Good afternoon, I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script: with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: lines=f.readlines() cluster_number = 1 for i in range(len(lines)): frame = i if mdInfo["frame number"] == frame: name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand('write format pdb 0 $name) which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered. However, this script is not working, and I would greatly thank any help you could provide me with. Lorena. -- <http://www.uab.cat> Lorena Roldán Martín *PhD Student in Bioinformatics* Departament de Química Unitat de Química Física Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 690799431 www.uab.cat <http://www.uab.cat> <https://orcid.org/0000-0002-6902-8285><https://www.linkedin.com/in/lorena-roldan-biomedica/>
Hi Lorena, I don't think a per-frame script is really the approach you want. What you want to do is open your trajectory, use "coordset" commands to go to the representative frames, and then write them out. Here's a possible script (that you would run simply be opening it with the "open" command [make sure the file name ends in '.py']): from chimera import runCommand with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: cluster_number = 1 for line in f: if line.startswith('#'): #comment line continue runCommand("coordset #0 " + line.strip().split()[0]) name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand("write format pdb 0 " + name) cluster_number += 1 --Eric Eric Pettersen UCSF Computer Graphics Lab
On Dec 23, 2020, at 8:20 AM, Lorena Roldán <Lorena.Roldan@uab.cat> wrote:
Good afternoon,
I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script:
with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: lines=f.readlines() cluster_number = 1 for i in range(len(lines)): frame = i if mdInfo["frame number"] == frame: name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand('write format pdb 0 $name)
which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered.
However, this script is not working, and I would greatly thank any help you could provide me with.
Lorena.
-- <http://www.uab.cat/> Lorena Roldán Martín PhD Student in Bioinformatics
Departament de Química Unitat de Química Física
Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain
+34 690799431 www.uab.cat <http://www.uab.cat/>
<https://orcid.org/0000-0002-6902-8285> <https://www.linkedin.com/in/lorena-roldan-biomedica/>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Eric, Thank you so much for your quick response. I have tried the script you sent me and the only problem with this is that all the PDBs saved correspond to the same frame, although I have tested that the frames are correctly parsed to the coordset command. I have also loaded the full trajectory to the MD movie and visualized every single frame. Do you know why this might happen? Thank you, Lorena
El 23 dic 2020, a las 19:31, Eric Pettersen <pett@cgl.ucsf.edu> escribió:
Hi Lorena, I don't think a per-frame script is really the approach you want. What you want to do is open your trajectory, use "coordset" commands to go to the representative frames, and then write them out. Here's a possible script (that you would run simply be opening it with the "open" command [make sure the file name ends in '.py']):
from chimera import runCommand with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: cluster_number = 1 for line in f: if line.startswith('#'): #comment line continue runCommand("coordset #0 " + line.strip().split()[0]) name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand("write format pdb 0 " + name) cluster_number += 1
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Dec 23, 2020, at 8:20 AM, Lorena Roldán <Lorena.Roldan@uab.cat <mailto:Lorena.Roldan@uab.cat>> wrote:
Good afternoon,
I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script:
with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: lines=f.readlines() cluster_number = 1 for i in range(len(lines)): frame = i if mdInfo["frame number"] == frame: name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand('write format pdb 0 $name)
which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered.
However, this script is not working, and I would greatly thank any help you could provide me with.
Lorena.
-- <http://www.uab.cat/> Lorena Roldán Martín PhD Student in Bioinformatics
Departament de Química Unitat de Química Física
Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain
+34 690799431 www.uab.cat <http://www.uab.cat/>
<https://orcid.org/0000-0002-6902-8285> <https://www.linkedin.com/in/lorena-roldan-biomedica/>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Finally solved! runCommand("coordset #0 " + line.strip().split()[0] + “; wait 1”) did the trick. Thank you so much, Merry Christmas and Happy New Year Lorena
El 23 dic 2020, a las 19:31, Eric Pettersen <pett@cgl.ucsf.edu> escribió:
Hi Lorena, I don't think a per-frame script is really the approach you want. What you want to do is open your trajectory, use "coordset" commands to go to the representative frames, and then write them out. Here's a possible script (that you would run simply be opening it with the "open" command [make sure the file name ends in '.py']):
from chimera import runCommand with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: cluster_number = 1 for line in f: if line.startswith('#'): #comment line continue runCommand("coordset #0 " + line.strip().split()[0]) name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand("write format pdb 0 " + name) cluster_number += 1
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Dec 23, 2020, at 8:20 AM, Lorena Roldán <Lorena.Roldan@uab.cat <mailto:Lorena.Roldan@uab.cat>> wrote:
Good afternoon,
I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script:
with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: lines=f.readlines() cluster_number = 1 for i in range(len(lines)): frame = i if mdInfo["frame number"] == frame: name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand('write format pdb 0 $name)
which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered.
However, this script is not working, and I would greatly thank any help you could provide me with.
Lorena.
-- <http://www.uab.cat/> Lorena Roldán Martín PhD Student in Bioinformatics
Departament de Química Unitat de Química Física
Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain
+34 690799431 www.uab.cat <http://www.uab.cat/>
<https://orcid.org/0000-0002-6902-8285> <https://www.linkedin.com/in/lorena-roldan-biomedica/>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Glad you were able to figure it out! I'm surprised that coordset requires a 'wait' to work, but not totally shocked I guess. :-) --Eric
On Dec 24, 2020, at 3:02 AM, Lorena Roldán Martín <lorena.roldan@uab.cat> wrote:
Finally solved! runCommand("coordset #0 " + line.strip().split()[0] + “; wait 1”) did the trick.
Thank you so much, Merry Christmas and Happy New Year Lorena
El 23 dic 2020, a las 19:31, Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> escribió:
Hi Lorena, I don't think a per-frame script is really the approach you want. What you want to do is open your trajectory, use "coordset" commands to go to the representative frames, and then write them out. Here's a possible script (that you would run simply be opening it with the "open" command [make sure the file name ends in '.py']):
from chimera import runCommand with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: cluster_number = 1 for line in f: if line.startswith('#'): #comment line continue runCommand("coordset #0 " + line.strip().split()[0]) name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand("write format pdb 0 " + name) cluster_number += 1
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Dec 23, 2020, at 8:20 AM, Lorena Roldán <Lorena.Roldan@uab.cat <mailto:Lorena.Roldan@uab.cat>> wrote:
Good afternoon,
I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script:
with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: lines=f.readlines() cluster_number = 1 for i in range(len(lines)): frame = i if mdInfo["frame number"] == frame: name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand('write format pdb 0 $name)
which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered.
However, this script is not working, and I would greatly thank any help you could provide me with.
Lorena.
-- <http://www.uab.cat/> Lorena Roldán Martín PhD Student in Bioinformatics
Departament de Química Unitat de Química Física
Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain
+34 690799431 www.uab.cat <http://www.uab.cat/>
<https://orcid.org/0000-0002-6902-8285> <https://www.linkedin.com/in/lorena-roldan-biomedica/>
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participants (3)
-
Eric Pettersen -
Lorena Roldán -
Lorena Roldán Martín