[sharp-discuss] Problem trying to use partial model as external phase information

Gupta, Yogesh yogesh.gupta at mssm.edu
Thu Apr 23 03:22:27 CEST 2015


Just add "model_"  to your pdb file name. For example, if your file name is test.pdb, change its name to


Yogesh Gupta, PhD
Assistant Professor
Dept. of Structural and Chemical Biology
Mount Sinai School of Medicine
1425 Madison Ave, Icahn/East Bldg. Room # 16-23B
New York, NY 10029
Tel: +1-212-659-8713
From: sharp-discuss [sharp-discuss-bounces at globalphasing.com] on behalf of Kevin [chenqf at gmail.com]
Sent: Wednesday, April 22, 2015 7:47 PM
To: sharp-discuss at globalphasing.com
Subject: [sharp-discuss] Problem trying to use partial model as external phase information

Hi all,

Recently I was able to get the density map of a protein at fairly low resolution (~3.8A) using SIRAS in SHARP. Since it is a membrane protein and the secondary structures are mostly transmembrane helices connected by loops, I was able to build a rough partial poly ala model except some broken loop regions. I wanted to try the external phase information feature in SHARP and followed the manual to generate Hendrickson-Lattman coefficients, however, I was not able to see my partial model in the drop down list in "Phase Improvement and Interpretation Panel". I can see some other pdb files but not the one I uploaded, which was in the datafiles directory when I manually checked it. Does the pdb file need some special headers in order to be visible in the list?

Any help will be appreciated.

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