Thanks a lot. Your method B is exactly what I want to get. As for the binding area, it seems that using different methods, I get different values. I tried surfcat command to get the surface area of D, E and DE. and then calculate by (D+E-DE)/2, it gave me 363. but using "measure buriedArea" command it gave me 372 for BaveSAS. Do you know why these two results are not the same even though the difference is small? thanks bobo On Thu, Jan 10, 2013 at 11:59 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Bobo, (A) If you mostly want the area measurement (not display), you can just use the command "measure buriedArea." Use the Favorites menu to show the Chimera command line. Structure 4GLN has 4 chains: D, E, F, and H ... I could see that by rainbow-coloring each chain a different color, for example with Chimera commands:

open 4gln rainbow chain

You can see which chain is which by putting the mouse cursor over them, which will show an information "balloon." So for example, I could measure area between chains E and F with:

measure buriedArea :.e :.f

...or between D+E and F+H with:

measure buriedArea :.d:.e :.f:.h

The information goes to the Reply Log (show using Favorites menu). For details on this command, see: < http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedAre...

...

(B) If you care about display too, then more steps are required. By default, Chimera will make one surface that includes all the protein chains. The "split" command will put each chain in a separate model, for example:

split surface rainbow model

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>

You can see what models you have by showing the Model Panel (also in Favorites menu).

Then you still want to show just the interface. For example, to show only surface of E within 1.5 Angstroms of surface of F:

~surface measure contactArea #0.2 #0.3 1.5 color orange offset 0.1

< http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#contactAr...

...

I had to look in the Model Panel to see what model numbers to use for the "measure contactArea" command. If offset is >0, this command will make a new model, also listed in the Model Panel. To also show the whole surface of E, for example, you could use the command:

surface :.e

(C) instead of B, a completely different approach is to use the Intersurf tool to show an interface surface instead of the molecular surface of either chain. This tool is in the menu under Tools... Surface/Binding Analysis. In that dialog you would choose the two chains and then Apply. You can use the histogram at the bottom to color by distance. You could also use the command "intersurf" to do the same thing. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/intersurf.html> < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/intersurf/intersurf...

...

Example Intersurf result is shown here: < http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/alphabeta/alphabeta.htm...

...

The Intersurf results are more "chunky," not as smooth as the molecular surface(s) shown by method B above.

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 Jan 10, 2013, at 8:21 AM, Bobo Dang wrote:

...

Dear Chimera Users,

I am trying to use Chimera to show the binding surface between two chains in one Model and measure the area of this binding surface,

but I don't know how I can select the bind surface, could anybody give me a hand? the model I am using is 4GLN from PDB.

thanks a lot

bobo

Thanks for the explanation, but still one more thing confuse me. Indeed weather delete waters first then measure buriedArea, or just use measure buriedArea :.d&protein :.e&protein command gave BaveSAS 349. But when I use surfcat, I mean I delete waters first. then use command surfcat 1 :.d surf 1 measure surface area of d, I got 2972.6, I do the same thing for e, surfcat 2 :.e surf 2 I got 5504; then I do that for d,e as one model, surfcat 3 :.d-e surf 3 I got 8117.6.

From these values I do the calculation (2972.6+5504-8117.6)/2=179.5.

This value does not match with BaveSAS 349.4, or BaveSES 186.2. Do you know where the difference come from? Does chimera define different surfaces based on different methods? thanks a lot bobo On Thu, Jan 10, 2013 at 1:54 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Bobo, One issue to be careful about with both "surfcat" and "measure buriedArea" is to NOT include stuff like waters. I forgot to mention that issue in my first reply. You could either delete water first, or when using the commands take care to use specifications that exclude water, something like this:

measure buriedArea :.d&protein :.e&protein

(because there are waters with chain ID D and waters with chain ID E)

When I did that, I got the same answer both ways, BaveSAS 349 for 4gln protein-only. I hope this helps, Elaine

On Jan 10, 2013, at 11:14 AM, Bobo Dang wrote:

...

Thanks a lot.

Your method B is exactly what I want to get.

As for the binding area, it seems that using different methods, I get different values.

I tried surfcat command to get the surface area of D, E and DE. and then calculate by (D+E-DE)/2, it gave me 363. but using "measure buriedArea" command it gave me 372 for BaveSAS. Do you know why these two results are not the same even though the difference is small?

thanks

bobo

On Thu, Jan 10, 2013 at 11:59 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Bobo, (A) If you mostly want the area measurement (not display), you can just use the command "measure buriedArea." Use the Favorites menu to show the Chimera command line. Structure 4GLN has 4 chains: D, E, F, and H ... I could see that by rainbow-coloring each chain a different color, for example with Chimera commands:

open 4gln rainbow chain

You can see which chain is which by putting the mouse cursor over them, which will show an information "balloon." So for example, I could measure area between chains E and F with:

measure buriedArea :.e :.f

...or between D+E and F+H with:

measure buriedArea :.d:.e :.f:.h

The information goes to the Reply Log (show using Favorites menu). For details on this command, see: < http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedAre...

(B) If you care about display too, then more steps are required. By default, Chimera will make one surface that includes all the protein chains. The "split" command will put each chain in a separate model, for example:

split surface rainbow model

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>

You can see what models you have by showing the Model Panel (also in Favorites menu).

Then you still want to show just the interface. For example, to show only surface of E within 1.5 Angstroms of surface of F:

~surface measure contactArea #0.2 #0.3 1.5 color orange offset 0.1

< http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#contactAr...

I had to look in the Model Panel to see what model numbers to use for the "measure contactArea" command. If offset is >0, this command will make a new model, also listed in the Model Panel. To also show the whole surface of E, for example, you could use the command:

surface :.e

(C) instead of B, a completely different approach is to use the Intersurf tool to show an interface surface instead of the molecular surface of either chain. This tool is in the menu under Tools... Surface/Binding Analysis. In that dialog you would choose the two chains and then Apply. You can use the histogram at the bottom to color by distance. You could also use the command "intersurf" to do the same thing. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/intersurf.html> < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/intersurf/intersurf...

Example Intersurf result is shown here: < http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/alphabeta/alphabeta.htm...

The Intersurf results are more "chunky," not as smooth as the molecular surface(s) shown by method B above.

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 Jan 10, 2013, at 8:21 AM, Bobo Dang wrote:

...

Dear Chimera Users,

I am trying to use Chimera to show the binding surface between two chains in one Model and measure the area of this binding surface,

but I don't know how I can select the bind surface, could anybody give me a hand? the model I am using is 4GLN from PDB.

thanks a lot

bobo

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hey Elaine, You are right, I think I didn't make it clear before. Here is where I got the different value: after surfcat, I selected the surface for d chain and use "measure volume and area" in tools->surface and binding assays, then I got a area value, that's where the difference come from. the function "measure volume and area" just gives a volume and a area value, it doesn't distinguish SAS or SES. I checked the manual guide more carefully, it says this function gives the "total surface area of a surface model", but again I don't really understand how chimera define the model. Thanks for your great help. bobo On Thu, Jan 10, 2013 at 4:25 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Bobo, Maybe you were looking at the wrong numbers? I bot 349 with both approaches, surfcat and measure buriedArea.

Here's what I did:

open 4gln delete solvent surfcat one :.d surfcat two :.e surf one surf two surfcat both :.d-e surf both start Reply Log

Reply Log shows total SASA (solvent-accessible surface area) values: one 3772 two 6927 both 10,000

0.5 (3772 + 6927 - 10,000) = 349

measure buriedArea :.d :.e

... also gives 349

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 Jan 10, 2013, at 2:10 PM, Bobo Dang wrote:

...

Thanks for the explanation, but still one more thing confuse me.

Indeed weather delete waters first then measure buriedArea, or just use measure buriedArea :.d&protein :.e&protein command gave BaveSAS 349.

But when I use surfcat, I mean I delete waters first.

then use command

surfcat 1 :.d surf 1

measure surface area of d, I got 2972.6,

I do the same thing for e,

surfcat 2 :.e surf 2

I got 5504;

then I do that for d,e as one model,

surfcat 3 :.d-e surf 3

I got 8117.6.

From these values I do the calculation (2972.6+5504-8117.6)/2=179.5.

This value does not match with BaveSAS 349.4, or BaveSES 186.2.

Do you know where the difference come from? Does chimera define different surfaces based on different methods?

thanks a lot

bobo

On Thu, Jan 10, 2013 at 1:54 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Bobo, One issue to be careful about with both "surfcat" and "measure buriedArea" is to NOT include stuff like waters. I forgot to mention that issue in my first reply. You could either delete water first, or when using the commands take care to use specifications that exclude water, something like this:

measure buriedArea :.d&protein :.e&protein

(because there are waters with chain ID D and waters with chain ID E)

When I did that, I got the same answer both ways, BaveSAS 349 for 4gln protein-only. I hope this helps, Elaine

I got it, thanks for your patient explanation! Really appreciate it. Bobo 发自我的 iPhone 在 Jan 10, 2013，18:10，Elaine Meng <meng@cgl.ucsf.edu> 写道：

Hi Bobo, The molecular surface areas (SASA, SESA) are calculated analytically by the MSMS module.

"Measure Volume and Area" does not perform any analytical calculation, it just adds up the areas of the flat triangles that make up the surface. The smaller the triangles (higher vertex density), the closer to the analytical value.

The "Measure Volume and Area" manual page mentions this a little bit, near the top... <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/measurev...>

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

On Jan 10, 2013, at 4:03 PM, Bobo Dang wrote:

...

Hey Elaine,

You are right, I think I didn't make it clear before.

Here is where I got the different value:

after surfcat, I selected the surface for d chain and use "measure volume and area" in tools->surface and binding assays, then I got a area value, that's where the difference come from.

the function "measure volume and area" just gives a volume and a area value, it doesn't distinguish SAS or SES.

I checked the manual guide more carefully, it says this function gives the "total surface area of a surface model", but again I don't really understand how chimera define the model.

Thanks for your great help.

bobo