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jmcookie

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[求助] 用DS进行蛋白同源建模时出现错误

以下是运行Build homology models后出现的错误，不知道有哪位了解的，还望指导小弟一下，在下不胜感激！

Build Homology Models

--------------------------------------------------------------------------------
Description
  Builds homology models of a protein sequence using one or more template structures.
Uses MODELER automodel (or loopmodel if Refine Loops is True) to build homology models. An accurate sequence alignment between the model and the template proteins are essential to achieve high quality models.

Set Disulfide Bridges, Cis-Prolines, and Additional Restraints to add modeling restraints. Set Copy Ligands to copy the ligands of the templates to the models as rigid body. If some sequence segments of the model sequence are not aligned with the templates, Refine Loops can be used to build additional refinement models for these segments.


The B-factors provided in homology models represent an average of the B-factors found in template structures from crystallographic origins. These B-factors may be useful for understanding the dynamics of the models, but should not be taken as accurate estimations of thermal motion.


Information
  Name Build Homology Models
Status Error
User jmcookie
DS Version 2.5.0.9167
DS Client Version 2.5.0.9164
System localhost (Windows32)
Start Time 2015-03-18 21:57:31
Finish Time 2015-03-18 21:57:58
Execution Time 00:00:27


Error Messages
  Model FK01.B99990001.pdb not found. Please check MODELER log file (modeler.log).
Model FK01.B99990002.pdb not found. Please check MODELER log file (modeler.log).
Model FK01.B99990003.pdb not found. Please check MODELER log file (modeler.log).
Model FK01.B99990004.pdb not found. Please check MODELER log file (modeler.log).
Model FK01.B99990005.pdb not found. Please check MODELER log file (modeler.log).
Engine failed to generate any model. Please check MODELER log file (modeler.log).
761 1 Traceback (most recent call last): File "modeler.py", line 21, in ? modeller.util.accelrys.generate_clean_pdb(env, code='gi|55669741|pdb|1SIR|A', use_only_aa_chains=True, ligands2copy=[], chains2copy=[], hetsyn=hetsyn) File "C:\Program Files (x86)\Accelrys\PipelinePilot\apps\scitegic\dscore\server\share\modeler\modlib\modeller\util\accelrys.py", line 320, in generate_clean_pdb mdl.read(file=code,model_format='PDB') File "C:\Program Files (x86)\Accelrys\PipelinePilot\apps\scitegic\dscore\server\share\modeler\modlib\modeller\model.py", line 117, in read model_format, model_segment) IOError: pdbnam_____E> Filename for PDB code not found: gi|55669741|pdb|1SIR|A Directories: Extensions : ;.atm;.pdb;.ent;.crd (Also tried prepending 'pdb', and looking for .Z, .gz, .bz2, .7z)  


Input Files
  Build Homology Models Protocol Protocol.pr_xml
Input Sequence Alignment FK01_profile-3SF6.bsml
Input Template Structures 1SIQ.dsv
Input Template Structures 1SIR.dsv
Input Template Structures 2R0M.dsv
Input Template Structures 3SF6.dsv


Output Files
  Build Homology Models Log Output.log


Summary
  Modeler Version : 9v4


Parameters
  Input Sequence Alignment ../Input/FK01_profile-3SF6.bsml
Input Model Sequence FK01
Input Template Structures ../Input/3SF6.dsv, ../Input/1SIQ.dsv, ../Input/1SIR.dsv, ../Input/2R0M.dsv
Cut Overhangs True
Disulfide Bridges  
Cis-Prolines  
Additional Restraints  
Copy Ligands  
Copy Chains  
Reference Template  
Reference Template Copy Regions  
Optimize Sidechains True
Number of Models 5
Start Model Index 1
Optimization Level Low
Refine Loops False
Refine Loops Number of Models 1
Refine Loops Optimization Level Medium
Refine Loops Use DOPE Method True
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