- Chimera-users - RBVI Mailing Lists

vop subtract map minRMS
by Roberto Marabini 16 Apr '20

16 Apr '20

Hi, I have two questions regarding the command "vop subtract" with the option "minRMS". 1st question) In the help page the option minRMS is defined as: "the min RMS option can be used to scale othermap automatically to minimize the root-mean-square sum of the resulting (subtracted) values at grid points within the lowest contour of othermap." Does this mean that the value that appears in the "Volume viewer" window and labeled as "Level" is used to create a contour and all the grid pints inside this counter are used to compute the scale factor? 2nd question) If I understand the command, minRMS assume that the maps (let us called them V1 and V2) are related by a multiplicative factor. That is V1 = V2 * f where f is a scalar In my case V1 = V2 * f1 + f2 that is, both maps are related by a multiplicative factor (f1) plus and additive factor (f2). Is there any chimera command that compute the average of a volume so I can force both volume to have the same average? Thanks in advance. Roberto

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Enquiry regarding electrostatics calculations of outersurface
by Jian Chen 16 Apr '20

16 Apr '20

Dear all Chimera users, Chimera has capability to color molecular surface by electrostatic potential using data calculated by apbs module, and the values could be exported into txt files using the surfval.py script. However, there are too many electrostatic potential values exported, and the number of values seems exceed that of atoms. My question is, how to define a surface point whose electrostatic potential value whoud be calculated? I want to obatain the values of outersurface, how to screen out the values of outersurface of protein from them? I would greatly appreciate your help. Best Regards, Jian Chen

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Help with symmetry of fusion protein
by Hasan khan 15 Apr '20

15 Apr '20

Hi there I was hoping I could get some help with a modelling challenge that I am having as I am very new to protein modelling as a whole and Chimera. So I developed a fusion protein of a single monomer of an encapsulin structure (PDB:3DKT), I wanted to build the final icosahedral structure with the added fusion protein. So I tried to align 10 of the fusion monomers to the di-pentamer of the original PDB file and ran the sym command generating the native structure with the added fusion protein. I am unable to save this symmetry structure and I'm not sure if its due to the alignment of the 10 monomers onto the di-pentamer that I did first and then ran the sym command using coordinates of the original PDB or if Chimera is not able to produce coordinates for the structure in a new PDB. When I export it as a PDB the coordinates are not saved. So I was wondering if there is a way I could save this newly generated structure as other methods are not currently working. Thank you Kind regards HK

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remove of the list
by Jose Alirio Mendoza Mesa 15 Apr '20

15 Apr '20

Please, could you remove my email from the list. *Qco. JOSE ALIRIO MENDOZA MESA* Candidato a Doctor en ciencias Universidad Nacional de Colombia. cel. 3173829637

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Saving changes made in PDB files
by Liam fletcher 15 Apr '20

15 Apr '20

Good day, I am hoping you may be able to help me with an enquire I have for current work I am performing using the Chimera software for my final year project. I am attempting to save a PDB file separately following changes made e.g. Highlighted reside(s), change the background. I am having trouble in saving these files separately. More specifically, I am attempting to save different file versions where changes have been made to the protein for predicting the function. Is there a way to save these PDB files as I have been following the instruction. But, I am confusion about which of these instructions is the right instructions to use. I thank you in advance and hope to hear from you soon. Kind regards, Liam Fletcher

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CSG of a kind
by Esser, Lothar (NIH/NCI) [E] 14 Apr '20

14 Apr '20

Hi, I am sure this is possible I just could not find it in the documentation: Can someone quickly remind me how to subtract density that surrounds a molecule so as to leave the extra density in the map ? Volume eraser seems to use a sphere but this is too crude. I am interested in an extra domain that is not (yet) in my model and it would help to remove the portion that I know from the density. There is probably a very simple solution that I just can't seem to find. Thanks, Lothar

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Charge assignment to a ligand
by Prabuddha Bhattacharya 14 Apr '20

14 Apr '20

Dear Sir, I had a query regarding charge assignment to any ligand in chimera. While minimizing the energy of a particular ligand (Tools --> Structure Editing --> Minimize Structure) and also during Dock Prep, I found that for most of the aliphatic and alicyclic amines, they are getting protonated with a residual positive charge; while the aromatic amines remain unprotonated (and hence no residual charge). I understand that this is because of their differential pKb values (basic strengths). On the other side, deprotonation never occurs with the carboxylic acid (-COOH) group. Does the Chimera (force fields) control this issue of protonation and deprotonation considering the physiological pH ? I will be extremely grateful if some one may kindly clarify my doubts. Thanking you in advance, With Best Regards, *Dr. Prabuddha Bhattacharya * *Dept. Of Chemistry* *Adamas University* *Kolkata 700126* *India*

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Re: [Chimera-users] [chimera-dev] icosahedron with a T number
by Wei Zhang 11 Apr '20

11 Apr '20

Hi Elaine, I am able to use hkcage and build a spherical sphere with pentagons and hexagons. Is there a way to color those pentagons differently? Thank you, Wei On Fri, Apr 10, 2020 at 10:41 AM Wei Zhang <zhangwei(a)umn.edu> wrote: > Hi Elaine, > > Thank you for the quick reply and the instructions. > I will use the other email address next time. > > Best regards, > > Wei > > On Fri, Apr 10, 2020 at 10:12 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > >> Hi Wei, >> >> Take a look at the "hkcage" command if you want hexagons and pentagons >> instead of triangles. You give it the h and k values which are related to >> T number by the equation shown in that page: >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html> >> >> For this kind of question (next time) you probably want the >> chimera-users(a)cgl.ucsf.edu mailing list, not chimera-dev which is more >> for programming questions. >> >> Thank you for the good wishes -- you stay safe too! >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> > On Apr 9, 2020, at 4:21 PM, Wei Zhang <zhangwei(a)umn.edu> wrote: >> > >> > Hello, >> > >> > I have been playing with the icosahedron utility in Chimera. I really >> like this feature, especially with the sphere factor. >> > >> > The current routine uses a subdivision factor to represent the number >> of triangles on an icosahedral surface. However this lattice is not the >> same as we see in icosahedral viruses, which use a T number to designate >> symmetry. With a subdivision number, there are always hexamers on any edge >> of the icosahedron, whereas in the virus structure this is not the case. >> > >> > I am wondering if Chimera has an utility that can use the T number as >> the basis for building an icosahedron surface. >> > >> > Thank you. >> > >> > Hope everything is going well and stay safe! >> > >> > Wei >> >>

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MINIMIZATION BY CHIMERA
by Jonathan Javid 09 Apr '20

09 Apr '20

Dear Instructor Please guide meabout how minization is performed of protein Structure from chimera.Guide me step by step kindly. Waitig for your positive response. Thank you Reagrds Jonathan Javid

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How to to do that in chimera?
by Krivic, Denis 09 Apr '20

09 Apr '20

To whom it may concern, I have just started working on a project which includes docking and analysis of the results several weeks ago. So figuring out software for docking and the docking procedure itself was one set of problems (solved), and now I could really use your help in order to analyze my data - docking results (output files). At the moment, I am using Windows 10 (x64), Chimera 1.14, AutoDock Vina 1.1.2 and AutoDock 4.2.6. So, I have a protein (ion-channel) and several different ligands, for which I want to see how they and if they (at all) may interact with the protein. Therefore I dock the ligand in the two mentioned programs and got different output files. Vina generates a single file with 9 different positions, and 4.2. generates 9 different files for each position. Now, the first problem I encountered was that in Chimera I can open and analyze only Vina output (single file). How do I open 4.2. output? The second problem is that I am able (know how) to analyze polar interactions (HBonds). But can I somehow check for hydrophobic or other kind of interactions? The third thing is that, for example, I have Vina output files for ligand docked in 2 different (but adjacent) places in protein (so 18 positions in total). Is there any chance to merge those files so I can see the energy differences among all of them? Fourthly, is there any way to merge vina and an other program's output (4.2 or DOCK for example) and see if there are common structures (same one generated by both) and the ones that are not common for the two? Finally, is there any graphical way of representing the docking poses and see the likeliness of the binding of a certain poses? Or some sort of clustering of poses into more probable binding candidates or something similar? Thank you in advance, Denis What kind of docking What you want to do, meaning achive Which steps have you carried out Description of the status, when you get stuck

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How to split multiple ligands in mol2 files
by sunyeping 09 Apr '20

09 Apr '20

Dear all, I seem to read some posts in the chimera email-list that discuss split combined mol2 files contains many compound into single mol2 files for virtual screening, but now I cannot find them. I wish to do some virtual screening with autodock 4. I have split a sdf file contains over a thousand compounds into single mol2 file with the linux shell "csplit" command. However, I find lots of such mol2 files still contain multiple ligands （LIG1, LIG2, LIG3, etc.) whose coordinates mix together and so can not be split by shell command "csplit". Please find three such examples at: https://drive.google.com/drive/folders/1AiW00lbA4tRfLu-l47QfxWVn8PqnQ-5J?us… I can split the ligands in a mol2 file manually in Chimera GUI: first open the mol2 file, then select the ligands and save them as pdb files respectively to get separate pdb files for these ligands. After then reopen these pdb files respectively and save them as mol2 file. However, to process a large amount of mol2 files manually is impossible, so I need a command or script to do this. I hope chimera can do this. Chimera has a command "split": split [ model_number(s) ] [ chains ] [ ligands ] [ connected ] [ atoms atom-spec ]n However, it doesn't seem to be suitable for my scenario. Does anyone know whether chimera can split such mol2 files and how? I will appreciate any help of you. Best regards. Yeping Sun

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Issue: laptop gets sooooo hot when running chimera
by Yangfeng Li 06 Apr '20

06 Apr '20

Hi, I've been using chimera for several years. Recently I used it on my macbook air (2019 model, macOS 10.14) and found that it gets extremely hot when operating chimera even for ten minutes. That doesn't occur on windows laptops. So I guess the software might have some further optimization to better work on macOS. Hope to see a new version of Chimera launched soon. Stay safe and healthy, Loyal user Yangfeng

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2D diagram and CDK-Depiction.jar
by David Ricardo Figueroa Blanco 06 Apr '20

06 Apr '20

Hi! I am trying to generate 2d diagrams with Dockview from autodock vina outputs but I get this problem : Web Service: cdkdepiction converts either SMILES strings or MOL2 files into 2D structure diagrams in PNG format Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/CDKDepictionService Opal job URL: http://webservices.rbvi.ucsf.edu/appCDKDepictionService1586137005272-807576… CDKDepictionService stderr ----- Error: Unable to access jarfile /usr/local/cdk/CDK-Depiction.jar ----- CDKDepictionService stdout ----- [no output] ----- Structure diagram generation failed; see Reply Log for more information Any suggestion or needed program to install? Thank you !

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Download Chimera using CLI
by Reza Khayat 06 Apr '20

06 Apr '20

?Hi, Is it possible to download chimera headless using the command line interface? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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chimera session does not save new position of map
by Irina P. Suarez 06 Apr '20

06 Apr '20

Hi, I have a problem, for some reason my chimera session stopped saving the new position of my maps, meaning I open a few maps I align them and save the session, I close chimera and open the session again and the maps are again in their original position. Do you have an idea of what could the problem be? Also it does not let me save the session with “save session”, the option appears in gray in the file menu, it only allows me to do “save session as…”. Thanks for your help! Best, Irina

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(no subject)
by Josef Stadelmann 06 Apr '20

06 Apr '20

confirm d9b43160fd8d6219836a2d9e8200e223df7ef733

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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

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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

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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

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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

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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>

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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

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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

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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

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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

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