[Chimera-users] (no subject)

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 28 15:55:05 PDT 2014


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 at 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 at 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 at cgl.ucsf.edu>
>> To: "Joshua Broyde" <jb3401 at c2b2.columbia.edu>
>> Cc: chimera-users at 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 at 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 at cgl.ucsf.edu 
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users 
>> 
>> 
> 
> 




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