problem in loading figures

[hema latha]

Dear Lars Skjaerven,

This is with respect to the figures. I am using core command in trajectory analysis. My input pdbs are 17. I was able to align them and everything was fine. But, when I wanted to plot the core, it is showing the following error message.

Error in plot.new() : figure margins too large

In addition to this, I am also finding difficulty in plotting the RMSD histogram figures as well. It's showing the same error as above. Please kindly let me know how to get out of it.

Thank you in advance.

Regards, Hema.

[Xinqiu Yao]

Hi Hema,

It seems like a problem of improper plotting device size.

Can you provide more information about the commands you used and especially the output message of dev.size()?

Are you plotting to a PDF file or on screen?

Have you closed all your previously opened devices before plotting with dev.off()?

[hema latha]

Dear Xin-Qin Yao, I have used the following commands. 1. files <- list.files("/home/hema/wkdir_R", ".pdb$", full.names = TRUE)

2. pdb <- pdbaln(files) this was done by aligning all the pdbs

3. core <- core.find(pdbs) It has executed successfully... at the end the message was as below

FINISHED: Min vol ( 0.5 ) reached

4.plot(core) Error in plot.new() : figure margins too large

and the dev.size() is as follows

dev.size() [1] 6.652778 1.388889

I have closed all the previously opened devices and re-run the analysis again. even then it's the same error. and I am plotting it on the screen.
Hope I have provided you with all the information.

[Xinqiu Yao]

This is the reason: The height of device, 1.389 inch, is too small. I resized my window and got the same error message.

But I am not sure how this could happen, since by default R pops up a squared window ( 7by7 inches in my case).

When you type the command dev.size(), is there a window showing up?

Can you adjust the window to normal squared size and try plot(core) again?

[hema latha]

Dear Xin-Qin Yao,

I did not see any window showing up when I used dev.size()

however, I got the following new dimensions for dev.size() now. it is

dev.size() [1] 1.388889 1.388889

I am using Rstudio in ubuntu. I have opened only the console window and adjusted to normal size. even then, its the same error.. as before Error in plot.new(): figure margins too large

[hema latha]

Dear Xin-Qin Yao,

I got it solved. I have closed Rstudio and opened R from terminal and have tried it. I got the plot. I could save it in jpeg format.

I have to see if I could plot the RMSD also. Hope it also works. Keep you informed. Thank you