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