- Chimera-users - RBVI Mailing Lists

segment and group density together
by Yangqi Gu 21 Jun '19

21 Jun '19

Hi Chinera users, I have a density map of a filament. After I segmented the map, I want to group all the outer globular domain (which is part of a monomer) together. Instead of group them one by one, is there a quicker way to do this? I have the helical symmetry of the filaments. Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

2 1

chimera help in spacing out two structures within the same session
by #LAI KEI ONN# 21 Jun '19

21 Jun '19

Dear Chimera team would appreciate if you have any advice in spacing out two/or more structures within the same chimera session (e.g. the green structure away from the beige ones) so as to clearly visualise the intercrosslinks (red and blue sticks) between two different structures. Currently everything is superimposed with one another and i tried separating all the structures into different sessions and recombining it again but it didnt work. I am using xlinkanalyzer plugin with chimera. Would appreciate your kind advice, [cid:a79ad9c6-047a-493c-abc9-3ac3d537f4df] thank you! Best Regards Kei Onn LAI|黎啟諳 Phd Student Lee Kong Chian School of Medicine

2 1

Chimera - mask after vop
by Ryan Harlich 18 Jun '19

18 Jun '19

Hi Chimera team, Is it possible to mask after vop. I got it to work in Chimera’s command line in the gui but when I run it from my python script it does not work. I am trying to change this working solution to this solution without ground truth: WORKING SOLUTION #chimera_script.write('open ' + paths['input'] + '\n' # 'open ' + paths['ground_truth'] + '\n' # 'molmap #1 6 gridSpacing 1\n' # 'volume #1.1 level 0.1\n' # 'mask #0 #1.1\n' # 'vop resample #2 onGrid #1.1\n' # 'volume #3 save ' + paths['cleaned_map']) NEW SOLUTION chimera_script.write('open ' + paths['input'] + '\n' 'vop gaussian #0 sDev 2\n' 'vop median #1 iterations 5 modelId #2.1\n' 'volume #2.1 level 0.1\n' 'mask #0 #2.1\n' 'vop resample #3 onGrid #2.1\n' 'volume #4 save ' + paths['cleaned_map']) While mask after vop works with GUI command line it gets a NoneType error when doing this: subprocess.run(['/usr/local/bin/chimera', '--nogui', chimera_script.name]). It seems like this might be a bug of chimera? Since it tries to return None to a tuple and crashes. For some reason no triangles in the new surface with vop. Here is a snippet from the depthmask.py where it crashes. [cid:image001.png@01D525AB.830ADC20] Thank you, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

2 1

Chimera local resolution color
by Dmitry Semchonok 14 Jun '19

14 Jun '19

Dear colleagues, I have a cryo-em map after resmap local resolution. I would like to see not just the 2D colored slices but the hole model (not in the movie mode). How to color the model model in chimera based o remap? I would like the final result be similar to https://discuss.cryosparc.com/t/view-coloured-3d-map-in-chimera-using-outpu… <https://discuss.cryosparc.com/t/view-coloured-3d-map-in-chimera-using-outpu…> Thank you. Sincerely, Dmitry

2 1

Stereo glasses
by Jonathan Sheehan 13 Jun '19

13 Jun '19

Hi all, What stereo setup are people recommending these days? It seems that NVIDIA has discontinued the 3D Vision 2 goggles+emitter. Is there something else that is available and works well? Thanks for any advice! -Jonathan

2 2

Script to generate and fit structures
by Ahmad Khalifa 12 Jun '19

12 Jun '19

I want to write a script that can copy combine my structure, translate it up, down, left or right a certain distance, fit it into its new place. Is it feasible, how can I do it? Regards.

2 3

counter ions
by patrizio.arrigo＠ge.ismac.cnr.it 12 Jun '19

12 Jun '19

Dear All I would like to use counter ions of nucleic acids not included in the default list of Chimera. I do not know how to perform this action. The option add ions offers only a limited set of ionic species I guess that is necessary to use amber18. Can you give me some suggestions Dr. Patrizio Arrigo CNR SMAC

2 1

Chimera silent installer options for RHEL 7.6
by Darin Lory 11 Jun '19

11 Jun '19

Chimera Gurus, Are there linux silent install options for the Chimera so I can specify the installation directory, etc. I have chimera working via the regular installation method. My team and I are trying to automate the installation via Ansible playbook. Kindly advise, -Darin "The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...'" -Issac Asimov [image: --] Darin S. Lory [image: https://]about.me/darin.lory <https://about.me/darin.lory?promo=email_sig&utm_source=email_sig&utm_medium…>

2 2

Chimera - can I tweak the red color on the Red-cyan stereo view
by Tweten, Rodney K. (HSC) 11 Jun '19

11 Jun '19

We are displaying our protein structures on a large TV in the Red-Cyan stereo view, which works pretty good for 3D viewing (except the required loss of specific colors). We tend to see a bit of ghosting of the red structure, which I suspect is that the red color lens of the Red-Cyan glasses we have (we’ve tried a few with the same results) is not quite matched to that being used by Chimera in its Red-Cyan stereo view. I was wondering if there is any way the user could tweak the red color being used by chimera in this stereo view to more closely match that of the glasses (assuming that this is responsible for the ghosting of the red structure). Thanks! Rodney Tweten George Lynn Cross Professor "Anti-intellectualism has been a constant thread winding its way through our political and cultural life, nurtured by the false notion that democracy means that my ignorance is just as good as your knowledge.” Isaac Asimov BMSB-1053 940 Stanton L. Young Blvd. The University of Oklahoma Health Sciences Center Oklahoma City OK 73104 USA Work phone: 405 271-1205 FAX: 405 271-3117 Skype: toxlab1

2 1

APBS
by Karl R Voigtritter 11 Jun '19

11 Jun '19

Hello, I am trying to display an APBS surface. I loaded a .pqr file that was generated using the http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1 server. I then ran the APBS tool in the surface/binding analysis tab in Chimera. I left everything to default and clicked OK. It launched the executable and then executed it. The newly generated files came into the Surface Color window correctly. Upon trying to color the surface with the "color" nothing happens. -Karl Voigtritter, Ph.D. California State University, Chico

2 3

Regarding MD simulation
by Divakar S 10 Jun '19

10 Jun '19

Hi, I have been trying to do MD simulation in chimera. However, i could not understand the exact procedure from the user help menu. Plz give us a detailed procedure for simulation and analysis if possible. I also tried to learn the procedures from previously published papers but i couldn't find any articles using MD simulation from chimera. Thank you -- *Dr. Divakar S, M. Pharm (Pharmacology), PhD.,* *Lecturer, **Department of Pharmacology,* *JSS College of Pharmacy,* *(A Constitute College of JSS Academy of Higher Education and Research, Mysuru)* *Ooty, The Nilgris, Tamilnadu.* *Mobile: +91-9944036345* *Email: divakar.s(a)jssuni.edu.in <divakar.s(a)jssuni.edu.in>, diva.niru(a)gmail.com <diva.niru(a)gmail.com>*

3 2

viewing same size atoms within multiple molecules
by Andrew Garven 10 Jun '19

10 Jun '19

Hi, I am trying to implement a script so that each individual atom in each molecule I view on chimera is the same size (ie each carbon atom i view, regardless of the size of the molecule views a the same size). I realize this must be a function of the scale factor which changes the size of the molecules to appropriate viewing size. Is there a way to properly scale each molecule so that they have a standard atom viewing size. I would appreciate any help in this regard. Andrew

2 3

voxel coordinates
by Andrew Garven 07 Jun '19

07 Jun '19

Hi I am trying to get a voxel encodings (coordinates) of molecules that are run through Chimera, as a deep learning model will have an easier time with such data. I am unsure how to retrieve such data from chimera. Any help would be greatly appreciated Andrew

2 1

Re: [Chimera-users] THANKS! Chimera question
by Mike de la Flor 06 Jun '19

06 Jun '19

Hello, Thank you to all of you for getting back to me so fast. Thanks for the help. I am looking forward to ChimeraX Best, Mike de la Flor, CMI Board Certified Medical Illustrator PhD Candidate Biology and Biochemistry Natural Sciences and Mathematics University of Houston From: Greg Couch [mailto:gregc@cgl.ucsf.edu] Sent: Thursday, June 06, 2019 1:28 AM To: Mike de la Flor; UCSF Chimera users mailing list Subject: Re: [Chimera-users] Chimera question 1f16 is a NMR structure and as such has 20 different variations of the structure. Using the command line, you can hide all except for the first structure with the command: ~modeldisplay #0.2-20. To do that graphically, bring up the Model Panel, then click on the group/ungroup button to show controls for the individual structures. Then select the structures you don't want (click, drag, control-click, and shift-click as appropriate), and click on the hide button to leave the one you want. HTH, Greg On 6/5/2019 8:44 PM, Mike de la Flor wrote: Hello Mr. Pettersen, I apologize for bothering you but I had a Chimera question that is best explained by the screenshot attached. For some reason Chimera is importing multiple copies of 1f16.pdb. PyMol does not do this, but I prefer to use Chimera. Do you have any suggestions as to how to fix this? Thank you in advance. Mike de la Flor, CMI Board Certified Medical Illustrator PhD Candidate Biology and Biochemistry Natural Sciences and Mathematics University of Houston _______________________________________________ Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

Chimera question
by Mike de la Flor 05 Jun '19

05 Jun '19

Hello Mr. Pettersen, I apologize for bothering you but I had a Chimera question that is best explained by the screenshot attached. For some reason Chimera is importing multiple copies of 1f16.pdb. PyMol does not do this, but I prefer to use Chimera. Do you have any suggestions as to how to fix this? Thank you in advance. Mike de la Flor, CMI Board Certified Medical Illustrator PhD Candidate Biology and Biochemistry Natural Sciences and Mathematics University of Houston

3 2

split map based on resolution or surface color
by Shu-Hao Liou 03 Jun '19

03 Jun '19

Hi Chimera User, Is that possible to split a density map base on its resolution? That means I have a surface color file contained all local resolution distribution through a density map. Best, Shu-hao

2 1

animation commands in a morph movie
by Natesh Singh 31 May '19

31 May '19

Dear Chimera development team, I am trying to add a simple animation into the morphed trajectory that was developed using two unique conformations (protein and proten-ligand complex). I want the ligand to fly into the binding site (of course ligand is not considered in the morph since it was not a part of a chain), but I guess this could be done. contents of my model panel. ID 0 ligand surface ID 0 conformation A (protein-ligand complex) ID 1 conformation B (protein) ID 2 Morph (400 frames) I am adding the following commands into the perframe box of md movie: # Save bound view. savepos p1 # Move ligand away and save unbound view. move y -10 model #0 ; turn z -30 model #0 center #0 scale 0.2 savepos p2 #fly ligand into the binding site reset p1 100 wait But it's not working the way I want. I just want the ligand to fly slowly into its original position may be within 25-50 frames. Could we execute the commands at a specific frame number? Kindly let me know what would be the correct commands to achieve this effect. Many thanks for your help. Sincerely, Natesh University of Lille

2 1

I forgot where I saved my Chimera session
by Ahmad Khalifa 31 May '19

31 May '19

Is there anyway I can know from logs, history etc where I had saved my session? Regards.

2 1

Select by attribute value in a .psf file
by MARIA CLARA BLANES MIRA 29 May '19

29 May '19

Hello Chimera users, I am trying to see the movement of some phospholipids in a lipid bilayer when a peptide is anchoring to this membrane. I have a .pdb, .psf and several .dcd files. When I select one of these phospholipids I obtain four molecules selected (with the same name due to the segments). I have been trying with ’Select by attribute value’/atoms/pdbSegment and it works perfect because this way I can specify the segment where it is. But I can’t find the way to do the same with the .psf file. Could you tell me how should I do it?. Thank you very much, clara

3 4

How to get the best references
by temban billyhp 28 May '19

28 May '19

HiI used UCSF chimera for MOLECULAR DOCKING. Are these citations below enough for me to cite. Could you please help me with more citations. 1.Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E., UCSF Chimera--a visualization system for exploratory research and analysis, J. Comput. Chem., 2004, vol. 25, p. 1605. 2. Maier, J.A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K.E., and C. Simmerling, ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB, J. Chem. Theory Comput., 2015, vol. 11, p. 3696. 3. Shapovalov, M.V. and Dunbrack, R.L., A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions, Structure, 2011, vol. 19, p. 844. 4. Trott, O. and Olson, A.J., AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry, 2010, vol. 31, p. 455. Best regards. Sent from Yahoo Mail on Android

2 1

How to get the best references
by temban billyhp 28 May '19

28 May '19

HiI used UCSF chimera for MOLECULAR DOCKING. Are these citations below enough for me to cite. Could you please help me with more citations. 1.Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E., UCSF Chimera--a visualization system for exploratory research and analysis, J. Comput. Chem., 2004, vol. 25, p. 1605. 2. Maier, J.A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K.E., and C. Simmerling, ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB, J. Chem. Theory Comput., 2015, vol. 11, p. 3696. 3. Shapovalov, M.V. and Dunbrack, R.L., A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions, Structure, 2011, vol. 19, p. 844. 4. Trott, O. and Olson, A.J., AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry, 2010, vol. 31, p. 455. Best regards. Sent from Yahoo Mail on Android

1 0

(no subject)
by MARIA CLARA BLANES MIRA 23 May '19

23 May '19

Dear Chimera users, I have a .psf and multiple .dcd files for a peptide movement and I need to make a movie combining certain frames for each dcd file. First, I have tried to load more than one dcd file in the MD movie interface but my computer hungs. I think I should use a metafile in this situation. Something like this: namd(psf/dcd) pam.psf pam1.dcd But I have all the other pam2.dcd, pam3.dcd, etc until 40, each having 3000 frames. How could I include them in the same metafile to be able to open one, record 20-30 frames, open the second, record some other frames and so on? And how could I include the frames number? Thank you in advance, Clara Blanes

4 8

Re: [Chimera-users] Question on chimera app
by Elaine Meng 22 May '19

22 May '19

On May 21, 2019, at 4:38 PM, temban billyhp <btemban(a)yahoo.com> wrote: > > Hi > During the auto dock vina operation, when building the grid box. What is the unit of the dimensions. I will equally like to know how to find the grid spacing value. > Best regards. Chimera questions should be sent to chimera-users(a)cgl.ucsf.edu (CC’d here). The Autodock Vina tool in Chimera does not have a grid spacing setting. It only has the box center and size, which are in X,Y,Z coordinates of your atomic structure. Atomic structures are generally in Angstrom units. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Maybe there is a setting to control grid spacing if you downloaded and used the Autodock Vina program directly (not using the tool in Chimera) but I do not know. You would have to look at the Autodock Vina website for that information. <http://vina.scripps.edu/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 2

Fwd: Re: ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var
by Greg Couch 20 May '19

20 May '19

Yes, this bug was fixed after the 1.13.1 release. -- Greg On 5/17/2019 6:52 AM, Thomas Evangelidis wrote: > Strangely, the alpha version (May 09, 2019) works fine! > > On Fri, 17 May 2019 at 12:19, Thomas Evangelidis <tevang3(a)gmail.com > <mailto:tevang3@gmail.com>> wrote: > > Greetings, > > I did a fresh installation of Chimera on Ubuntu 19.04 but although > the installation finished successfully, I get this error message > whenever I launch the executable: > > > Traceback (most recent call last): > File > "/home2/thomas/Programs/Chimera-1.13.1/share/__main__.py", > line 73, in <module> > value = chimeraInit.init(sys.argv) > File > "/home2/thomas/Programs/Chimera-1.13.1/share/chimeraInit.py", > line 666, in init > import chimera > File > "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/__init__.py", > line 2777, in <module> > from SimpleSession import BEGIN_RESTORE_SESSION, > END_RESTORE_SESSION > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/__init__.py", > line 14, in <module> > from save import saveSession, sessionID, noAutoRestore, > autoRestorable, \ > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/save.py", > line 13, in <module> > from chimera import replyobj, selection, SessionPDBio, version > File > "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/replyobj.py", > line 24, in <module> > import Tkinter > File > "/home2/thomas/Programs/Chimera-1.13.1/lib/python2.7/lib-tk/Tkinter.py", > line 39, in <module> > import _tkinter # If this fails your Python may not be > configured for Tk > ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: > undefined symbol: FT_Done_MM_Var > > > What is strange is that the following works without error: > > /home2/thomas/Programs/Chimera-1.13.1/bin/python2.7 -c 'import > _tkinter' > > > Any idea what might be wrong? > > Best, > Thomas > > > -- > > ====================================================================== > > Dr. Thomas Evangelidis > > Research Scientist > > IOCB - Institute of Organic Chemistry and Biochemistry of the > Czech Academy of Sciences > <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, > Czech Republic > > & > CEITEC - Central European Institute of Technology > <https://www.ceitec.eu/>, Brno, Czech Republic > > email: tevang3(a)gmail.com <mailto:tevang3@gmail.com>, Twitter: > tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas > Evangelidis > <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > > > -- > > ====================================================================== > > Dr. Thomas Evangelidis > > Research Scientist > > IOCB - Institute of Organic Chemistry and Biochemistry of the Czech > Academy of Sciences > <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech > Republic > > & > CEITEC - Central European Institute of Technology > <https://www.ceitec.eu/>, Brno, Czech Republic > > email: tevang3(a)gmail.com <mailto:tevang3@gmail.com>, Twitter: > tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas > Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > > _______________________________________________ > Chimera-users mailing list:Chimera-users@cgl.ucsf.edu > Manage subscription:http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

Help in validation of Mutant Structure
by carlo cast 20 May '19

20 May '19

Good Morning to everyone, it’s my first time here writing at you, I hope I’m doing right. The point is that I’m working with a wild type enzyme from which I got mutant versions by using swap aa command. My goal is to look at the effects that mutations have on the structure by superimposing the mutant form with the wild type one. When I perform matchmaker command, RMSD is equal to 0 and the structures overlap perfectly; thus I thought to minimize structure before superimposing and in this way I see a little difference in RMSD but it could be due to the different steps of the minimize process (e.g. adding protons) than the actual effect of mutations. Moreover when I perform multiple sequence alignment, the amminoacids I swapped actually are not different from the Wild type ones. If I point the cursor on the swapped aa I see the difference in name and side chain but by doing multiple sequence alignment they do not appear. Any suggestions? Inviato da Posta<https://go.microsoft.com/fwlink/?LinkId=550986> per Windows 10

2 1

Re: [Chimera-users] Contact area between 2 Proteins
by Elaine Meng 17 May '19

17 May '19

Dear Fer Villa, (better to send questions to chimera-users(a)cgl.ucsf.edu, CC’d here) It is not really a matter of right and wrong. Instead it depends on what you want… If you want to measure buried solvent-accessible and solvent-excluded surface areas of atomic structures, use “measure buriedArea”. The “measure contactArea” command is similar but if the goal is measurement (rather than coloring for a figure), it is generally used for other kinds of surfaces that are not necessarily associated with any atoms, like density map isosurfaces. In that case, the appropriate cutoff value really depends on the judgment of the user based on what kinds of surfaces these are and what the user is trying to do. The tutorial you mention is for making a figure where the interaction surfaces of two proteins are colored, which is a different purpose than getting a measurement value. It explains that different cutoffs could be used with “measure contactArea", but the example has 2.5 because it gave similar appearance to using the other (buriedArea) method. The tutorial shows both methods because if you are making a figure, you could use either one as you like. It actually discusses three methods. For the other people on the list, here is that tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html> … 3 methods of coloring the interface: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#in…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2019, at 12:17 AM, Fernando Villa <fer.vdl1928(a)gmail.com> wrote: > > Dear Chimera users, > I would like to know which is the correct method to know what is the surface area of contact between two proteins: > measure contactArea or measure buriedArea? > When I apply the command: measure contactArea # 0.1 # 0.2 2.5 color yellow offset 0 that comes in the tutorial, it says that the cutting distance is equal to 2.5 A2 > But, is it correct? > How can I know that? > this example states that if this cut-off distance (2.5 A) is applied compared with a cut distance for measure buriedArea: > Command: measure buriedArea # 0.1 # 0.2 > Command: color yellow #0.1@/buriedSESArea> 1 > Command: color hot pink #0.2@/buriedSESArea> 1 > measure buried Area # 0.1 & protein # 0.2 & protein > atoms with> 1.0 Å2 > How can I know which is the correct contact area (protein protein interaction) of two models or crystals? > What is the correct cutting area that I should apply? > Could it be the default cut area of 1A? > Which method of calculation is better, measure contactArea or measure buriedArea? > I would thank you in advance for a possible solution to my problem. > > Best regards. > > Fer Villa. > Enviar comentarios > Historial > Guardadas > Comunidad > > <image.png> > > Command:open 1avx > Command: ~longbond > Command: split > Command: preset apply int 2 > Command: repr stick > Command: delete solvent > Command: color sea green #0.1 > Command: color medium purple #0.2 > Command: surface > Command: measure contactArea #0.1 #0.2 2.5 color yellow offset 0 > Command: measure contactArea #0.2 #0.1 2.5 color hotpink offset 0 > > > or > > Command: measure buriedArea #0.1 #0.2 > Command: color yellow #0.1@/buriedSESArea>1 > Command: color hot pink #0.2@/buriedSESArea>1 > > Command: measure buriedArea #0.1&protein #0.2&protein > > ATTE > Fernando Villa Díaz >

2 6

display bond lengths and angles
by Thomas Evangelidis 17 May '19

17 May '19

Hello, Is it possible to load a small molecule in Chimera and display all bond lengths and angle values, pretty much as you can do using labelopt option for the atom names? If not directly, could you please give me some hints about how to write a Python script to do it? I thank you in advance for your help. Thomas -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: tevang3(a)gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/

2 1

ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var
by Thomas Evangelidis 17 May '19

17 May '19

Greetings, I did a fresh installation of Chimera on Ubuntu 19.04 but although the installation finished successfully, I get this error message whenever I launch the executable: > > Traceback (most recent call last): > File "/home2/thomas/Programs/Chimera-1.13.1/share/__main__.py", line 73, > in <module> > value = chimeraInit.init(sys.argv) > File "/home2/thomas/Programs/Chimera-1.13.1/share/chimeraInit.py", line > 666, in init > import chimera > File "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/__init__.py", > line 2777, in <module> > from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/__init__.py", > line 14, in <module> > from save import saveSession, sessionID, noAutoRestore, > autoRestorable, \ > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/save.py", line > 13, in <module> > from chimera import replyobj, selection, SessionPDBio, version > File "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/replyobj.py", > line 24, in <module> > import Tkinter > File > "/home2/thomas/Programs/Chimera-1.13.1/lib/python2.7/lib-tk/Tkinter.py", > line 39, in <module> > import _tkinter # If this fails your Python may not be configured for > Tk > ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: > FT_Done_MM_Var > What is strange is that the following works without error: /home2/thomas/Programs/Chimera-1.13.1/bin/python2.7 -c 'import _tkinter' > Any idea what might be wrong? Best, Thomas -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: tevang3(a)gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/

1 1

Still won't work after libfreetype.so* and libz.so* removal
by Яцкевич Максим 14 May '19

14 May '19

Hi! I am running Fedora 29. Now I'm trying to install chimera-1.13.1-linux_x86_64.bin. After successful installation it failed to create a window in a desktop applecation menu. So I followed the instructions on the web-site (http://www.cgl.ucsf.edu/chimera/data/downloads/1.13.1/linux_x86_64.html) After running the command <dir_name>/bin/xdg-setup install it stumbled upon the same error that was discussed in this thread (https://www.cgl.ucsf.edu/pipermail/chimera-users/2018-November/015237.html) Traceback (most recent call last): File "/home/sec/.local/chimera/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/home/sec/.local/chimera/share/chimeraInit.py", line 666, in init import chimera File "/home/sec/.local/chimera/share/chimera/__init__.py", line 2777, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/home/sec/.local/chimera/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/home/sec/.local/chimera/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/home/sec/.local/chimera/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/home/sec/.local/chimera/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: /usr/lib64/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var So I followed your advise and removed the corresponding files: > rm ~/.local/chimera/lib/libz.so* > rm ~/.local/chimera/lib/libfreetype.so* Unfortunately it didn't solve the problem. So after typing: > ~/.local/chimera/bin/xdg-setup install It complained that it cannot find the libz.so file! Traceback (most recent call last): File "/home/sec/.local/chimera/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/home/sec/.local/chimera/share/chimeraInit.py", line 659, in init initialize_ssl_cert_dir() File "/home/sec/.local/chimera/share/chimeraInit.py", line 309, in initialize_ssl_cert_dir import ssl File "/home/sec/.local/chimera/lib/python2.7/ssl.py", line 146, in <module> import base64 # for DER-to-PEM translation File "/home/sec/.local/chimera/lib/python2.7/base64.py", line 11, in <module> import binascii ImportError: libz.so: cannot open shared object file: No such file or directory I will be grateful for any help. Best regards, Maxim. PhD Student, Physical Faculty, Lomonosov Moscow State University

2 1

Upload color scheme
by Cornelius Hunter 10 May '19

10 May '19

I am looking for a 3D protein viewer that allows me to visualize the protein tertiary structure using my own color assignments, for each residue (or alpha carbon). In other words I would upload a file, with a value for each residue, which would drive the color assignments. Thx

2 2

Volume Step default
by Rebecca Swett 10 May '19

10 May '19

HI all, I was wondering if it was possible to set the Volume Viewer step to 1 as default instead of 4. Is this something I could add to my .chimera/preferences file? Cheers, Rebecca This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

2 1

to hide atoms using command lines
by C.J. 08 May '19

08 May '19

Dear specialist, I know how to use hide selected atoms (Menu: Actions => Atoms/Bonds => Hide), but I would like to use command lines instead. Anyone could help me with that? Thank you! Best regards! C.J.

2 2

FW: Association info
by Hernando J Sosa 08 May '19

08 May '19

Thanks Eric, it works. To summarize: #---------------------------------------------------------------------- def findMAV(): from chimera.extension import manager from MultAlignViewer.MAViewer import MAViewer mavs = [inst for inst in manager.instances if isinstance(inst, MAViewer)] if not mavs: raise AssertionError("No MAV instances") return mavs[-1] #---------------------------------------------------------------------- mav = findMAV() mav.saveAssocInfo('myfile.asc') #---------------------------------------------------------------------- Best Hernando

2 1

Re: [Chimera-users] Non-standard atom names
by Sid Majaha 08 May '19

08 May '19

Hi Eric So I have been only using dock6 for docking and now want to venture in using dock3. I tried checking online for tutorials that I could look at but there are just a couple of them. On the UCSF website, there is a tutorial but requires the use of dock blaster. I just have a few questions; Is there another way of using dock3.6 without using dock blaster? Is there another simpler tutorial for dock3.6 that you could recommend me to use? Are the dock 3.6 steps similar to the steps of dock6? Sid Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Sent: Tuesday, April 16, 2019 6:46:31 AM To: Sid Majaha Cc: Elaine Meng Subject: Re: [Chimera-users] Non-standard atom names You’re welcome. AM1-BCC does take considerably longer than Gasteiger, but in this case the great majority of the time is spent adding the missing side chains. —Eric > On Apr 15, 2019, at 1:18 AM, Sid Majaha <sidumomajaha(a)live.com <mailto:sidumomajaha@live.com>> wrote: > > Hi Eric > > Thank you so much for your help. I was able to see as well that my protein might have been too large for the calculations of the charges to take place efficiently because after following the procedure you gave me, it took a much longer time than using Gasteiger. Thank you so much for your help. > > Sid > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 > > From: Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> > Sent: Saturday, April 13, 2019 2:18:39 AM > To: Sid Majaha > Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > Subject: Re: [Chimera-users] Non-standard atom names > > Hi Sid, > The 2BXF structure has many, many missing heavy side-chain atoms. I recommend using the Dock Prep tool (Tools→Structure Editing→Dock Prep), which will use a rotamer library to fill out missing/incomplete side chains before adding hydrogens and assigning charges. Use the dialog check boxes to turn off any Dock Prep steps you don’t want (e.g. Write Mol2 file). Applying a lot of rotamers takes a few minutes, so you might want to bring up the Reply Log first (Favorites→Reply Log) so you can keep an eye on the Dock Prep progress while you possibly do something else. > > ―Eric > > Eric Pettersen > UCSF Computer Graphics Lab > >> On Apr 11, 2019, at 8:26 PM, Sid Majaha <sidumomajaha(a)live.com <mailto:sidumomajaha@live.com>> wrote: >> >> >> Hi Eric >> >> Problems with atom names in adding charge to a receptor using Chimera v1.13.1 >> (ToolsàSurface Binding/AnalysisàAdd charge) >> I first added my H to prepare my receptor. And I am using the protein PDB ID 2BXF. >> Net Charge is +0 for the residue HIS using charge method AM1_BCC >> >> Chimera warning received >> Correct charges are unknown for 9 non-standard atom names in otherwise standard residues. >> Charges of 0.0 were assigned to the unknown atoms. >> 1 model(s) had non-intergral total charge. >> >> Reply log is as follows, >> >> Charge model: AMBER ff14SB >> Assigning partial charges to residue HIS (net charge +0) with am1-bcc method >> Running ANTECHAMBER command: C:/Program Files/Chimera 1.13.1/bin/amber16/bin\antechamber -ek qm_theory='AM1', -i c:\users\hp\appdata\local\temp\tmplj8p6o\ante.in.mol2 -fi mol2 -o c:\users\hp\appdata\local\temp\tmplj8p6o\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n >> (HIS) >> >> (HIS) Welcome to antechamber 17.3: molecular input file processor. >> >> (HIS) >> >> (HIS) Info: Finished reading file (c:\users\hp\appdata\local\temp\tmplj8p6o\ante.in.mol2). >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac >> >> (HIS) >> >> (HIS) >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff >> >> (HIS) Info: Total number of electrons: 78; net charge: 0 >> >> (HIS) >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/sqm" -O -i sqm.in -o sqm.out >> >> (HIS) >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/Chimera 1.13.1/bin/amber16/dat/antechamber/BCCPARM.DAT" -s 2 -j 1 >> >> (HIS) >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC >> >> (HIS) >> >> Charges for residue HIS determined >> Non-standard atom names: >> VAL HB1 (VAL 551.A HB1) >> VAL HB2 (VAL 551.A HB2) >> ILE HB3 (ILE 509.A HB3, ILE 1087.B HB3) >> VAL HB3 (VAL 551.A HB3) >> ILE HB2 (ILE 509.A HB2, ILE 1087.B HB2) >> THR HB1 (THR 79.A HB1, THR 621.B HB1, THR 657.B HB1) >> ILE HB1 (ILE 509.A HB1, ILE 1087.B HB1) >> THR HB3 (THR 79.A HB3, THR 621.B HB3, THR 657.B HB3) >> THR HB2 (THR 79.A HB2, THR 621.B HB2, THR 657.B HB2) >> Total charge for #0: -66.402 >> The following residues had non-integral charges: >> LYS 16.A 0.0867 >> LEU 27.A -0.0471 >> GLN 29.A 0.0392 >> LYS 37.A 0.0867 >> LYS 47.A 0.0733 >> ASP 52.A -0.2088 >> GLU 53.A -0.2103 >> GLU 56.A -0.1137 >> LYS 69.A 0.0867 >> ARG 77.A 0.0612 >> GLU 78.A -0.1137 >> THR 79.A 0.3128 >> TYR 80.A 0.0451 >> GLU 82.A -0.1137 >> GLN 90.A 0.0152 >> GLU 91.A -0.1137 >> GLU 93.A -0.1137 >> ARG 94.A 0.0612 >> PHE 98.A 0.0352 >> GLN 100.A 0.0392 >> ASN 107.A 0.0397 >> ARG 110.A 0.0612 >> LYS 132.A 0.0867 >> LYS 133.A 0.2148 >> LYS 155.A 0.0867 >> LYS 158.A 0.0733 >> GLN 166.A 0.0152 >> LYS 170.A 0.0733 >> LEU 174.A -0.0471 >> LYS 186.A 0.0867 >> GLN 200.A 0.0152 >> LYS 201.A 0.0733 >> ARG 205.A 0.153 >> LYS 221.A 0.0867 >> LYS 229.A 0.0733 >> LYS 236.A 0.0733 >> LEU 247.A -0.0471 >> LYS 272.A 0.0733 >> GLU 273.A -0.1137 >> GLU 276.A -0.1137 >> LYS 277.A 0.0733 >> GLU 281.A -0.1137 >> LYS 282.A 0.0733 >> GLU 293.A -0.1137 >> LEU 298.A -0.0471 >> LYS 309.A 0.0733 >> LYS 319.A 0.0867 >> ASP 320.A -0.2088 >> LYS 355.A 0.0867 >> ASP 361.A -0.2088 >> LYS 368.A 0.0867 >> LYS 374.A 0.0733 >> GLU 378.A -0.1137 >> GLU 392.A -0.1137 >> GLN 393.A 0.0152 >> LYS 398.A 0.0733 >> LEU 404.A -0.0471 >> LYS 428.A 0.0867 >> LYS 432.A 0.0867 >> LYS 462.A 0.0733 >> LYS 496.A 0.0867 >> GLU 497.A -0.2103 >> ASN 499.A 0.0397 >> ILE 509.A 0.0431 >> LYS 515.A 0.0733 >> GLU 516.A -0.1137 >> LYS 520.A 0.0733 >> LEU 528.A -0.0471 >> LYS 532.A 0.0733 >> LYS 534.A 0.0733 >> LYS 537.A 0.0733 >> LYS 541.A 0.0733 >> PHE 547.A 0.0352 >> VAL 551.A 0.1935 >> LYS 553.A 0.2148 >> LYS 556.A 0.0733 >> ASP 558.A -0.2088 >> LYS 560.A 0.0733 >> GLU 561.A -0.1137 >> GLU 566.A -0.2103 >> LYS 569.A 0.0733 >> LYS 570.A 0.0733 >> GLN 576.A 0.0152 >> LYS 586.B 0.0733 >> LEU 605.B -0.0471 >> GLN 606.B 0.0152 >> THR 621.B 0.3128 >> LYS 625.B 0.0733 >> ASP 630.B -0.2088 >> GLU 634.B -0.1137 >> ASN 635.B 0.0397 >> LYS 638.B 0.0867 >> GLU 656.B -0.1137 >> THR 657.B 0.3128 >> TYR 658.B 0.0451 >> GLU 660.B -0.1137 >> MET 661.B 0.0564 >> LYS 667.B 0.0733 >> GLN 668.B 0.0152 >> GLU 671.B -0.1137 >> ARG 672.B 0.0612 >> PHE 676.B 0.0352 >> GLN 678.B 0.0152 >> ARG 688.B 0.0612 >> LEU 689.B -0.0471 >> LYS 733.B 0.0733 >> GLN 744.B 0.0152 >> LYS 748.B 0.0733 >> LEU 752.B -0.0471 >> LYS 755.B 0.0733 >> ARG 760.B 0.0612 >> GLU 762.B -0.1137 >> LYS 764.B 0.2148 >> GLN 778.B 0.0152 >> LYS 779.B 0.0867 >> ARG 783.B 0.3792 >> LYS 799.B 0.0867 >> LYS 807.B 0.0733 >> LYS 814.B 0.0733 >> LEU 849.B -0.0471 >> LYS 850.B 0.0733 >> GLU 851.B -0.1137 >> GLU 854.B -0.1137 >> LYS 855.B 0.0867 >> LYS 860.B 0.0733 >> GLU 871.B -0.1137 >> ASP 875.B -0.2088 >> LYS 887.B 0.0733 >> LYS 891.B 0.0733 >> GLU 895.B -0.1137 >> LYS 897.B 0.0867 >> LYS 933.B 0.2148 >> GLU 942.B -0.1137 >> LYS 952.B 0.0867 >> GLU 956.B -0.1137 >> LYS 963.B 0.2148 >> LYS 976.B 0.0867 >> ARG 984.B 0.3792 >> LYS 1010.B 0.0867 >> LYS 1018.B 0.2148 >> LYS 1040.B 0.0733 >> GLU 1075.B -0.1137 >> ASP 1086.B -0.2088 >> ILE 1087.B 0.0431 >> LYS 1093.B 0.0733 >> GLU 1094.B -0.1137 >> GLN 1096.B 0.0152 >> LYS 1098.B 0.0867 >> LYS 1099.B 0.0867 >> LYS 1110.B 0.0733 >> LYS 1115.B 0.0733 >> LYS 1119.B 0.2148 >> ASP 1124.B -0.2088 >> PHE 1128.B 0.0352 >> LYS 1131.B 0.0733 >> ASP 1136.B -0.2088 >> LYS 1138.B 0.0733 >> GLU 1139.B -0.1137 >> GLU 1144.B -0.1137 >> LYS 1147.B 0.0733 >> LYS 1148.B 0.0733 >> LEU 1149.B -0.0471 >> GLN 1154.B 0.0152 >> Correct charges are unknown for 9 non-standard atom names in otherwise standard residues >> >> Charges of 0.0 were assigned to the unknown atoms >> >> 1 model(s) had non-integral total charge >> Details in reply log. >> >> How do I work around this? >> >> Sid >> >> >> _______________________________________________ >> 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> > _______________________________________________ > 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>

2 3

RR distance map, scale normalization
by Arvind SHARMA 07 May '19

07 May '19

Hi, I am comparing four drug bound structures of homologous proteins to their unbound structures in chimera RR distance maps. These structures vary to different degree to unbound structures and I want to show that in four individual RR distance maps (each bound structure to unbound structure). The problem is that the scale varies each time and I was wondering if there is a way to normalize the scale? or set the color code so that, for e.g, for stdv of 10 its red in all cases and below 5 its always white. Thanks. Best wishes, Arvind.

4 10

Handling electrostatic potential in cube format
by Boaz Shaanan 06 May '19

06 May '19

Hi, It seems as if the new Delphi version (v8.4) only knows to produce potential phi files in cube format. Oh well. I'm beginning to play with this format via the volume viewer but so far the fit of the surface to the atomic model is bad, let alone that potential values on the surface (as reported by moving the mouse on the surface) make no sense. I'm wondering whether there is a chance to achieve as nice a fit of the cube surface to the protein model as is easily achieved with the good old .phi format and surface command. So far I'm lost. I'd appreciate any clues. Luckily, I still keep the older version but there might be some improvements in the potential calculations in the newer version. Thanks for your help. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

3 4

Re: [Chimera-users] [chimera-dev] Loop refinement in chain A and Chain B
by Elaine Meng 06 May '19

06 May '19

Hi Aashish, The address for questions about using Chimera is chimera-users(a)cgl.ucsf.edu (CC’d here). Chimera-dev is for programming questions. It sounds like you did find the “model/refine loops” dialog for using the Modeller web service. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> In that dialog, you would need to choose either “non-terminal missing structure” (if the missing residues are in the middle) or “all missing structure” (if some of the missing residues are in the termini), and also enter a license key for running Modeller. However, I have no idea what you mean by “not running,” so I can’t give any more help than that. Also, be aware that in Chimera using this dialog, you can only model one chain at a time. I.e. when it is adding the residues to chain A it does not care if they are in a bad place relative to chain B, and vice versa. Our newer program ChimeraX has the advantage that you can sensibly model the dimer using the Modeller web service, with the two chains “seeing” each other. However, to use that you would have to download and learn a different program. <http://www.rbvi.ucsf.edu/chimerax/index.html> <http://www.rbvi.ucsf.edu/chimerax/download.html> <http://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html#comparative> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 6, 2019, at 5:39 AM, Aashish Bhatt <aashish.ph16221(a)inst.ac.in> wrote: > > Dear Sir/ Ma'am > > I have dimer PDB structure in which 40 amino acid is missing in both chain A and B. > Is it possible to make a model with a chimera? I have tried the same with chain A and but it is not running. > > Can you please give me an idea of how to build the complete structure? > > Best regards > > Aashish > INST-Mohali > India

1 0

How do I find the active site?
by Abryn Jeuness Luna 06 May '19

06 May '19

Good day! I am currently using UCSF Chimera for my protein structure analysis. However, I cannot find the active site of my protein structure. How do I find the active site, including the amino acids in it using UCSF Chimera? Thank you. Regards, Abryn

2 1

regarding to minimization and preparation of sdf files for docking.
by prasad ssv 05 May '19

05 May '19

hi, i had a database which contains a set of molecules,all molecules in sdf format i would like to minimize all sdf files and dock preparation.can you please help me do that. i had performed dock prep for those sdf files but it showing some reply log and bugs.when i am adding hydrogens it is gvng reply log as attached in below files. can you please go through and suggest me a solution. thanking you,

3 4

Re: [Chimera-users] Chimera-users Digest, Vol 193, Issue 5
by Boaz Shaanan 05 May '19

05 May '19

Hi Again, Following my complaint on the cube format I started to play with .dx format of APBS which so far seems more promising in how it projects on the protein surface. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Sunday, May 5, 2019 8:18 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 193, Issue 5 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. save sequence alignment (Hernando J Sosa) 2. Re: save sequence alignment (Eric Pettersen) 3. Re: RR distance map, scale normalization (Arvind SHARMA) 4. Handling electrostatic potential in cube format (Boaz Shaanan) 5. How to select residues/atoms only those within my cryo-EM map region (Kim, Doo Nam) ---------------------------------------------------------------------- Message: 1 Date: Fri, 3 May 2019 21:03:33 +0000 From: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> To: Chimera <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] save sequence alignment Message-ID: <F0E461AAE34D0448B6EE7D31E433B7080154B87577(a)AEWEXCPM21.yuad.uds.yu.edu> Content-Type: text/plain; charset="utf-8" Dear Chimera, Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script? Thanks H. ------------------------------ Message: 2 Date: Fri, 3 May 2019 15:19:36 -0700 From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> Cc: Chimera <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] save sequence alignment Message-ID: <EFACEFC8-FD06-4C10-AE7B-704CD8925BCF(a)cgl.ucsf.edu> Content-Type: text/plain; charset="utf-8" Hi Hernando, This old chimera-users message shows how to find the alignment in Python and save it: [Chimera-users] easy way to make alignments in chimera <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html>. You can?t do it in nogui mode since the MAV window has the alignment data. You would be able to do it in nogui mode in ChimeraX, but the code would be significantly different of course. Anyway, if you are doing this in a loop you may want to call mav.Quit() after saving your alignment in order to quit MAV and conserve memory. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On May 3, 2019, at 2:03 PM, Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> wrote: > > Dear Chimera, > > Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script? > > Thanks > > H. > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

AutoDock Vina
by Hernando J Sosa 02 May '19

02 May '19

Is it possible to specify more than 10 'Number of Binding models' on the AtoDock Vina dialogue? Thanks Hernando

3 5

get_view, set_view
by Pranav Shah 02 May '19

02 May '19

Dear Devs, Apologies for asking a naive question, but i was wondering if there exists a function similar to pymols' get_view and set_view in chimera/chimeraX? If yes, is there a way to do this? Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

2 3

Installing vina webserver?
by Antoine Daina 01 May '19

01 May '19

Dear, Is there any possibility to install a local AutoDock Vina webserver (not the executable, really the WS) through the scripts I can see in the Chimera install directories? Thanks a lot in advance fro your help. Best, Antoine. -- Antoine Daina, PhD SIB | Swiss Institute of Bioinformatics | Molecular Modeling Group Quartier Sorge | Bâtiment Amphipôle | CH-1015 Lausanne | Switzerland

2 1

Re: [Chimera-users] Reading electrostatic potential map in cube format into Chimera
by Boaz Shaanan 30 Apr '19

30 Apr '19

1 0

Reading electrostatic potential map in cube format into Chimera
by Boaz Shaanan 30 Apr '19

30 Apr '19

Hi, Does Chimera accept electrostatic potential in cube format (apparently that's what the new Delphi version 8.4 produces). I noticed a cube input under gaussian cube grid, is that the one I should use? Apparently the source of my recent problem with reading an electrostatic potential map had to do with this change of format. I'd appreciate your input. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

2 1

Deleting data contained in a session
by David Sáez 29 Apr '19

29 Apr '19

Dear Chimera experts: I have saved multiple sessions of molecular dynamics trajectories. Each session is about 5MB. Nevertheless, one of those files is huge, about 120MB. Checking the differences, I noticed that one of the files contained in the session, which normally is a one-frame .pdb, in the large case corresponds to a .nc file, a whole trajectory containing a large number of frames. I did not notice this before because when I opened the .py file, the MD movie box is not shown. As I am only interested in the currently displayed frame of this .nc file, is there a way to delete the additional frames? Some command line trick that would allow me to get rid of the uninteresting frames, and decrease the file size, without having to re-make the whole session again? My most immediate concern is that the file size is too large to be uploaded to a journal online platform. Any help is appreciated, Regards.

2 2

How to join two modelled chain of protein using chimera
by Bhanu Sharma 29 Apr '19

29 Apr '19

I have modelled two chains of protein(A,B) sepratrely. now i want to join these two chains as like of original protein and want to save it as a pdb file format . Can anyone please help me? Best regards, Bhanu sharma

2 2

A query
by Bhanu Sharma 26 Apr '19

26 Apr '19

Dear sir/mam I have done homology modelling for a protein having two chains (A,B). I have modelled them seprately one after another. Now i want to join these two chains to make complete protein. And i want to do it using chimera. Can you please help me how to do this. Best regards, Bhanu sharma

1 0

Changing the default temp folder for chimera
by Yehuda Halfon 25 Apr '19

25 Apr '19

Hi all, I try to make a movie in chimera and it fills my C drive. Can I change the temp folder, in which the pics are stored, to another empty drive? Thanks, Yehuda Halfon

2 1

Surface representation
by MARIA CLARA BLANES MIRA 25 Apr '19

25 Apr '19

Hello, I would like to know if Chimera could show the surfaces like VMD does with the command QuickSurf (I attach the image with the protein in yellow and the lipids in green). I have been trying with a lot of different variations of the surface command but I can not find the way to make the surface ’softer'…. I have also been trying with spheres representation but the image shows too much information. I need a simplest view, similar to the image because this way it is easier see them move in the .dcd file. It not so important for the protein, just for the lipids. Could you help me with this, please? Thank you very much, clara

2 7