[phenixbb] FW: need suggestion

Terwilliger, Thomas C terwilliger at lanl.gov
Fri May 24 07:53:36 PDT 2013

Hi Afshan,

For building protein into your RNA:protein complex at a resolution of 4.2 A you can:

1. use a protein from the PDB and place it by MR using your RNA as a fixed model. This is the best if you have a search model.

2. take the map at 4.2 A and run phenix.find_helices_strands and set "trace_chain=False" and then try to find helices and strands. This might work.

3. take the RNA and data and current map and run autobuild with input_lig_file_list=my_rna.pdb to mark the RNA positions.   This won't work well at this resolution.

all the best,
Tom T

On May 24, 2013, at 12:00 AM, <afshan490 at yahoo.com<mailto:afshan490 at yahoo.com>>
 <afshan490 at yahoo.com<mailto:afshan490 at yahoo.com>> wrote:

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From: Afshan Begum <afshan490 at yahoo.com<mailto:afshan490 at yahoo.com>>;
To: phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> <phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>>;
Subject: need suggestion
Sent: Thu, May 23, 2013 9:40:15 AM

 Dear ALL,

I need the suggetion s from you to solve my problem, I have having one complex data set RNA and protein complex which obtained at 4.2 A, RNA molecules is placed at the right place where it would be after running MR in ccp4, and after that i have seen clear density for the protein which is near about 14 KDa but i can not bulid it manually as i know there would be some option in phaser to place protein moleuules in that proper palce but i dont know how to do it, could you kindly help me i would be really appreciate for your kind help.

Many thanks

Best Regards


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