Chimera - Saving multiple files
Dear all, I am Elza Fonseca, a PhD student of the University of Porto and I am now learning to do dockings. I am using Chimera for open the results from SwissDock and I would like to save it like a multiple file. However I always get the same error message: "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". I don't understand what "$name or $number" means... May you please help me solving it? I apologize for my ignorance. Best regards, -- Elza Fonseca 00351 966 199 802 PhD student CIIMAR – AGE/EDEC http://www.ciimar.up.pt/researchgroup.php?id=AGE
Hi Elza, This is not a bug, just a question (so it should go to the chimera-users email address only, not chimera-bugs). Literally, you must enter a name that includes either “$name” or “$number” into the output-filename area. Then that part will be replaced by the model name or model number of the individual docking, to create multiple different output filenames. You can’t just enter a name without one of those because multiple names are required for multiple output files, not a single name. You can see the model names and model numbers of the docking results in the “Save models” area of the PDB-saving dialog (Chimera menu: File… Save PDB). For example, if you enter File name in the PDB-saving dialog as: docking$number.pdb It will write model #1.1 to a file named docking1.1.pdb, model #1.2 to a file named docking1.2.pdb, etc. 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 Jun 16, 2016, at 3:48 AM, Elza Sofia Fonseca <fonseca.ess@gmail.com> wrote:
Dear all,
I am Elza Fonseca, a PhD student of the University of Porto and I am now learning to do dockings.
I am using Chimera for open the results from SwissDock and I would like to save it like a multiple file. However I always get the same error message: "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". I don't understand what "$name or $number" means... May you please help me solving it? I apologize for my ignorance.
Hi Elaine, Thank you for your help, but it didn't work... I want the protein - target.pdb (#0) - and the model (#1.1), so I selected these ones and in the name I wrote docking1.1.pdb and the error meaage appeared again... Best regards, 2016-06-16 18:02 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi Elza, This is not a bug, just a question (so it should go to the chimera-users email address only, not chimera-bugs).
Literally, you must enter a name that includes either “$name” or “$number” into the output-filename area. Then that part will be replaced by the model name or model number of the individual docking, to create multiple different output filenames. You can’t just enter a name without one of those because multiple names are required for multiple output files, not a single name.
You can see the model names and model numbers of the docking results in the “Save models” area of the PDB-saving dialog (Chimera menu: File… Save PDB).
For example, if you enter File name in the PDB-saving dialog as:
docking$number.pdb
It will write model #1.1 to a file named docking1.1.pdb, model #1.2 to a file named docking1.2.pdb, etc.
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 Jun 16, 2016, at 3:48 AM, Elza Sofia Fonseca <fonseca.ess@gmail.com> wrote:
Dear all,
I am Elza Fonseca, a PhD student of the University of Porto and I am now learning to do dockings.
I am using Chimera for open the results from SwissDock and I would like to save it like a multiple file. However I always get the same error message: "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". I don't understand what "$name or $number" means... May you please help me solving it? I apologize for my ignorance.
-- *Elza Fonseca* 00351 966 199 802 PhD student *CIIMAR – AGE/EDEC* http://www.ciimar.up.pt/researchgroup.php?id=AGE
Hi Elza, As I tried to describe before, you would NOT enter docking1.1.pdb. You would enter: docking$number.pdb and choose (highlight with mouse) only those two models in the Models part of the dialog. That would give you two output files with names automatically including the numbers. Elaine On Jun 17, 2016, at 12:45 PM, Elza Sofia Fonseca <fonseca.ess@gmail.com> wrote:
Hi Elaine,
Thank you for your help, but it didn't work... I want the protein - target.pdb (#0) - and the model (#1.1), so I selected these ones and in the name I wrote docking1.1.pdb and the error meaage appeared again...
Best regards,
2016-06-16 18:02 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>: Hi Elza, This is not a bug, just a question (so it should go to the chimera-users email address only, not chimera-bugs).
Literally, you must enter a name that includes either “$name” or “$number” into the output-filename area. Then that part will be replaced by the model name or model number of the individual docking, to create multiple different output filenames. You can’t just enter a name without one of those because multiple names are required for multiple output files, not a single name.
You can see the model names and model numbers of the docking results in the “Save models” area of the PDB-saving dialog (Chimera menu: File… Save PDB).
For example, if you enter File name in the PDB-saving dialog as:
docking$number.pdb
It will write model #1.1 to a file named docking1.1.pdb, model #1.2 to a file named docking1.2.pdb, etc.
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 Jun 16, 2016, at 3:48 AM, Elza Sofia Fonseca <fonseca.ess@gmail.com> wrote:
Dear all,
I am Elza Fonseca, a PhD student of the University of Porto and I am now learning to do dockings.
I am using Chimera for open the results from SwissDock and I would like to save it like a multiple file. However I always get the same error message: "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". I don't understand what "$name or $number" means... May you please help me solving it? I apologize for my ignorance.
-- Elza Fonseca
00351 966 199 802
PhD student CIIMAR – AGE/EDEC
http://www.ciimar.up.pt/researchgroup.php?id=AGE _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, I didn't understand the first time, but now it finally worked!!! Thank you very much! Best regards, 2016-06-19 17:13 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi Elza,
As I tried to describe before, you would NOT enter docking1.1.pdb. You would enter: docking$number.pdb
and choose (highlight with mouse) only those two models in the Models part of the dialog. That would give you two output files with names automatically including the numbers.
Elaine
On Jun 17, 2016, at 12:45 PM, Elza Sofia Fonseca <fonseca.ess@gmail.com> wrote:
Hi Elaine,
Thank you for your help, but it didn't work... I want the protein - target.pdb (#0) - and the model (#1.1), so I selected these ones and in the name I wrote docking1.1.pdb and the error meaage appeared again...
Best regards,
2016-06-16 18:02 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>: Hi Elza, This is not a bug, just a question (so it should go to the chimera-users email address only, not chimera-bugs).
Literally, you must enter a name that includes either “$name” or “$number” into the output-filename area. Then that part will be replaced by the model name or model number of the individual docking, to create multiple different output filenames. You can’t just enter a name without one of those because multiple names are required for multiple output files, not a single name.
You can see the model names and model numbers of the docking results in the “Save models” area of the PDB-saving dialog (Chimera menu: File… Save PDB).
For example, if you enter File name in the PDB-saving dialog as:
docking$number.pdb
It will write model #1.1 to a file named docking1.1.pdb, model #1.2 to a file named docking1.2.pdb, etc.
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 Jun 16, 2016, at 3:48 AM, Elza Sofia Fonseca <fonseca.ess@gmail.com> wrote:
Dear all,
I am Elza Fonseca, a PhD student of the University of Porto and I am now learning to do dockings.
I am using Chimera for open the results from SwissDock and I would like to save it like a multiple file. However I always get the same error message: "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". I don't understand what "$name or $number" means... May you please help me solving it? I apologize for my ignorance.
-- Elza Fonseca
00351 966 199 802
PhD student CIIMAR – AGE/EDEC
http://www.ciimar.up.pt/researchgroup.php?id=AGE _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- *Elza Fonseca* 00351 966 199 802 PhD student *CIIMAR – AGE/EDEC* http://www.ciimar.up.pt/researchgroup.php?id=AGE
participants (2)
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Elaine Meng -
Elza Sofia Fonseca