Bug (?) with EnsembleCluster
I was trying to carry out a cluster analysis from three mdcrd trajectories from Amber 9. I reported here yesterday that I was unable to input more that one mdcrd (in gz form) to Chimera. Therefore, I combined the mdcrd files with ptraj in Amber 9, while stripping all water molecules, all lipid, and box information, leaving only the protein with ligand. That combined mdcrd loaded perfectly into Chimera MD Movie saving a pdb file (there was no option "save all frames" suggested by Elaine's email; I did not select anything else than "untranformed coordinates") Opened successfully this pdb into Chimera, Tools, MD/EnsembleAnalysis, EnsembleCluster, select the new file, finally click on OK: that resulted in Chimera Error. This was a first trial, though I have right taken the opportunity to submit an alleged bug from the window inviting to do so. From a perusal of Reply Log, I was unable to grasp the nature of the failure. In particular, lacking documentation for ksdssp, I was unable to run it (to assign the lacking secondary structure of the protein) with different parameters from used energy cutoff -0.5 minimum helix length 3 minimum strand length 3 and commands as from Log. Perhaps I should also mention that lack of secondary structure is typical of the long procedure through different programs to carry our (1) model building, (2) docking, (3) MD. Thanks francesco ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping
Hi Francesco, On Jan 5, 2008, at 12:34 AM, Francesco Pietra wrote:
I was trying to carry out a cluster analysis from three mdcrd trajectories from Amber 9.
I reported here yesterday that I was unable to input more that one mdcrd (in gz form) to Chimera. Therefore, I combined the mdcrd files with ptraj in Amber 9, while stripping all water molecules, all lipid, and box information, leaving only the protein with ligand.
That combined mdcrd loaded perfectly into Chimera MD Movie saving a pdb file (there was no option "save all frames" suggested by Elaine's email; I did not select anything else than "untranformed coordinates")
As I said in previous messages, you have to view all the frames you want to save (actually play through the trajectory) before you can save them. Even if the dialog says "N frames" the coordinates are not read until they are viewed. So if you didn't view them, there is no "save all frames" option, it won't save multiple structures, and the saved PDB will not work in the ensemble tools.
Opened successfully this pdb into Chimera, Tools, MD/EnsembleAnalysis, EnsembleCluster, select the new file, finally click on OK:
that resulted in Chimera Error. This was a first trial, though I have right taken the opportunity to submit an alleged bug from the window inviting to do
Probably your file did not contain multiple structures, as explained above.
so. From a perusal of Reply Log, I was unable to grasp the nature of the failure. In particular, lacking documentation for ksdssp, I was unable to run it (to assign the lacking secondary structure of the protein) with different parameters from used
energy cutoff -0.5 minimum helix length 3 minimum strand length 3
and commands as from Log.
Perhaps I should also mention that lack of secondary structure is typical of the long procedure through different programs to carry our (1) model building, (2) docking, (3) MD.
We realize this is a common situation, and that is why Chimera is able to calculate secondary structure automatically. The message about lack of secondary structure is not an error message or complaint about a problem. It is just an "informational message" that Chimera is automatically running ksdssp for you to calculate the secondary structure assignments since they weren't in the file. Thus, you do not need to run ksdssp yourself unless you wanted to, and I don't think ksdssp is involved in your problems here. However, you can run ksdssp with a command or from the Model Panel. Documentation: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html If you choose Help... Search Documentation from the Chimera menu and search for "ksdssp" that is the top hit. I hope this clarifies things, Elaine
Elaine: Although I could argue that the "Report Bug" window was misleading, I am better saying that I was stupid enough. francesco --- Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco,
On Jan 5, 2008, at 12:34 AM, Francesco Pietra wrote:
I was trying to carry out a cluster analysis from three mdcrd trajectories from Amber 9.
I reported here yesterday that I was unable to input more that one mdcrd (in gz form) to Chimera. Therefore, I combined the mdcrd files with ptraj in Amber 9, while stripping all water molecules, all lipid, and box information, leaving only the protein with ligand.
That combined mdcrd loaded perfectly into Chimera MD Movie saving a pdb file (there was no option "save all frames" suggested by Elaine's email; I did not select anything else than "untranformed coordinates")
As I said in previous messages, you have to view all the frames you want to save (actually play through the trajectory) before you can save them. Even if the dialog says "N frames" the coordinates are not read until they are viewed. So if you didn't view them, there is no "save all frames" option, it won't save multiple structures, and the saved PDB will not work in the ensemble tools.
Opened successfully this pdb into Chimera, Tools, MD/EnsembleAnalysis, EnsembleCluster, select the new file, finally click on OK:
that resulted in Chimera Error. This was a first trial, though I have right taken the opportunity to submit an alleged bug from the window inviting to do
Probably your file did not contain multiple structures, as explained above.
so. From a perusal of Reply Log, I was unable to grasp the nature of the failure. In particular, lacking documentation for ksdssp, I was unable to run it (to assign the lacking secondary structure of the protein) with different parameters from used
energy cutoff -0.5 minimum helix length 3 minimum strand length 3
and commands as from Log.
Perhaps I should also mention that lack of secondary structure is typical of the long procedure through different programs to carry our (1) model building, (2) docking, (3) MD.
We realize this is a common situation, and that is why Chimera is able to calculate secondary structure automatically. The message about lack of secondary structure is not an error message or complaint about a problem. It is just an "informational message" that Chimera is automatically running ksdssp for you to calculate the secondary structure assignments since they weren't in the file.
Thus, you do not need to run ksdssp yourself unless you wanted to, and I don't think ksdssp is involved in your problems here. However, you can run ksdssp with a command or from the Model Panel. Documentation: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html If you choose Help... Search Documentation from the Chimera menu and search for "ksdssp" that is the top hit.
I hope this clarifies things, Elaine
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Hi Francesco, I agree it can be confusing - the error dialog always includes the "report bug" button, but it is not always a bug when that dialog appears. We will have to look at your report to try to figure out what was happening in your case. We are still looking into the mdcrd.gz file issue. In my tests, I could successfully specify multiple (uncompressed) mdcrd files as input to MD Movie. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 5, 2008, at 1:26 PM, Francesco Pietra wrote:
Elaine: Although I could argue that the "Report Bug" window was misleading, I am better saying that I was stupid enough. francesco
Hi Elaine: As I said privately, ptraj failed to remove one molecule of water. I loaded mdcr pmrtop to Chimera, saved the pdb, stripped that water (better: wrote the lines that do not contain water) from the 549 models with f=open("prod1-3.pdb", "r") for line in f: line=line.rstrip() if "WAT" not in line: print line f.close() outputting the edited file with tee. The file is nice, it starts with 13 instances of helix (built by Chimera, as there was no such information at any stage), and contains 549 models. With the desktop I use for Chimera (total 1GB ram) there is no way to open this pdb. I removed from gnome all that was possible to remove except Chimera. Opened top -i in parallel, which showed python to take rapidly about 99% memory. I left the system on overnight: little mem and cpu were in use, though Chimera had not opened the file. This is not to compare, simply to assure that the pdb is not bad: it can be rapidly opened with vmd, which play all 549 models. Though, I have to go through Chimera. So that, it seems to me that pure python finds problems with long trajectories. As a naive user (who might well be wrong) I would add some fast code to help python. An alternative is to add ram; don't know if my old mainboard can add ram. I can't install Chimera on the amd64 parallel machine, where ram is plenty (4GB per processor). I can't even install X. --- Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, I agree it can be confusing - the error dialog always includes the "report bug" button, but it is not always a bug when that dialog appears. We will have to look at your report to try to figure out what was happening in your case.
We are still looking into the mdcrd.gz file issue. In my tests, I could successfully specify multiple (uncompressed) mdcrd files as input to MD Movie. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Jan 5, 2008, at 1:26 PM, Francesco Pietra wrote:
Elaine: Although I could argue that the "Report Bug" window was misleading, I am better saying that I was stupid enough. francesco
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The only advice I have (which you may have already tried) is to also strip the lipid bilayer using basically the same method as you did with the water. --Eric On Jan 6, 2008, at 11:15 PM, Francesco Pietra wrote:
Hi Elaine: As I said privately, ptraj failed to remove one molecule of water.
I loaded mdcr pmrtop to Chimera, saved the pdb, stripped that water (better: wrote the lines that do not contain water) from the 549 models with
f=open("prod1-3.pdb", "r") for line in f: line=line.rstrip() if "WAT" not in line: print line f.close()
outputting the edited file with tee.
The file is nice, it starts with 13 instances of helix (built by Chimera, as there was no such information at any stage), and contains 549 models.
With the desktop I use for Chimera (total 1GB ram) there is no way to open this pdb. I removed from gnome all that was possible to remove except Chimera. Opened top -i in parallel, which showed python to take rapidly about 99% memory. I left the system on overnight: little mem and cpu were in use, though Chimera had not opened the file.
This is not to compare, simply to assure that the pdb is not bad: it can be rapidly opened with vmd, which play all 549 models. Though, I have to go through Chimera. So that, it seems to me that pure python finds problems with long trajectories. As a naive user (who might well be wrong) I would add some fast code to help python. An alternative is to add ram; don't know if my old mainboard can add ram. I can't install Chimera on the amd64 parallel machine, where ram is plenty (4GB per processor). I can't even install X.
--- Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, I agree it can be confusing - the error dialog always includes the "report bug" button, but it is not always a bug when that dialog appears. We will have to look at your report to try to figure out what was happening in your case.
We are still looking into the mdcrd.gz file issue. In my tests, I could successfully specify multiple (uncompressed) mdcrd files as input to MD Movie. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Jan 5, 2008, at 1:26 PM, Francesco Pietra wrote:
Elaine: Although I could argue that the "Report Bug" window was misleading, I am better saying that I was stupid enough. francesco
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The lipid, all solvation water, and box information were removed by ptraj. I used python to remove the single water molecule of crystallization. There is nothing else than the protein and the ligand in the pdb. This is clear both from vmd and a text editor. francesco --- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
The only advice I have (which you may have already tried) is to also strip the lipid bilayer using basically the same method as you did with the water.
--Eric
On Jan 6, 2008, at 11:15 PM, Francesco Pietra wrote:
Hi Elaine: As I said privately, ptraj failed to remove one molecule of water.
I loaded mdcr pmrtop to Chimera, saved the pdb, stripped that water (better: wrote the lines that do not contain water) from the 549 models with
f=open("prod1-3.pdb", "r") for line in f: line=line.rstrip() if "WAT" not in line: print line f.close()
outputting the edited file with tee.
The file is nice, it starts with 13 instances of helix (built by Chimera, as there was no such information at any stage), and contains 549 models.
With the desktop I use for Chimera (total 1GB ram) there is no way to open this pdb. I removed from gnome all that was possible to remove except Chimera. Opened top -i in parallel, which showed python to take rapidly about 99% memory. I left the system on overnight: little mem and cpu were in use, though Chimera had not opened the file.
This is not to compare, simply to assure that the pdb is not bad: it can be rapidly opened with vmd, which play all 549 models. Though, I have to go through Chimera. So that, it seems to me that pure python finds problems with long trajectories. As a naive user (who might well be wrong) I would add some fast code to help python. An alternative is to add ram; don't know if my old mainboard can add ram. I can't install Chimera on the amd64 parallel machine, where ram is plenty (4GB per processor). I can't even install X.
--- Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, I agree it can be confusing - the error dialog always includes the "report bug" button, but it is not always a bug when that dialog appears. We will have to look at your report to try to figure out what was happening in your case.
We are still looking into the mdcrd.gz file issue. In my tests, I could successfully specify multiple (uncompressed) mdcrd files as input to MD Movie. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Jan 5, 2008, at 1:26 PM, Francesco Pietra wrote:
Elaine: Although I could argue that the "Report Bug" window was misleading, I am better saying that I was stupid enough. francesco
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Hi Francesco, I guess I do have a further suggestion which is to reduce the structure to just those residues that are interacting with the ligand at any time during the trajectory. The basic idea would be to run the trajectory to select those residues and then write a PDB file with just selected residues in it. Here's a recipe: open your trajectory delete solvent delete the lipid bilayer bring up the "Define script..." dialog from MD Movie's Per-Frame menu define a "Chimera commands" script that is just: select ligand z<N [where N is the distance you want to consider as "interacting"] click OK this will select the appropriate residues in the first frame. We want the selection to aggregate as the trajectory plays so we need to change the selection mode... choose Select->Selection Mode->append run the trajectory once the trajectory has played through, all residues that were ever within the cutoff distance will be selected. You may be interested in the list itself. You can write it out with: Actions->Write List... You can write a PDB limited to just the selected residues the same way you wrote the PDB before, just with the "Save selected atoms only" check button on. --Eric On Jan 7, 2008, at 12:50 PM, Francesco Pietra wrote:
The lipid, all solvation water, and box information were removed by ptraj. I used python to remove the single water molecule of crystallization. There is nothing else than the protein and the ligand in the pdb. This is clear both from vmd and a text editor. francesco --- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
The only advice I have (which you may have already tried) is to also strip the lipid bilayer using basically the same method as you did with the water.
--Eric
On Jan 6, 2008, at 11:15 PM, Francesco Pietra wrote:
Hi Elaine: As I said privately, ptraj failed to remove one molecule of water.
I loaded mdcr pmrtop to Chimera, saved the pdb, stripped that water (better: wrote the lines that do not contain water) from the 549 models with
f=open("prod1-3.pdb", "r") for line in f: line=line.rstrip() if "WAT" not in line: print line f.close()
outputting the edited file with tee.
The file is nice, it starts with 13 instances of helix (built by Chimera, as there was no such information at any stage), and contains 549 models.
With the desktop I use for Chimera (total 1GB ram) there is no way to open this pdb. I removed from gnome all that was possible to remove except Chimera. Opened top -i in parallel, which showed python to take rapidly about 99% memory. I left the system on overnight: little mem and cpu were in use, though Chimera had not opened the file.
This is not to compare, simply to assure that the pdb is not bad: it can be rapidly opened with vmd, which play all 549 models. Though, I have to go through Chimera. So that, it seems to me that pure python finds problems with long trajectories. As a naive user (who might well be wrong) I would add some fast code to help python. An alternative is to add ram; don't know if my old mainboard can add ram. I can't install Chimera on the amd64 parallel machine, where ram is plenty (4GB per processor). I can't even install X.
--- Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, I agree it can be confusing - the error dialog always includes the "report bug" button, but it is not always a bug when that dialog appears. We will have to look at your report to try to figure out what was happening in your case.
We are still looking into the mdcrd.gz file issue. In my tests, I could successfully specify multiple (uncompressed) mdcrd files as input to MD Movie. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Jan 5, 2008, at 1:26 PM, Francesco Pietra wrote:
Elaine: Although I could argue that the "Report Bug" window was misleading, I am better saying that I was stupid enough. francesco
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Eric: I installed the 8 JAN DailyBuild of Chimera. Still found difficulties in loading more than one mdcrd, though this should be my fault. I was not sure if the list of mdcrd is to be given at beginning or if the other mdcrd files after the first one are to be given subsequently from the menu. I tried with the "list" option but only the first mdcrd was opened. Forget about that as not the focus here. I took the combined mdcrd from ptraj, where the lipid had been wholly stripped, while one water molecule of the many was not stripped (for unclear reasons). Gave this combined mdcrd to Chimera using the prmtop used before embedding the protein complex into lipid and solvate. This should be correct as that prmtop was from DOCK amber_score_everything, i.e. concerned the best scored protein-ligand complex that was used for MD after embedding into the membrane. All docking had been carried out with a crystallization molecule of water in the protein, so that WAT was in prmtop, as well as in mdcrd. With the opened trajectory in Chimera, without playing, i.e. with the first frame (where the water molecule was at the border of the protein, showing up as a triangle because of SHAKE; if movie is started, that triangle moves around within the protein from snapshot to snapshot). In the "Define script.." I defined "select ligand z<10", then OK and a BUG window was presented. Attached is the reply log (bug). I tried with z<4 with the same result (actually, I don't remember if attached bug file refers to z<10 or z<4). Thanks francesco --- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Francesco, I guess I do have a further suggestion which is to reduce the structure to just those residues that are interacting with the ligand at any time during the trajectory. The basic idea would be to run the trajectory to select those residues and then write a PDB file with just selected residues in it. Here's a recipe:
open your trajectory delete solvent delete the lipid bilayer bring up the "Define script..." dialog from MD Movie's Per-Frame menu define a "Chimera commands" script that is just: select ligand z<N [where N is the distance you want to consider as "interacting"] click OK
this will select the appropriate residues in the first frame. We want the selection to aggregate as the trajectory plays so we need to change the selection mode...
choose Select->Selection Mode->append run the trajectory
once the trajectory has played through, all residues that were ever within the cutoff distance will be selected. You may be interested in the list itself. You can write it out with:
Actions->Write List...
You can write a PDB limited to just the selected residues the same way you wrote the PDB before, just with the "Save selected atoms only" check button on.
--Eric
On Jan 7, 2008, at 12:50 PM, Francesco Pietra wrote:
The lipid, all solvation water, and box information were removed by ptraj. I used python to remove the single water molecule of crystallization. There is nothing else than the protein and the ligand in the pdb. This is clear both from vmd and a text editor. francesco --- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
The only advice I have (which you may have already tried) is to also strip the lipid bilayer using basically the same method as you did with the water.
--Eric
On Jan 6, 2008, at 11:15 PM, Francesco Pietra wrote:
Hi Elaine: As I said privately, ptraj failed to remove one molecule of water.
I loaded mdcr pmrtop to Chimera, saved the pdb, stripped that water (better: wrote the lines that do not contain water) from the 549 models with
f=open("prod1-3.pdb", "r") for line in f: line=line.rstrip() if "WAT" not in line: print line f.close()
outputting the edited file with tee.
The file is nice, it starts with 13 instances of helix (built by Chimera, as there was no such information at any stage), and contains 549 models.
With the desktop I use for Chimera (total 1GB ram) there is no way to open this pdb. I removed from gnome all that was possible to remove except Chimera. Opened top -i in parallel, which showed python to take rapidly about 99% memory. I left the system on overnight: little mem and cpu were in use, though Chimera had not opened the file.
This is not to compare, simply to assure that the pdb is not bad: it can be rapidly opened with vmd, which play all 549 models. Though, I have to go through Chimera. So that, it seems to me that pure python finds problems with long trajectories. As a naive user (who might well be wrong) I would add some fast code to help python. An alternative is to add ram; don't know if my old mainboard can add ram. I can't install Chimera on the amd64 parallel machine, where ram is plenty (4GB per processor). I can't even install X.
--- Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, I agree it can be confusing - the error dialog always includes the "report bug" button, but it is not always a bug when that dialog appears. We will have to look at your report to try to figure out what was happening in your case.
We are still looking into the mdcrd.gz file issue. In my tests, I could successfully specify multiple (uncompressed) mdcrd files as input to MD Movie. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Jan 5, 2008, at 1:26 PM, Francesco Pietra wrote:
Elaine: Although I could argue that the "Report Bug" window was misleading, I am better saying that I was stupid enough. francesco
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On Jan 9, 2008, at 3:32 PM, Francesco Pietra wrote:
In the "Define script.." I defined "select ligand z<10", then OK and a BUG window was presented. Attached is the reply log (bug). I tried with z<4 with the same result (actually, I don't remember if attached bug file refers to z<10 or z<4).
In the script-definition dialog you need to have "Interpret script as" set to "Chimera commands". You had it set to "Python".
Still found difficulties in loading more than one mdcrd, though this should be my fault. I was not sure if the list of mdcrd is to be given at beginning or if the other mdcrd files after the first one are to be given subsequently from the menu. I tried with the "list" option but only the first mdcrd was opened.
When you run MD Movie and the dialog comes up where you specify the prmtop/trajectory files, you can use the "Add..." button to add as many trajectory files as needed. I think this means you "give it at the beginning" rather than "subsequently from the menu" in your terminology. You can also just list the files in a "metafile" for the command line. For instance, this file works for me: amber leap.top md01.crd md02.crd md03.crd md04.crd md05.crd md06.crd Note that there _still_ seems to be something funky with Amber compressed trajectories, so don't use them for now but I should have things fixed in a day or so with that. --Eric
Eric: I followed previous route from combined mdcrd from ptraj. Removed remaining water. select ligand z<2.5 as Chimera command; (this was the minimum, selecting 244 atoms, 118 of which for the ligand; with z<2.0 the ligand only is selected) On playing the pdb (saved for selected atoms only) (with LOOP deselected) the atom selection increased, reaching 5365 atoms at the last (549) frame. In another run, with z<4.0 the course of atom selection was similar, reaching 5993 atoms at frame 549. This huge number of atoms proved problematic for opening pdb. For the z<2.5 case I left the computer on for 4h and half, with python occupying 98% of the available MEM (nearly 1GB). I had to kill gnome to recover command. May be with much more MEM it will work, though I can't check that now. I did not try to combine the trajectories with Chimera as I have no indication that those from ptraj are faulty. The pdb files for both z<2.5 and z<4.0 open in vmd. francesco --- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
On Jan 9, 2008, at 3:32 PM, Francesco Pietra wrote:
In the "Define script.." I defined "select ligand z<10", then OK and a BUG window was presented. Attached is the reply log (bug). I tried with z<4 with the same result (actually, I don't remember if attached bug file refers to z<10 or z<4).
In the script-definition dialog you need to have "Interpret script as" set to "Chimera commands". You had it set to "Python".
Still found difficulties in loading more than one mdcrd, though this should be my fault. I was not sure if the list of mdcrd is to be given at beginning or if the other mdcrd files after the first one are to be given subsequently from the menu. I tried with the "list" option but only the first mdcrd was opened.
When you run MD Movie and the dialog comes up where you specify the prmtop/trajectory files, you can use the "Add..." button to add as many trajectory files as needed. I think this means you "give it at the beginning" rather than "subsequently from the menu" in your terminology.
You can also just list the files in a "metafile" for the command line. For instance, this file works for me:
amber leap.top md01.crd md02.crd md03.crd md04.crd md05.crd md06.crd
Note that there _still_ seems to be something funky with Amber compressed trajectories, so don't use them for now but I should have things fixed in a day or so with that.
--Eric
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5365 atoms? Given average atom counts in protonated protein residues that means your ligand came in close contact with ~340 residues over the course of the trajectory -- so it's wandering all over the place. I can see why you want to use cluster analysis. Oh well, I guess we're stuck until I have time to coordinate with Conrad and integrate his clustering code with MD Movie. --Eric On Jan 10, 2008, at 6:38 AM, Francesco Pietra wrote:
Eric: I followed previous route from combined mdcrd from ptraj.
Removed remaining water.
select ligand z<2.5
as Chimera command; (this was the minimum, selecting 244 atoms, 118 of which for the ligand; with z<2.0 the ligand only is selected)
On playing the pdb (saved for selected atoms only) (with LOOP deselected) the atom selection increased, reaching 5365 atoms at the last (549) frame. In another run, with z<4.0 the course of atom selection was similar, reaching 5993 atoms at frame 549.
This huge number of atoms proved problematic for opening pdb. For the z<2.5 case I left the computer on for 4h and half, with python occupying 98% of the available MEM (nearly 1GB). I had to kill gnome to recover command.
May be with much more MEM it will work, though I can't check that now.
I did not try to combine the trajectories with Chimera as I have no indication that those from ptraj are faulty. The pdb files for both z<2.5 and z<4.0 open in vmd.
francesco
--- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
On Jan 9, 2008, at 3:32 PM, Francesco Pietra wrote:
In the "Define script.." I defined "select ligand z<10", then OK and a BUG window was presented. Attached is the reply log (bug). I tried with z<4 with the same result (actually, I don't remember if attached bug file refers to z<10 or z<4).
In the script-definition dialog you need to have "Interpret script as" set to "Chimera commands". You had it set to "Python".
Still found difficulties in loading more than one mdcrd, though this should be my fault. I was not sure if the list of mdcrd is to be given at beginning or if the other mdcrd files after the first one are to be given subsequently from the menu. I tried with the "list" option but only the first mdcrd was opened.
When you run MD Movie and the dialog comes up where you specify the prmtop/trajectory files, you can use the "Add..." button to add as many trajectory files as needed. I think this means you "give it at the beginning" rather than "subsequently from the menu" in your terminology.
You can also just list the files in a "metafile" for the command line. For instance, this file works for me:
amber leap.top md01.crd md02.crd md03.crd md04.crd md05.crd md06.crd
Note that there _still_ seems to be something funky with Amber compressed trajectories, so don't use them for now but I should have things fixed in a day or so with that.
--Eric
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Yes, 5365. What happened will be discovered. Up to the stage on amber_score_everything, all was perfectly OK. Minimization and heating was also OK. As to MD, the situation could not be clarified so far. In view of your comments below, I carried out a check with proven MD. I went to Amber tutorial B3, took equil1.mdcrd.gz, decompressed, took the related prmtop, and fed the two files to Chimera, last Daily Building. After all 5000 steps had been acquired, saved pdb, all frames. Quit MD Movie. Try to open this pdb. Well, with my modest desktop, Debian Linux i386, 1GB ram, this pdb could not be opened: rapidly the memory was exhausted and to get control of the computer I had to kill gnome. With vmd, this pdb developed rapidly with all 5000 frames. Exactly as with the pdb from MD with my protein. This does not mean that my MDs are OK. I'll look for what may be wrong there. Thanks francesco --- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
5365 atoms? Given average atom counts in protonated protein residues that means your ligand came in close contact with ~340 residues over the course of the trajectory -- so it's wandering all over the place. I can see why you want to use cluster analysis. Oh well, I guess we're stuck until I have time to coordinate with Conrad and integrate his clustering code with MD Movie.
--Eric
On Jan 10, 2008, at 6:38 AM, Francesco Pietra wrote:
Eric: I followed previous route from combined mdcrd from ptraj.
Removed remaining water.
select ligand z<2.5
as Chimera command; (this was the minimum, selecting 244 atoms, 118 of which for the ligand; with z<2.0 the ligand only is selected)
On playing the pdb (saved for selected atoms only) (with LOOP deselected) the atom selection increased, reaching 5365 atoms at the last (549) frame. In another run, with z<4.0 the course of atom selection was similar, reaching 5993 atoms at frame 549.
This huge number of atoms proved problematic for opening pdb. For the z<2.5 case I left the computer on for 4h and half, with python occupying 98% of the available MEM (nearly 1GB). I had to kill gnome to recover command.
May be with much more MEM it will work, though I can't check that now.
I did not try to combine the trajectories with Chimera as I have no indication that those from ptraj are faulty. The pdb files for both z<2.5 and z<4.0 open in vmd.
francesco
--- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
On Jan 9, 2008, at 3:32 PM, Francesco Pietra wrote:
In the "Define script.." I defined "select ligand z<10", then OK and a BUG window was presented. Attached is the reply log (bug). I tried with z<4 with the same result (actually, I don't remember if attached bug file refers to z<10 or z<4).
In the script-definition dialog you need to have "Interpret script as" set to "Chimera commands". You had it set to "Python".
Still found difficulties in loading more than one mdcrd, though this should be my fault. I was not sure if the list of mdcrd is to be given at beginning or if the other mdcrd files after the first one are to be given subsequently from the menu. I tried with the "list" option but only the first mdcrd was opened.
When you run MD Movie and the dialog comes up where you specify the prmtop/trajectory files, you can use the "Add..." button to add as many trajectory files as needed. I think this means you "give it at the beginning" rather than "subsequently from the menu" in your terminology.
You can also just list the files in a "metafile" for the command line. For instance, this file works for me:
amber leap.top md01.crd md02.crd md03.crd md04.crd md05.crd md06.crd
Note that there _still_ seems to be something funky with Amber compressed trajectories, so don't use them for now but I should have things fixed in a day or so with that.
--Eric
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Just FYI, when you open a 5000 MODEL structure with Chimera's normal File...Open, you get 5000 completely separate models (and will likely exhaust memory unless its a small molecule). Each model can be colored individually, moved, mutated, closed, etc. individually. When you open the same 5000 MODEL file with the MD Movie extension you get _one_ model with 5000 sets of coordinates, which takes much less memory. On the other hand, each frame shares colors and so forth with all the other frames, cannot be moved with respect to the other frames, etc. VMD undoubtedly uses the latter approach. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 11, 2008, at 3:04 PM, Francesco Pietra wrote:
Yes, 5365. What happened will be discovered. Up to the stage on amber_score_everything, all was perfectly OK. Minimization and heating was also OK. As to MD, the situation could not be clarified so far.
In view of your comments below, I carried out a check with proven MD. I went to Amber tutorial B3, took equil1.mdcrd.gz, decompressed, took the related prmtop, and fed the two files to Chimera, last Daily Building. After all 5000 steps had been acquired, saved pdb, all frames. Quit MD Movie. Try to open this pdb. Well, with my modest desktop, Debian Linux i386, 1GB ram, this pdb could not be opened: rapidly the memory was exhausted and to get control of the computer I had to kill gnome. With vmd, this pdb developed rapidly with all 5000 frames. Exactly as with the pdb from MD with my protein. This does not mean that my MDs are OK. I'll look for what may be wrong there.
Thanks francesco
--- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
5365 atoms? Given average atom counts in protonated protein residues that means your ligand came in close contact with ~340 residues over the course of the trajectory -- so it's wandering all over the place. I can see why you want to use cluster analysis. Oh well, I guess we're stuck until I have time to coordinate with Conrad and integrate his clustering code with MD Movie.
--Eric
On Jan 10, 2008, at 6:38 AM, Francesco Pietra wrote:
Eric: I followed previous route from combined mdcrd from ptraj.
Removed remaining water.
select ligand z<2.5
as Chimera command; (this was the minimum, selecting 244 atoms, 118 of which for the ligand; with z<2.0 the ligand only is selected)
On playing the pdb (saved for selected atoms only) (with LOOP deselected) the atom selection increased, reaching 5365 atoms at the last (549) frame. In another run, with z<4.0 the course of atom selection was similar, reaching 5993 atoms at frame 549.
This huge number of atoms proved problematic for opening pdb. For the z<2.5 case I left the computer on for 4h and half, with python occupying 98% of the available MEM (nearly 1GB). I had to kill gnome to recover command.
May be with much more MEM it will work, though I can't check that now.
I did not try to combine the trajectories with Chimera as I have no indication that those from ptraj are faulty. The pdb files for both z<2.5 and z<4.0 open in vmd.
francesco
--- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
On Jan 9, 2008, at 3:32 PM, Francesco Pietra wrote:
In the "Define script.." I defined "select ligand z<10", then OK and a BUG window was presented. Attached is the reply log (bug). I tried with z<4 with the same result (actually, I don't remember if attached bug file refers to z<10 or z<4).
In the script-definition dialog you need to have "Interpret script as" set to "Chimera commands". You had it set to "Python".
Still found difficulties in loading more than one mdcrd, though this should be my fault. I was not sure if the list of mdcrd is to be given at beginning or if the other mdcrd files after the first one are to be given subsequently from the menu. I tried with the "list" option but only the first mdcrd was opened.
When you run MD Movie and the dialog comes up where you specify the prmtop/trajectory files, you can use the "Add..." button to add as many trajectory files as needed. I think this means you "give it at the beginning" rather than "subsequently from the menu" in your terminology.
You can also just list the files in a "metafile" for the command line. For instance, this file works for me:
amber leap.top md01.crd md02.crd md03.crd md04.crd md05.crd md06.crd
Note that there _still_ seems to be something funky with Amber compressed trajectories, so don't use them for now but I should have things fixed in a day or so with that.
--Eric
____________________________________________________________________ __ ______________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http:// mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
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Got FMI, thanks. That seems a reasonable rationalization. Though, if I understand, importing pdb files without saturating memory (may be importing one "model", analyzing it, and then removing it from memory before importing next "model", or any other better idea) is something to overcome in order to have Chimera carrying out cluster analysis. Or I do not understand or cluster analysis is of minor interest, both equally possible. francesco --- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Just FYI, when you open a 5000 MODEL structure with Chimera's normal File...Open, you get 5000 completely separate models (and will likely exhaust memory unless its a small molecule). Each model can be colored individually, moved, mutated, closed, etc. individually. When you open the same 5000 MODEL file with the MD Movie extension you get _one_ model with 5000 sets of coordinates, which takes much less memory. On the other hand, each frame shares colors and so forth with all the other frames, cannot be moved with respect to the other frames, etc. VMD undoubtedly uses the latter approach.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jan 11, 2008, at 3:04 PM, Francesco Pietra wrote:
Yes, 5365. What happened will be discovered. Up to the stage on amber_score_everything, all was perfectly OK. Minimization and heating was also OK. As to MD, the situation could not be clarified so far.
In view of your comments below, I carried out a check with proven MD. I went to Amber tutorial B3, took equil1.mdcrd.gz, decompressed, took the related prmtop, and fed the two files to Chimera, last Daily Building. After all 5000 steps had been acquired, saved pdb, all frames. Quit MD Movie. Try to open this pdb. Well, with my modest desktop, Debian Linux i386, 1GB ram, this pdb could not be opened: rapidly the memory was exhausted and to get control of the computer I had to kill gnome. With vmd, this pdb developed rapidly with all 5000 frames. Exactly as with the pdb from MD with my protein. This does not mean that my MDs are OK. I'll look for what may be wrong there.
Thanks francesco
--- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
5365 atoms? Given average atom counts in protonated protein residues that means your ligand came in close contact with ~340 residues over the course of the trajectory -- so it's wandering all over the place. I can see why you want to use cluster analysis. Oh well, I guess we're stuck until I have time to coordinate with Conrad and integrate his clustering code with MD Movie.
--Eric
On Jan 10, 2008, at 6:38 AM, Francesco Pietra wrote:
Eric: I followed previous route from combined mdcrd from ptraj.
Removed remaining water.
select ligand z<2.5
as Chimera command; (this was the minimum, selecting 244 atoms, 118 of which for the ligand; with z<2.0 the ligand only is selected)
On playing the pdb (saved for selected atoms only) (with LOOP deselected) the atom selection increased, reaching 5365 atoms at the last (549) frame. In another run, with z<4.0 the course of atom selection was similar, reaching 5993 atoms at frame 549.
This huge number of atoms proved problematic for opening pdb. For the z<2.5 case I left the computer on for 4h and half, with python occupying 98% of the available MEM (nearly 1GB). I had to kill gnome to recover command.
May be with much more MEM it will work, though I can't check that now.
I did not try to combine the trajectories with Chimera as I have no indication that those from ptraj are faulty. The pdb files for both z<2.5 and z<4.0 open in vmd.
francesco
--- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
On Jan 9, 2008, at 3:32 PM, Francesco Pietra wrote:
In the "Define script.." I defined "select ligand z<10", then OK and a BUG window was presented. Attached is the reply log (bug). I tried with z<4 with the same result (actually, I don't remember if attached bug file refers to z<10 or z<4).
In the script-definition dialog you need to have "Interpret script as" set to "Chimera commands". You had it set to "Python".
Still found difficulties in loading more than one mdcrd, though this should be my fault. I was not sure if the list of mdcrd is to be given at beginning or if the other mdcrd files after the first one are to be given subsequently from the menu. I tried with the "list" option but only the first mdcrd was opened.
When you run MD Movie and the dialog comes up where you specify the prmtop/trajectory files, you can use the "Add..." button to add as many trajectory files as needed. I think this means you "give it at the beginning" rather than "subsequently from the menu" in your terminology.
You can also just list the files in a "metafile" for the command line. For instance, this file works for me:
amber leap.top md01.crd md02.crd md03.crd md04.crd md05.crd md06.crd
Note that there _still_ seems to be something funky with Amber compressed trajectories, so don't use them for now but I should have things fixed in a day or so with that.
--Eric
____________________________________________________________________ __ ______________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http:// mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
______________________________________________________________________ ______________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/ newsearch/category.php?category=shopping
____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
participants (3)
-
Elaine Meng -
Eric Pettersen -
Francesco Pietra