how to write script that can run chemera command
Dear professor: I find a command "delete ligand" can delete ligand from a protein. Then I have thousands of protein contain ligands, how can I write a script to do this command automotically, Thanks for your kindly help.
Best regard Haiping Zhang
Dear Haiping Zhang, Please see this page for instructions on how to write Chimera scripts to process multiple structures:
http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html
Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 18, 2013, at 8:05 PM, 张海平 spr8249618@163.com wrote:
Dear professor: I find a command "delete ligand" can delete ligand from a protein. Then I have thousands of protein contain ligands, how can I write a script to do this command automotically, Thanks for your kindly help.
Best regard Haiping Zhang
Dear professor： Thanks for your help.
Best regards Haiping Zhang
At 2013-09-20 02:02:42,"Elaine Meng" meng@cgl.ucsf.edu wrote:
Dear Haiping Zhang, Please see this page for instructions on how to write Chimera scripts to process multiple structures:
http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html
Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 18, 2013, at 8:05 PM, 张海平 spr8249618@163.com wrote:
Dear professor: I find a command "delete ligand" can delete ligand from a protein. Then I have thousands of protein contain ligands, how can I write a script to do this command automotically, Thanks for your kindly help.
Best regard Haiping Zhang
Dear professor Elaine C. Meng： I have a structure that miss some resides, I want to add a loop to fed the gap. How can I accomplish this by chimera? The structure is as bellow, I want to add some residus to the place where shows dot line. Thanks for your help.
在 2013-09-20 02:02:42，"Elaine Meng" meng@cgl.ucsf.edu 写道：
Dear Haiping Zhang, Please see this page for instructions on how to write Chimera scripts to process multiple structures:
http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html
Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 18, 2013, at 8:05 PM, 张海平 spr8249618@163.com wrote:
Dear professor: I find a command "delete ligand" can delete ligand from a protein. Then I have thousands of protein contain ligands, how can I write a script to do this command automotically, Thanks for your kindly help.
Best regard Haiping Zhang
Dear Haiping Zhang, You can use the Modeller interface for building loops. First show the Sequence for that protein chain (menu: Tools… Sequence… Sequence). This sequence comes from the SEQRES in the PDB file and includes the whole sequence. The part that is missing from the structure is shown with a red outline box. To build the missing part, from the Sequence window menu choose Structure… Modeller (loops/refinement). The Modeller loop-building interface is described here:
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 26, 2013, at 2:59 AM, 张海平 spr8249618@163.com wrote:
Dear professor Elaine C. Meng： I have a structure that miss some resides, I want to add a loop to fed the gap. How can I accomplish this by chimera? The structure is as bellow, I want to add some residus to the place where shows dot line. Thanks for your help.
<截图1.png>
Dear professor Elaine Meng： I can not add a GGGGGGG sequence to the place between 182 and 183 residues by the Modeller interface for building loops. My structure is in a attachment file. Thanks for your help.
best wishes Haiping zhang
在 2013-09-27 04:16:42，"Elaine Meng" meng@cgl.ucsf.edu 写道：
Dear Haiping Zhang, You can use the Modeller interface for building loops. First show the Sequence for that protein chain (menu: Tools… Sequence… Sequence). This sequence comes from the SEQRES in the PDB file and includes the whole sequence. The part that is missing from the structure is shown with a red outline box. To build the missing part, from the Sequence window menu choose Structure… Modeller (loops/refinement). The Modeller loop-building interface is described here:
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 26, 2013, at 2:59 AM, 张海平 spr8249618@163.com wrote:
Dear professor Elaine C. Meng： I have a structure that miss some resides, I want to add a loop to fed the gap. How can I accomplish this by chimera? The structure is as bellow, I want to add some residus to the place where shows dot line. Thanks for your help.
<截图1.png>
Dear Haiping Zhang, I see, your PDB file does not have SEQRES. My previous instructions assumed you had a structure from the PDB database that was missing coordinates for residues that were in SEQRES.
In your case, PDB file without SEQRES, you need to make a sequence file that has the GGGGGG included in the sequence where you want it, in plain text FASTA format: http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
Then open both the structure PDB file (yourfile.pdb) and the sequence FASTA file (yourfile.fasta) in Chimera. Make sure the sequence is associated with the structure (sequence window menu: Structure… Associations), http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association
and then proceed to use the Modeller loop-building interface as in my previous message.
If you never used Modeller with Chimera before, you have to get a Modeller license key to enter into the interface (it is free for noncommercial use, you just have to go to the Modeller website and sign up, they will email it to you).
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 26, 2013, at 6:29 PM, 张海平 spr8249618@163.com wrote:
Dear professor Elaine Meng： I can not add a GGGGGGG sequence to the place between 182 and 183 residues by the Modeller interface for building loops. My structure is in a attachment file. Thanks for your help. best wishes Haiping zhang
I forgot to mention an easy way to get the sequence file in FASTA format:
(1) open your PDB file, then show its Sequence (Chimera menu: Tools… Sequence… Sequence)
(2) save the sequence as FASTA file (sequence window menu: File… Save As, choose file type: aligned FASTA)
(3) in a text-editing program, edit the FASTA file to add the GGG… part. Save yourfile.fasta as plain text from the text-editing program.
Quit from the first sequence window. Open your new fasta file (yourfile.fasta) in Chimera. Associate it with the structure (sequence window menu: Structure… Associations, change from "none" to the hlaa1… sequence, OK. Then use the Modeller interface (sequence window menu: Structure… Modeller (loops/refinement)) to model "non-terminal missing structure" or "all missing structure"
Elaine
On Sep 30, 2013, at 9:45 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Haiping Zhang, I see, your PDB file does not have SEQRES. My previous instructions assumed you had a structure from the PDB database that was missing coordinates for residues that were in SEQRES.
In your case, PDB file without SEQRES, you need to make a sequence file that has the GGGGGG included in the sequence where you want it, in plain text FASTA format: http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
Then open both the structure PDB file (yourfile.pdb) and the sequence FASTA file (yourfile.fasta) in Chimera. Make sure the sequence is associated with the structure (sequence window menu: Structure… Associations), http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association
and then proceed to use the Modeller loop-building interface as in my previous message.
If you never used Modeller with Chimera before, you have to get a Modeller license key to enter into the interface (it is free for noncommercial use, you just have to go to the Modeller website and sign up, they will email it to you).
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 26, 2013, at 6:29 PM, 张海平 spr8249618@163.com wrote:
Dear professor Elaine Meng： I can not add a GGGGGGG sequence to the place between 182 and 183 residues by the Modeller interface for building loops. My structure is in a attachment file. Thanks for your help. best wishes Haiping zhang
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