Subject: WHATIF

From: Deepak Singh <[email-masked]>
Date: Wed, 11 Mar 1998 09:08:16 -0800

Dear CCLers,

	I have several WHAT IF related questions, the answers to which, I will
be glad to summarize.

(i) When I add hydrogens to a pdb file for rhodopsin (without rh loops)
I lose my retinal chromophore on using the MAKMOL command after ADDHYD. 
I have no idea why.

(ii) On trying to model another visual protein with the PIRPSQ menu, I
get trouble too.  I create a .pir file for rhodopsin using the command
SOUPIR. Somehow I seem to lose a few residues here.  Anyway after making
all the mutations right in the .pir sequence manually comparing
sequences on paper, I use the BLDPIR command ad get the following error
message :

ERROR. There are not enough residues in the soup. This could be a bug...

Could anybody explain these?

Thanks

Deepak.

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Deepak Singh			    Tel : (315)443 1739 (w)
Graduate Student			  (315)472 9659 (h)	
Dept. of Chemistry		    Fax : (315)443 4070
Syracuse University		  email : [email-masked]
1-104 Scitech Syracuse		    URL : http://web.syr.edu/~desingh
NY 13210

 ......there is no dark side of the moon
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