- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Calculation of the average isoelectric point of a proteins solvation shell
by Elaine Meng 23 Nov '15

23 Nov '15

> On Nov 21, 2015, at 11:54 AM, Csaba Nagy <csaba.nagy(a)utu.fi> wrote: > > Dear Elaine, > > thank you for your kind reply, and for the instructions regarding the surface charge of the protein. I just realized, that I phrased my question wrong, actually I wanted to calculate the average isoelectric constant of the proteins surface-amino acids in order to apply the most optimal buffer system to solubilize my protein. > Thank you again. > > Best wishes, > Csaba > Dear Csaba, Sorry, Chimera does not calculate isoelectric points or constants, it only estimates charge in aqueous solution near neutral pH. You would need to find some other program to do what you want. It is best to send Chimera questions to the chimera-users(a)cgl.ucsf.edu list, CC’d here. Apologies if you got this message more than once, I was having trouble sending the e-mail. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

How to insert a morph into a movie command file?
by Christina Bourne 23 Nov '15

23 Nov '15

Dear all, Is there a straightforward way to insert a morph within a larger movie? We are working from command scripts but see that the command "morph" is not recognized.Any help is appreciated,Christina

2 1

Dock prep with multiple structures - endless loop?
by Oliver Clarke 20 Nov '15

20 Nov '15

Hi, Would it be possible to add a progress bar (with ETA) for Dock prep at some point? I ran it overnight to fill partial sidechains on six structures (each ~6000aas), and it still isn’t finished, but I can’t tell whether it is just taking a really long time or whether something has gone wrong. The status bar is still updating with “Matching donors”, “finding acceptors” and “building search tree” messages, but it seems to be giving these messages multiple times for each structure - is that normal? Cheers, Oliver.

2 3

Inter-molecular H-bonds between water molecules not displayed in per-frame script
by George Green 20 Nov '15

20 Nov '15

Hi, I'm trying to get a per-frame script going which shows the inter-molecular H-bonds within a protein binding site. It is working in that all H-bonds show apart from water-water h-bonds. Is there any fix for this at all? My code is below: Water molecules are residues :159-162 I would be very grateful for any assistance. :) sg ################################################ #################### # per-frame H-bond repr bs :158 color hot pink :158 color byhet :158 # disp :60,37,85,112,109,35,158,84,60,40,38,114,69,90,58,61-68,56,21,45,52,101,15,92,40,105,116,24,42,54,40,24,10,97,120,159,160,161,162 disp :WAT # select :1-162; hbonds intramodel true intermodel true line 5 color gold ; ~select select :90 ################################################

2 8

Calculation of the average isoelectric point of a proteins solvation shell
by Csaba Nagy 20 Nov '15

20 Nov '15

Dear Chimera Developers and -Users, I am struggling with the overexpression and purification of a cytoplasmic protein that looks to be soluble only in a very narrow pH range. I know the average isoelectric point of the whole protein, but there would be much more informative, to know what is the average isoelectric point of the proteins solvation shell, I think. Therefore I modeled the 3D structure of the protein and I tried several other visualization programs to calculate this pI value, but I was not successful. Could you tell me please, if there is any option to make this estimation in Chimera? Thank you very much in advance! Best regards, Csaba Nagy ------------------------------- Csaba I. Nagy, PhD Postdoctoral Researcher, PharmaCity, Itäinen Pitkäkatu 4 C, 6th floor, room 6049 Molecular Plant Biology University of Turku FI-20014 TURKU, Finland Phone +358 2 333 7914 Fax +358 2 333 8075 Email csaba.nagy(a)utu.fi --------------------------------

2 1

command line issues
by liz kellogg 19 Nov '15

19 Nov '15

Hi, I've been using chimera quite happily for the past couple of years. I especially like the command line, as it makes operations much faster to complete (once you know the commands!) I've been using the command-line, in chimera, on my mac (osx yosemite version 10.10.3) for a while now, but just today my command-line would not display the text I'm entering into the command-line bar. This is odd, I've never seen this before, and I don't know what the problem is due to. I tried restarting chimera, I tried restarting my computer, and I tried re-installing chimera, but the command-line prompt is the same.. it doesn't display the text as I'm entering it.. though if I type a command, it does execute it and it shows up in the command history.. so it looks like a problem in displaying text as it's being entered. Has anyone else run into this problem? And how do you fix it? I'd be so much happier if I could see what I'm typing! thanks Liz

2 2

Uploading to Microsoft Word
by Austin Brown 19 Nov '15

19 Nov '15

Hello, I am working on a project that involves uploading 10-15 Chimera images to a Microsoft Word document. The first time I got all of them on there, they looked great. However, upon opening my project the next morning, all the images were blank with a small red X in the corner. There was an error message that read "The image part with relationship ID rld5 was not found in the file." I am not sure what went wrong, but it's just a .png picture that I saved through Chimera. I am running on a Mac with Microsoft Word 2013. Any help is appreciated. Thanks, Austin

2 1

Calculation of the average isoelectric point of a proteins solvation shell
by Csaba Nagy 19 Nov '15

19 Nov '15

Dear Chimera Developers, I am struggling with the overexpression and purification of a cytoplasmic protein that looks to be soluble only in a very narrow pH range. I know the average isoelectric point of the whole protein, but there would be much more informative, to know what is the average isoelectric point of the proteins solvation shell, I think. Therefore I modeled the 3D structure of the protein and I tried several other visualization programs to calculate this pI value, but I was not successful. Could you tell me please, if there is any option to make this estimation in Chimera? Thank you very much in advance! Best regards, Csaba Nagy ------------------------------- Csaba I. Nagy, PhD Postdoctoral Researcher, PharmaCity, Itäinen Pitkäkatu 4 C, 6th floor, room 6049 Molecular Plant Biology University of Turku FI-20014 TURKU, Finland Phone +358 2 333 7914 Fax +358 2 333 8075 Email csaba.nagy(a)utu.fi --------------------------------

1 0

Re: [Chimera-users] RMSD script
by Elaine Meng 18 Nov '15

18 Nov '15

Yes, as described in more detail in the “RMSD Analysis” description you can select specific atoms (for example command “select protein & @n,ca,c,o” to select the peptide backbone atoms) and use the “Restrict map to current selection, if any” option. That option is on by default. If it was on and you didn’t select any atoms, it used all atoms. > See MD Movie manpage, especially sections “Startup and Input” and “RMSD Analysis" > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> More about selection: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> Best, Elaine On Nov 18, 2015, at 2:47 PM, Ruth Nelson <Ruth.Nelson.180(a)nd.edu> wrote: > Hi Elaine, thank you for your response. > > Using MD Movie worked to calculated the RMSDs, but I am unsure if the output values are full atom or for the backbone (Ca, C, N, O) only. Is there some way I can specify this? > > Thank you very much, > Ruthie > > On Wed, Nov 18, 2015 at 5:06 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Ruthie, > If all of the PDB files have exactly the same atoms with the same names, and no END lines, you could try opening all of them as one trajectory in MD Movie. That tool has an all-by-all RMSD calculation option and you can save the results to a text file. You would still have to process that file into CSV, however, as there is no CSV output option, but this would greatly decress the number of steps you have to script yourself, and it would be done outside of Chimera in whatever type of scripting you prefer. > > I.e. you would start MD Movie ( in menu under Tools… MD/Ensemble Analysis) and then choose to open the trajectory as PDB, multiple files. They have be named similarly with numbers but the numbers don’t have to be consecutive. If loading the trajectory is successful, the MD Movie playback dialog will appear, and from that dialog you could choose Analysis…RMSD Map. The RMSD can be calculated from all atoms or only specify ones that you have selected. Then there is a button to “Save RMSDs” on the resulting map window. > > See MD Movie manpage, especially sections “Startup and Input” and “RMSD Analysis" > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Nov 18, 2015, at 9:38 AM, Ruth Nelson <Ruth.Nelson.180(a)nd.edu> wrote: > > > Hello, > > > > I have a matrix of 10x10 .pdb files, and I need to calculate the RMSD from each PDB file to every other PDB file in that matrix. When I do this in the command line of Chimera, I type something like "match #0 #1" or "match #0 #2" for each of my PDB files, but I would like to automate this process so that it does not take as long. I have hundreds of files and they are all are named similarly (file_1.pdb, for example) but they are not numbered consecutively (file_1.pdb, file_17.pdb, file_43.pdb, for example). If possible, I would like the RMSD values to be output into a CSV file so that I can open it in excel. > > > > I have very little experience writing scripts and no idea where to begin to write this one, so I would greatly appreciate any help. I have been reading some of the responses given to other people regarding similar scripts, but I am having a hard time translating that to what I would like to do. > > > > Thank you very much, > > Ruthie > > > > > > > -- > Ruth Nelson, Graduate Student > Department of Chemistry and Biochemistry > University of Notre Dame > rnelson9(a)nd.edu

1 0

RMSD script
by Ruth Nelson 18 Nov '15

18 Nov '15

Hello, I have a matrix of 10x10 .pdb files, and I need to calculate the RMSD from each PDB file to every other PDB file in that matrix. When I do this in the command line of Chimera, I type something like "match #0 #1" or "match #0 #2" for each of my PDB files, but I would like to automate this process so that it does not take as long. I have hundreds of files and they are all are named similarly (file_1.pdb, for example) but they are not numbered consecutively (file_1.pdb, file_17.pdb, file_43.pdb, for example). If possible, I would like the RMSD values to be output into a CSV file so that I can open it in excel. I have very little experience writing scripts and no idea where to begin to write this one, so I would greatly appreciate any help. I have been reading some of the responses given to other people regarding similar scripts, but I am having a hard time translating that to what I would like to do. Thank you very much, Ruthie

2 1

Changing default framerate of Animation tool
by Eiros Zamora, Juan 17 Nov '15

17 Nov '15

Dear Chimera experts, I would like to know if there’s a way to increase the default 25 fps framerate when using the ‘Animation' tool to make movies. I tried increasing it from the ‘Movie Recorder’ menu, but it’s still producing the video at 25 fps. Also, I am not sure about what does the ‘Nth frame for discrete transitions’ property of items in the timeline mean. Should I increase this to get more FPS? I would like to do this because I am trying to do a video of an MD trajectory showing at the beginning the water box (and then hiding it), but at the moment the videos that I am getting feel very ‘clunky’ Cheers Juan

2 1

how to prepare ligand by command line?
by Albert 17 Nov '15

17 Nov '15

Hello: I've got a ligand in 2D .sdf format without any hydrogens. I am just wondering how can we prepare this compound for docking? Is it possible to run it by command from Chimera? Thanks a lot Albert

3 2

Problem using Chimera
by BRUXELLES Tatiana (ETU VIE) 17 Nov '15

17 Nov '15

Dear Sir, dear Madam I am a Master student at the Université de Strasbourg in France and I am currently doing an internship in a bioinformatics lab : the LBGI in Strasbourg. One of my tasks during this internship is to make Chimera read about 80 files with the extensions .scf. The problem is that software doesn't to be able to read my command file. I can't even make it read a print instruction. To execute those files I use the command : read File_name in command line on chimera. I am gonna join the files so you can see. Could you suggest a solution to my problem ? Kind regards, Bruxelles Tatiana

2 1

helices
by A G Szabo 17 Nov '15

17 Nov '15

I sent a message yesterday regarding how I can change helices from ribbons to smooth wires. I am pleased that I can indicate that I figured it out.. Arthur G Szabo Professor Emeritus Wilfrid Laurier University

1 0

smooth backbones
by A G Szabo 16 Nov '15

16 Nov '15

I have no problems with ribbons. However I would like to show some helices as backbones only. How can I achieve the result shown on the attachment for this helix. Don't know where to start looking. Any " Actions" only gave me this. Thank you Arthur G. Szabo Professor Emeritus Wilfrid Laurier University

1 0

isosurface and blobs
by Raffaele Raucci 12 Nov '15

12 Nov '15

Hi all, I imported in chimera a map file with .cube extension. I was able to show isosurface after setting specific isovalue. Can you tell me if it is possible, by command line, count the number of different blobs displayed as isosurface? Is it also possible determine the area and volume of each blob? Thanks in advance, Raphael

3 4

Volume transformation based on Phenix symmetry operators
by Morris, Kyle 12 Nov '15

12 Nov '15

Dear Chimera developers and community, I have a volume and an associated symmetry operator identified by another software package for this map. I would like to transform the map according to the symmetry operator to inspect what the symmetry related map looks like, does anyone know how to do this based on the appended matrix? Thanks in advance for your help! Best wishes, Kyle ================================== >From Phenix: new_operator rota_matrix -0.0877 -0.5114 0.8549 rota_matrix 0.9251 -0.3601 -0.1206 rota_matrix 0.3695 0.7803 0.5047 tran_orth 578.6845 434.1862 -508.9168 center_orth 918.6495 790.3525 1034.0200

2 1

ESP
by Putkey, John 12 Nov '15

12 Nov '15

I have a question about electrostatic surface potential coloring. It works fine when only one .pqr and .dx file is open. I can uncolor, recolor and adjust the ESP color scale, but odd things happen when muliple .pqr and .dx files are open. Strange color patterns are obtained even though the correct MSMS surface and .dx file are selected in the Surface Color dialog box. Its as if the program is reading two .dx files. Is it me or a bug with the system? Cheers John John A. Putkey Professor Biochemistry and Molecular Biology University of Texas Medical School 6431 Fannin Houston Texas, 77030 John.Putkey(a)uth.tmc.edu<mailto:John.Putkey@uth.tmc.edu> (713) 500-6061 Office (713) 500-6062 Laboratory (713) 500-5073 NMR Laboratory

2 1

Chimera 2 release date
by Markus Heller 12 Nov '15

12 Nov '15

Hello, Just curious, what's the anticipated release date for Chimera 2? Couldn't find it on the homepage ... Thanks Markus

2 1

Built-in residue specific annotations in mmCIF?
by Oliver Clarke 12 Nov '15

12 Nov '15

Hi all, As discussed on the ccp4bb (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511>), the mmCIF format incorporates an atom_sites_foornote record (http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_site…) which allows for the direct association of specific comments/annotations with particular atoms/residues. As part of expanding mmCIF support in Chimera2, would it be possible to consider incorporating the capacity to read, write, and display these records as labels or notes? This could be a great way of incorporating built-in-annotations in a structure pertaining to specific features that could potentially be readable by other software such as Coot and pymol. Cheers, Oliver.

2 4

Re: [Chimera-users] compounds
by Elaine Meng 09 Nov '15

09 Nov '15

Dear Dwey, You can use “Join Models” to join any structures that are open as two separate models (from two separate input files). You just couldn’t use the “peptide” option in that tool if they are not peptides; you would have to use the “other bond” option. See the Join Models part of the Build Structure tool for details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> You are more likely to find answers to questions in the User’s Guide than in the chimera-users archive. You can search the User’s Guide with menu: Help… Search Documentation. If that doesn’t help, then emailing the forum (CC’d here) is recommended unless you are including private data. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 9, 2015, at 2:05 PM, MPI <mpi566(a)gmail.com> wrote: > > Dear Elaine > Thanks for kindly answering my questions in Chimera forum. > > I have a question related to compounds and I appreciate your > valuable oppions. > > Let's say I have compound A and compund B. Both have strucctures. > > I would like to use a moiety (part) of compound A and a moeity > (part) of compound B. I wonder if Chimera can combine the desired > moeities of compound A and compound B to generate a new compound C. > > Another simpler version. Can Cimera merge compound A and > compound B into compound D ? > > I checked Chimera list but I found that Chimera provides a > function of joining models NOT for "compounds/drugs" but rather for > "Proteins". I also see you made comments in the past. I wonder if > you can provide insights into "compounds" or some hints to allow me > working on compounds in Chimera. > Many thanks, > Dwey

1 0

obj file origin
by Erin Cutts 08 Nov '15

08 Nov '15

I am trying to use the .obj file generated as a surface mesh. Where the chimera outputs it as a list of vertices (points in 3D), a list of nomals (which I ignore) and a list of faces defined by 3 vertex reference numbers, it is super easy to import this into any mesh handling software. The problem is it seems to reset the orgin (the 0,0,0 point) to some mysterious location. As I am trying to compare this to electrostatics stored in a grid mesh format, where the orgin is specified, it would be nice if I could find out where the .obj has translated the axis coordinates too... The problem could also be caused by Chimera loading the molecule with a translation. All this gets very hard to deal with and trace...Any ideas that doesn't lead to me getting lost in cartesian space?

2 2

3D dashed pseudobond styles?
by Oliver Clarke 07 Nov '15

07 Nov '15

Hi all, Feature request - more 3D psuedobond styles (for missing segments and metal coordination) would be nice. Specifically, small spheres (3D equivalent of dotted line) and cylinders with either rounded or flat ends (3D equivalent of dashed lines) would be very helpful. Often when used in combination with 3X3 or 4X4 supersampling, pseudobonds drawn in wire representation become too thin to see, whereas this is not the case for bonds or other 3D elements of the structure. Normally this doesn’t matter, because I can just redraw these bonds in a vector graphics program, but for stereo figures this doesn’t work. There is already one such option (representing pseudo bonds as sticks), but this looks weird - dashing or dotting is I think desirable to avoid confusion with regular bonds. Also, is there any way to add a custom pseudo bond (not a distance, no label) between a single pair of selected atoms? Similar to the dist command? This would be very helpful, for example, when trying to highlight a handful of specific interactions of a ligand with active site residues. One more while I’m thinking of it - a bit out there and certainly not for chimera 1 - it would be great to have a way of arranging 3D labels for residues such that they are displaced from the structure (perhaps arranged in a circle on the x-y plane), but with lines or arrows connecting them back to the residues they are labeling - this would be particularly great for generating labeled stereo figures, which is otherwise hard to do. Cheers, Oliver.

3 17

resmap
by R.I.Koning＠lumc.nl 05 Nov '15

05 Nov '15

I want to use the colors representing resolution in Resmap to color the surface of my map. From what I understand from the documentation the script that automatically runs after Resmap is finished and “… color the surface of your input map with the results of ResMap…”. This last thing does not happen. Though this script seems to run (I see a slice depicting the remap (in 2D) moving back and forth in chimera somehow only a map with 1 slice opens in Chimera afterwards and I cannot use the resolution color coding for my surface. Should some sort of 3D file be generated that can be used to do this via Surface color or should the coloring be on the surface map by default? Both is not possible now. Best regards, Roman

3 3

Using pip/easy install in Python 2.7.8 included in Chimera
by Ahir Pushpanath 05 Nov '15

05 Nov '15

Dear Chimera Team, As I specifically want to use the python included with chimera as the main python distribution available on my system, I am limited to using the python version shipped with it, as a standard. This is no problem for me, however, I am struggling to get pip /easy install working with the inbuilt python, namely because of errors between "urllib3" and python versions below 2.7.10. So, I keep getting HTTPS errors. Is there any way to use pip and easy install properly with the inbuilt Chimera Python? I did see a section called "import python modules into Chimera", but it appears as though that requires an additional python distribution to be present on the system? Please do let me know. Ahir If the reader of this email is not the intended recipient(s), please be advised that any dissemination, distribution or copying of this information is strictly prohibited. Johnson Matthey Plc has its main place of business at 5th Floor, 25 Farringdon Street, London (020 7269 8400). Johnson Matthey Public Limited Company Registered Office: 5th Floor, 25 Farringdon Street, London EC4A 4AB Registered in England No 33774 Whilst Johnson Matthey aims to keep its network free from viruses you should note that we are unable to scan certain emails, particularly if any part is encrypted or password-protected, and accordingly you are strongly advised to check this email and any attachments for viruses. The company shall not accept any liability with regard to computer viruses transferred by way of email. Please note that your communication may be monitored in accordance with Johnson Matthey internal policy documentation.

1 0