April 2014 - Chimera-users - RBVI Mailing Lists

Question About Using Chimera In Python Scripts with Other Features
by John Dougherty 28 Apr '14

28 Apr '14

Hello, I am not very computer savvy and very new to programming. I am using Windows 7, Python 2.7.3 32 bit I would like to know if it is possible to use features from Chimera in a python script. For example: from chimera import * from otherprogram import * otherprogram stuff runCommand('blah blah blah') Chimera does some things the other program does not and vice versa. My life would be made much easier if I could just integrate them into one script. I do not understand the instructions about this matter which are posted on the FAQs on the website. Sincerely, -- John J. Dougherty III Biomathematics Major Rutgers, New Brunswick (P) 856 981 9491

2 1

Re: [Chimera-users] (no subject)
by Elaine Meng 28 Apr '14

28 Apr '14

Hi Joshua, The linewidth issue is mentioned in the supersampling documentation, but you wouldn't be expected to know that your problem was related to supersampling in the first place! Most people report encounter it as the lines being too thin rather than being completely invisible. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#supersampling> If you use the Image Save dialog, it reports near the bottom of the dialog the "effective maximum linewidth" given the specified level of supersampling and image pixel dimensions. Elaine On Apr 28, 2014, at 3:43 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Joshua, > I'm glad to hear it worked! And of course you're welcome. Don't hesitate to send other problems or concerns to the list, and I'm sure you're right that others will benefit from having the info Googlable from the list archive. > > --Eric > > On Apr 28, 2014, at 3:39 PM, Joshua Broyde <jb3401(a)c2b2.columbia.edu> wrote: > >> Dear Eric, >> Thank you so much. The first thing I did is change the supersampling from 3x3 to 1x1 and it worked! Thanks so much! >> >> Sincerel, >> Joshua Broyde >> p.s. feel free to share this email with others who have this problem. When I googled "dashed lines not saving chimera".Thanks again! >> >> ----- Original Message ----- >> From: "Eric Pettersen" <pett(a)cgl.ucsf.edu> >> To: "Joshua Broyde" <jb3401(a)c2b2.columbia.edu> >> Cc: chimera-users(a)cgl.ucsf.edu >> Sent: Monday, April 28, 2014 2:06:04 PM >> Subject: Re: [Chimera-users] (no subject) >> >> Hi Joshua, >> The first thing you should do is make sure you have the latest driver installed for your graphics card. Based on the info you provided, I believe the latest release for your card was 4/24/14 -- only 4 days ago! Go to the AMD drivers site here: >> >> >> Download Drivers >> >> >> and input the values for your system to get to the latest drivers. >> If that doesn't help, my best guess as to the issue is that the card/driver can't show dashed lines beyond a certain thickness and that the supersampling done while saving the image requires lines thicker than the card supports (each "tile" of the supersampled image is essentially a zoomed-in depiction of that part of the image and is later sampled down to its final size -- which reduces aliasing artifacts). Therefore the two things to try are to reduce the amount of supersampling as you save the image, or reduce the thickness of the dashed lines before you save the image. >> There is a "Supersample" control on the Save-Image dialog, and there is a "supersample" keyword to the "copy" command, if that's what you're using. >> You can reduce the line width of the hydrogen bonds by bringing up the PseudoBond Panel (in the General Controls tool category) and double clicking on the "hydrogen bonds" group (assuming you've made some hydrogen bonds). The "line width" control is in the lower part of the inspector that comes up. >> I hope one of these things work! :-) >> >> >> --Eric >> >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >> >> >> On Apr 27, 2014, at 3:24 PM, Joshua Broyde < jb3401(a)c2b2.columbia.edu > wrote: >> >> >> Hi, >> >> >> I had a chimera-related problem. When saving images from chimera, chimera is not saving the dashed hbonds (I am NOT using POV-Ray), in the images, even though they appear on the screen. Does this have to do with the graphics driver, or is is there something internally in chimera that is likely causing this? >> I am using the AMD Radeon HD 6450 graphics driver on ubuntu 12.04. When I tried this on another computer with ubuntu 12.10 (using Gallium .04 graphics driver) , it worked fine and the image came out perfectly. This problem happens whether I use chimera 1.8, 1.8.1, or any release after that. >> >> Sincerely, >> Joshua Broyde >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > >

1 0

(no subject)
by Joshua Broyde 28 Apr '14

28 Apr '14

Hi, > I had a chimera-related problem. When saving images from chimera, chimera is not saving the dashed hbonds (I am NOT using POV-Ray), in the images, even though they appear on the screen. Does this have to do with the graphics driver, or is is there something internally in chimera that is likely causing this? > I am using the AMD Radeon HD 6450 graphics driver on ubuntu 12.04. When I tried this on another computer with ubuntu 12.10 (using Gallium .04 graphics driver) , it worked fine and the image came out perfectly. This problem happens whether I use chimera 1.8, 1.8.1, or any release after that. > > Sincerely, > Joshua Broyde

2 1

Print selected
by m.maletta＠nki.nl 28 Apr '14

28 Apr '14

Dear all, I would like to select all the atoms of the chain B that are less than 3.5A far away from chain A. And I would also like to print out all the distances that Chimera finds. I manage to do the first part with this command, but I do not manage to have a list of all the distances found. select #0:.A za<3.5 & #0:.B Is there a way to get the list? Best and thank you in advance Max __________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta(a)nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029

2 2

Multiscale models color
by Hernando J Sosa 26 Apr '14

26 Apr '14

Hi, How do you control the color of the surfaces generated by the multi-scale models command "Make models" so that the user can specify the color associated with each chain? I tried to follow the documentation on how to do this but still I don't get it right as I didn't manage to change the colors assigned by default. Thanks Hernando

2 2

1.9 release candidate
by Eric Pettersen 24 Apr '14

24 Apr '14

Hi everybody, There is a release candidate of Chimera 1.9 on the download page. If you can, please try it out and let us know if you have any problems or questions. The differences between 1.9 and 1.8 are covered in the release notes. Thanks! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Export Pov-Ray file with a python script.
by jiserte＠unq.edu.ar 23 Apr '14

23 Apr '14

I'm writing a small python script to generate Pov-Ray with chimera. The script loads a pdb file containing a protein and a ligand, modifies the protein view to ribbon and the ligand to surface. Then exports the .pov file. However the image created by Pov-Ray shows only the surface of ligand. The image is shown correctly in the chimera GUI. If I run the commands one by one in the chimera command line, the .pov file generated is ok. The script is: ----------------------------------------- import chimera from chimera import runCommand runCommand('windowsize 800 600') runCommand('open ../../kinase.domain.2/A.4K9Y.pdb') runCommand('ribbon #0') runCommand('surf ligand') runCommand('export test.pov') ------------------------------------------ After running the script the ReplyLog contains: ----------------------------------------- A.4K9Y.pdb opened /opt/UCSF/Chimera64-1.7/bin/mscalc 1.400000 2.000000 1 MSMSLIB 1.3 started on hamal Copyright M.F. Sanner (March 2000) Compilation flags Surface A.4K9Y.pdb, category ligand, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 436.845 Total solvent accessible surface area = 772.871 ----------------------------------------- Javier Iserte

3 2

Transparency of selected atoms
by Chinaza Egbuta 23 Apr '14

23 Apr '14

Hi, Is there a way to change the transparency of selected atoms in a model? I am trying to visualize what is behind the plane of my model without using the surface capping function. Thanks! CE Chinaza Egbuta Ph.D. Candidate Department of Pharmacology & SUNY Upstate Cancer Research Institute SUNY Upstate Medical University Syracuse, NY 13210

2 1

Re: [Chimera-users] [chimera-dev] read file by python script and color pdb file with script
by Eric Pettersen 22 Apr '14

22 Apr '14

Hi Sariya, Your "check" file contains this (one) line: 67 23 which means that the residue range you generate is ":67-23" which contains nothing. You want "check" to contain "23 67" so that your residue range becomes ":23-67". --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 21, 2014, at 8:33 PM, Sanjeev Sariya <s.sariya_work(a)ymail.com> wrote: > > I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. > I have chimera in my ~/bin/ > System specs: ubuntu 64 bit, 13.10, 4gb ram > > Below is the command I have used for script-chimera communication > > $ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb > > > I am storing values in listu and want to use them for coloring my file loaded. > > rc("color blue :"+listu[0]+"-"+listu[1]) > > This works well, if hard coded > rc ("color red :55-86") > > I do not get any error. The particular protein length is not colored. > > attached 3 files. > Kindly suggest, how do I proceed. > > > -- > Regards > Sariya > > <Q6UXT6.pdb><y.py><check>_______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

1 0

read file by python script and color pdb file with script
by Sanjeev Sariya 21 Apr '14

21 Apr '14

Hello Chimera team, I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. I have chimera in my ~/bin/ System specs: ubuntu 64 bit, 13.10, 4gb ram Below is the command I have used for script-chimera communication $ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb I am storing values in listu and want to use them for coloring my file loaded. rc("color blue :"+listu[0]+"-"+listu[1]) This works well, if hard coded rc ("color red :55-86") I do not get any error. The particular protein length is not colored. attached 3 files. Kindly suggest, how do I proceed. PS: I had sent the same mail to chimera-dev(a)cgl.ucsf.edu <chimera-dev(a)cgl.ucsf.edu>; Sorry, I didn't find this mailing list before. -- Regards Sariya

1 1

Chimera-users April 2014