Elaine Thanks for your message. I was able to find that page by typing the url into my browser. There are six subunits that I wish to show the surfaces in different colors. After splitting the model, I was able to visualize the surfaces of the first four of the subunits, #0.15 to #0.18. I at first was not able to image the surface of #0.19, nor of #0.20 So in the case of #0.19 I changed vdwdefine +.01 and it worked. I selected #0.20, set my cursor after vdwdefine +.01 hit return and it did not work. Eventually it did work with vbdwdefine .03 oK good so far. I decided to change the color of the last C-terminal residues of #0.20 - success. I went back to #0.16 and selected the last three residues and tried to change the color, nothing happened. So I selected the entire chain of #0.16 and attempted to change the color, and again nothing happened. I can tell it was selected because the sequence of#0.16 is highlighted in green, and I can see parts of the green outline under its surface. I changed the vdwdefine command to have +.00, nothing happened, deleted vdwdefine from the command line, again nothing happened, even when I tried to hide the surface. I am likely not doing something in the correct sequence, but cannot figure out what is the problem As I indicated I was able to image the surface of #0.16 before without using vdwdefine. Help!!!! Thanks arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: August-18-16 2:43 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] splitting and surfaces Hi Arthur, Yes it would be better if the URL in the message was more usable, but I’d asked the other developers before, and for some reason it wasn’t possible to make it a link or copyable there (however, the same text is also shown in the Reply Log, and you can copy the URL from there). Anyway, you can use this link: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> ...or you can reach your own copy using menu: Help… Search Documentation, searching for “surface failures” and using the top link in the results. Similar to your problem, it is difficult for us to access anything that you attach as winmail.dat. I can only suggest you try the molmap method in the page linked above, for example, command: molmap #0.7&protein 4 The last number is an adjustable parameter, see the page linked above for links to the molmap manpage and information how to otherwise deal with the resulting surface. 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 Aug 18, 2016, at 10:57 AM, A G Szabo <agszabo@bell.net> wrote:

I am working on a large multi subunit structure (4CR2). Originally I selected one of the subunits, and received the error message that suggested I should use the split command. Which I did and obviously I must have been successful in splitting the subunits.

Each of the subunits is now labelled as being split, i.e. (#0.14) etc.

I was successful in showing the surfaces of 4 subunits, and colored them differently.

However, when I tried to show the surface of one of the subunits with 437 residues, (several residues cannot be resolved) I received this error message

One subunit which I successfully was able to show the surface in the image had 467 residues and also had a large number of residues that were not resolvable.

So I am stuck!

Your help would be appreciated.

AGSzabo <winmail.dat>

Further to my last message regarding surfaces it would be highly convenient to have the url listed at the bottom of the error message open as a link. Secondly it is not even possible to copy it and paste it into my browser.

ags

Elaine I too do not know what was happening but I seem to have been able to sort things out. Your suggestion of using “vdwdefine +.01 #0.15" may prove useful in the future. Thanks arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: August-18-16 3:23 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] splitting and surfaces Hi Arthur, I really can’t tell what is going on. I would just say that if you use command “vdwdefine” without specifying the model in the command, it will apply to all models. It will not automatically use what is selected unless you enter “sel” as the specification. Actually, don’t bother selecting for that purpose, just use a command like “vdwdefine +.01 #0.15" “vdwdefine +0” does nothing, it adds zero to current radius. If you want to back to defaults, command is “~vdwdefine” As for coloring, I can’t tell what you mean by “attempted to change the color” … if you mean you used the menu Actions… Color, then I can only say to check on what the coloring is applying to, menu: Actions… Color… all options, see “Coloring applies to” on the right side of the resulting dialog. Best, Elaine

On Aug 18, 2016, at 12:13 PM, A G Szabo <agszabo@bell.net> wrote:

Elaine

Thanks for your message. I was able to find that page by typing the url into my browser.

There are six subunits that I wish to show the surfaces in different colors. After splitting the model, I was able to visualize the surfaces of the first four of the subunits, #0.15 to #0.18. I at first was not able to image the surface of #0.19, nor of #0.20

So in the case of #0.19 I changed

vdwdefine +.01

and it worked.

I selected #0.20, set my cursor after vdwdefine +.01 hit return and it did not work. Eventually it did work with vbdwdefine .03

oK good so far.

I decided to change the color of the last C-terminal residues of #0.20 - success.

I went back to #0.16 and selected the last three residues and tried to change the color, nothing happened. So I selected the entire chain of #0.16 and attempted to change the color, and again nothing happened. I can tell it was selected because the sequence of#0.16 is highlighted in green, and I can see parts of the green outline under its surface. I changed the vdwdefine command to have +.00, nothing happened, deleted vdwdefine from the command line, again nothing happened, even when I tried to hide the surface.

I am likely not doing something in the correct sequence, but cannot figure out what is the problem As I indicated I was able to image the surface of #0.16 before without using vdwdefine.

Help!!!!

Thanks

arthur