, I would like to place the numbers (markers) inside/on our map. Could you please prompt how to do that ? Thank you. Sincerely, Dmitry

2 1

Regarding Structure minimize
by Yash Bahl 08 Mar '20

08 Mar '20

To do structure minmization, what is the adequate values? Steepest descent should be changed to 75 from 100. What else? Should intervals be also changed to 25? Thanks

2 1

visualizing potential with volume data
by Christos Deligkaris 06 Mar '20

06 Mar '20

dear all, I have obtained a cube file from NWChem with the electrostatic potential around a molecule. I visualized the molecular surface using Actions->Surface->Show and then colored it using the volume data (followed instructions https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html in tools->surface color (electrostatic surface coloring)) . Since I do not have my data stored in a potential file, can I still do the surface offset? The chimera tool webpage discusses why that is preferred than showing the potential on the solvent excluded surface and it seems to me that option to not be available with volume data. Also, my surface does not look like the electrostatic potential surface shown here: https://www.cgl.ucsf.edu/chimera/data/tutorials/maps08/volume-basics.html . The molecular surface we get with Action->Surface->Show seems to be constructed with greater atomic radii than the one shown in that image. I am not sure how important that is though. Is there a way to ask Chimera to visualize the electrostatic potential volume data with the same options Chimera would use if it was reading a Delphi, PBS file? Best wishes, Christos Deligkaris, PhD Assistant Professor of Physics

2 5

move labels
by Dieter Blaas 06 Mar '20

06 Mar '20

Hi, I once knew but forgot and spent hours not finding it: How do I select a label by clicking and then move it with the mouse? Thank you very much, bw 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 ------------------------------------------------------------------------

2 8

Choosing Help->Search Documentation causes seg fault
by Hua tiger 05 Mar '20

05 Mar '20

Hello, First of all thank you for your good work and assistance. Core dump trace is attached and a snippet follows. Choosing Help->Search Documentation causes seg fault. The remaining help menu items work fine. Please see below. Thank you so much. John ------------------------------------------------------------------- huatiger@huatiger:debug$ coredumpctl debug PID: 23503 (python2.7) UID: 1000 (huatiger) GID: 1000 (huatiger) Signal: 11 (SEGV) Timestamp: Sat 2020-02-29 14:35:13 EST (1min 8s ago) Command Line: /opt/UCSF/Chimera64-1.14/bin/python2.7 /opt/UCSF/Chimera64-1.14/share/__main__.py --debug Executable: /opt/UCSF/Chimera64-1.14/bin/python2.7 ... Core was generated by `/opt/UCSF/Chimera64-1.14/bin/python2.7 /opt/UCSF/Chimera64-1.14/share/__main__.'. Program terminated with signal SIGSEGV, Segmentation fault. #0 0x00007fe3a31c51f8 in uncompress2 () from /lib/x86_64-linux-gnu/libz.so.1 ---------------------------------------------------------------------------------------- huatiger@huatiger:Downloads$ cat /etc/os-release NAME="Ubuntu" VERSION="19.10 (Eoan Ermine)" ID=ubuntu ID_LIKE=debian PRETTY_NAME="Ubuntu 19.10" VERSION_ID="19.10" HOME_URL="https://www.ubuntu.com/" SUPPORT_URL="https://help.ubuntu.com/" BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/" PRIVACY_POLICY_URL=" https://www.ubuntu.com/legal/terms-and-policies/privacy-policy" VERSION_CODENAME=eoan UBUNTU_CODENAME=eoan huatiger@huatiger:Downloads$ uname -a Linux huatiger 5.3.0-40-generic #32-Ubu

2 1

LINK record not honoured in Chimera?
by Kate Kim 04 Mar '20

04 Mar '20

Hello, I would like to visualize a thioester bond between a CYS residue of my protein and a carbonyl carbon of ligand (DCR) in my model. I have a LINK record for the DCR-CYS thioester bond created from Jligand and inserted in the PDB right before the CRYST1 line. However, when I open this PDB in Chimera, the thioester linkage is not drawn. The distance between the C1 of DCR and SG of CYS is 1.79 angstrom. Does Chimera need something else other than the LINK record in the PDB to display the bond? Thank you, Kate

4 4

desktop hardware
by joe viterbo 04 Mar '20

04 Mar '20

Hi everyone, I am about to purchase a PC desktop computer to run Chimera. Regarding the hardware, should I focus more on CPU speed & cores or should I focus more on a powerful GPU? Or should I try to find both? Thanks for your time! Best, Joe

2 2

how to create a sphere in Chimera
by Ke Shyue-Chu 04 Mar '20

04 Mar '20

Hi, I would like to know how to create a sphere of certain radius around a selected atom, for visualization purpose. Thank you. Sc Ke Professor Department of Physics National Dong Hua University Hualien, Taiwan

2 1

Auto-Stereo 3D
by Engelhardt, Peter 28 Feb '20

28 Feb '20

Dear Chimera developers, We are most interested of always using stereo in Chimera. Lately there have been presented Auto-Stereo 3D displays: https://www.tri-evolution.com/en/auto-stereo-3d/ Auto-Stereo 3D - TRI Evolution – 3D without glasses<https://www.tri-evolution.com/en/auto-stereo-3d/> We unfold digital vision. We unfold your product and video data in “GLASSES-FREE 3D”. We offer numerous services and solutions for perfect handling of the latest auto stereo 3D technology. We are an official Solutions Partner of 3D Global. Find out everything worth knowing about our AS3D offer in this section. AS3D Hardware AS3D Hardware More […] www.tri-evolution.com Because of this convenience in 'no need to use any stereo glasses' we wonder if Chimera is supporting Auto-stereo 3D displays, now or in near future. We thank you in advance Cheers Peter

4 4

Comparison of cryo-em maps
by Dmitry Semchonok 28 Feb '20

28 Feb '20

Dear colleagues, I have similar cryo-em maps that have also some differences. I want to compare them. Is there a tool in chimera that can compare the cryo-em maps? Thank you! Sincerely, Dmitry

2 1

debug
by 陈文心 27 Feb '20

27 Feb '20

When I open chimera, introduction webpages will continuously open and many interfaces pop out. Could you please help me solve the problem? Thanks a lot. 发送自 Windows 10 版邮件应用

2 1

Contour plot of intersurf surface
by Miguel Romero 27 Feb '20

27 Feb '20

Hello, I am looking for a way to generate a contour plot from the interface surface generated with the intersurf command. The idea is to have a 2D representation of the interface. I would really appreciate any suggestion. Thanks in advance, Miguel

2 4

Ctrl-Shift-click iimpaired on MacOS Mojave
by Visvaldas K. 27 Feb '20

27 Feb '20

Dear Chimera Users, recently I noticed a bug (?): I am not able to multiple select atoms using Ctrl-Shift-click easily, as I was able before (I am not sure when the problem started). If I use mouse, sometimes I am able to select two atoms after a while by going back and forth between the two atoms and keep clicking, and after some time I succeed to select, but but the required number of tries is unpredictable. However, with the touchpad, forget it, it does not work at all. Needless to say, I find this to be very annoying. I tried today's Chimera daily build, versions 14 and 13.1 with the same results. I am running MacOS Mojave. Sincerely yours, Visvaldas

2 1

How to change font size for scale bar
by Engelhardt, Peter 27 Feb '20

27 Feb '20

Hi We can’t find any options for font size in scale bar wondering if possible. Any suggestions Cheers Peter Sent from my iPhone

2 2

Unable to Install ChimeraX 1.14 on MacOS 10.15.3
by Shawn Rumrill 26 Feb '20

26 Feb '20

Hello, I recently tried installing ChimeraX 1.14 on my MacBook Pro OS 10.15.3. I receive a message that the software cannot be installed because it cannot be verified and needs to be updated. So you have any solution to this problem? Screenshot of error message attached. Best, Shawn Rumrill srr131(a)cabm.rutgers.edu<mailto:srr131@cabm.rutgers.edu> [cid:F2EDAD80-53DE-442C-B590-72AD2EE15870@ruw.rutgers.edu]

2 1

Biological assembly from the asymmetric unit and using it for MD
by David Sáez 26 Feb '20

26 Feb '20

Hi, very basic question here. I found ways to generate the tetramer biological assembly starting from the monomer asymmetric unit . (Downloading the BA directly from RCSB and alternatively using the BU function in Chimera's Model panel). The procedures are equivalent AFAIU. Now, this generated structure should be a valid starting point for molecular dynamics simulations? Does anybody have experience with that?. There are other structures showing the tetramer, but the resolution is too low. Thanks! David.

2 2

Font size in menu bar
by svle＠tiscali.it 25 Feb '20

25 Feb '20

Hi, there exists a method to increase the font size for the menu bar? Thanks in advance Saverio Con Tiscali Mobile Smart 30 4G hai minuti illimitati, 100 SMS e 30 Giga in 4G a soli 8,99€ al mese. http://tisca.li/smart30

2 1

FW: website broken?
by Cain, Cheryl A 25 Feb '20

25 Feb '20

Hello, Passing on this message to the help desk. Thanks, Cheryl Cheryl Cain Operations Coordinator Department of Pharmaceutical Chemistry UCSF ***Please note that my work hours are Tu-Wed-Th, 9am-4pm*** On 2/24/20, 7:56 AM, "Hoover, David (NIH/CIT) [E]" <hooverdm(a)hpc.nih.gov> wrote: Hi, The homepage for Chimera (https://www.cgl.ucsf.edu/chimera/) appears to be down or blocked. Is everything ok? David -- David Hoover, Ph.D. Computational Biologist High Performance Computing Services, Center for Information Technology, National Institutes of Health 12 South Dr., Rm 2N207 Bethesda, MD 20892, USA TEL: (+1) 301-435-2986 Email: hooverdm(a)hpc.nih.gov

2 1

visualizing formal charges
by Tasneem Vaid 24 Feb '20

24 Feb '20

Hi everyone, I want to see the formal charges on the ligand as well as the receptor. Is there a way to get that in Chimera? There is an option of setting charges under ‘label’, but that gives partial charges and not formal. Thanks, Tasneem

3 2

chimera exiting every time after clicking browse
by Dominique Gutierrez 24 Feb '20

24 Feb '20

Hello, I have MacOS Catalina 10.15.3. Chimera is exiting every time after clicking browse. Versions 1.13 and 1.14 are doing this. Best, Dominique

2 5

Color surface by electrostatic potential vs color by value at atom position
by Yu Zhou 21 Feb '20

21 Feb '20

Hi there, I want to color protein surface by electrostatic potential datacalculated using APBS 1.5. I tried two methods in Chimera and got quite differentresults. The resulted images can be found in attachment. In the first attached figure (fig1_ep surface) the surface wascolored by the “Electrostatic Surface Coloring” tool, in the second attachedfigure (fig2_value atom) the surface was colored by the “Values at AtomPositions” tool. Same color palette (red: -35, white: 0, blue: +35) and potential file was used in bothcases. Thanks for your help. Yu Zhou

2 2