Hello Herman and others,

I am somewhat concerned after reading the following comment:

"In pymol there is the infamous carve option, which can be used to select density for specific fragments and which can make bad density look good if you carve very tightly around your fragment."

I have been using PyMol to generate figures of electron density by creating .ccp4 format maps and displaying them in PyMol, using the option carve=1.6 as recommended by the PyMol Wiki. After reading Herman's reply, I am concerned that the figures I have been making don't accurately represent my density map. I haven't really found any information about what the "carve" option is actually doing. Can anyone comment on the proper way to display .ccp4 maps in PyMol so that they accurately depict the map without "making bad density look good" (or good density look bad for that matter)? Alternatively, is there a better method for making figures of density that does not involve PyMol, or eliminates any potential problems related to the carve option as Herman alluded to?

Thanks in advance for any advice,

Mike Thompson




----- Original Message -----
From: "Herman Schreuder" <[log in to unmask]>
To: [log in to unmask]
Sent: Friday, January 14, 2011 7:08:48 AM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] how to generate density map of selected residues

Hi Jie,

What is the purpose of generating density of a selected fragment? In
pymol there is the infamous carve option, which can be used to select
density for specific fragments and which can make bad density look good
if you carve very tightly around your fragment.

I usually delete the residues of interest from the pdb and calculate an
omit map. The resulting difference (FOFCWT) map will show a relatively
unbiased density for the omitted residues.

Best,
Herman

-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of jy
Sent: Friday, January 14, 2011 2:03 PM
To: [log in to unmask]
Subject: [ccp4bb] how to generate density map of selected residues

Hi All,

I tried the "mask map" function in COOT to generate density map of
selected fragment. However, the map looked much better than the original
2Fo-Fc map. For example, weak density now became strong density.

I am wondering whether the mask map I generated using default is
actually a Fc map? is there a parameter setting to make it reflect the
true map?

Also, is there a way to select non-continuous residues other than a
segment? or what is a better program to do the job?

Thanks a lot!

Jie Yang

-- 
Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

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