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lose c-term with protein.pdb to protein.dssp conv
- stevesei
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10 years 5 months ago #2981
by stevesei
lose c-term with protein.pdb to protein.dssp conv was created by stevesei
Martini users
I am finding that when I use dssp-2.0.4-linux-i386 to convert my pdb file to a dssp file that my dssp file loses the last residue from the pdb file and I go from a 322 residue protein to a 321 protein (in the dssp file). Has this occured with anyone else...I'm not sure how to fix this..??
The last residue in pdb file is:
ATOM 5086 N CYS 322 139.820 66.470 53.020 1.00 0.00
ATOM 5087 HN CYS 322 139.080 67.050 53.350 1.00 0.00
ATOM 5088 CA CYS 322 139.740 65.110 53.140 1.00 0.00
ATOM 5089 HA CYS 322 140.630 64.640 52.750 1.00 0.00
ATOM 5090 CB CYS 322 139.510 64.570 54.540 1.00 0.00
ATOM 5091 HB1 CYS 322 138.800 65.130 55.180 1.00 0.00
ATOM 5092 HB2 CYS 322 139.290 63.490 54.480 1.00 0.00
ATOM 5093 SG CYS 322 141.140 64.810 55.360 1.00 0.00
ATOM 5094 HG1 CYS 322 141.000 66.040 55.840 1.00 0.00
ATOM 5095 C CYS 322 138.570 64.660 52.220 1.00 0.00
ATOM 5096 OT1 CYS 322 138.720 63.850 51.280 1.00 0.00
ATOM 5097 OT2 CYS 322 137.440 65.210 52.480 1.00 0.00
Does any see a problem with this??
Thanks, Steve
I am finding that when I use dssp-2.0.4-linux-i386 to convert my pdb file to a dssp file that my dssp file loses the last residue from the pdb file and I go from a 322 residue protein to a 321 protein (in the dssp file). Has this occured with anyone else...I'm not sure how to fix this..??
The last residue in pdb file is:
ATOM 5086 N CYS 322 139.820 66.470 53.020 1.00 0.00
ATOM 5087 HN CYS 322 139.080 67.050 53.350 1.00 0.00
ATOM 5088 CA CYS 322 139.740 65.110 53.140 1.00 0.00
ATOM 5089 HA CYS 322 140.630 64.640 52.750 1.00 0.00
ATOM 5090 CB CYS 322 139.510 64.570 54.540 1.00 0.00
ATOM 5091 HB1 CYS 322 138.800 65.130 55.180 1.00 0.00
ATOM 5092 HB2 CYS 322 139.290 63.490 54.480 1.00 0.00
ATOM 5093 SG CYS 322 141.140 64.810 55.360 1.00 0.00
ATOM 5094 HG1 CYS 322 141.000 66.040 55.840 1.00 0.00
ATOM 5095 C CYS 322 138.570 64.660 52.220 1.00 0.00
ATOM 5096 OT1 CYS 322 138.720 63.850 51.280 1.00 0.00
ATOM 5097 OT2 CYS 322 137.440 65.210 52.480 1.00 0.00
Does any see a problem with this??
Thanks, Steve
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- xavier
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10 years 5 months ago #2983
by xavier
Replied by xavier on topic lose c-term with protein.pdb to protein.dssp conv
Hi,
yes we have seen this earlier but no one has had time to look at it yet …
Thanks for remanding us. I hope we can fix it soon.
yes we have seen this earlier but no one has had time to look at it yet …
Thanks for remanding us. I hope we can fix it soon.
stevesei wrote: Martini users
I am finding that when I use dssp-2.0.4-linux-i386 to convert my pdb file to a dssp file that my dssp file loses the last residue from the pdb file and I go from a 322 residue protein to a 321 protein (in the dssp file). Has this occured with anyone else...I'm not sure how to fix this..??
The last residue in pdb file is:
ATOM 5086 N CYS 322 139.820 66.470 53.020 1.00 0.00
ATOM 5087 HN CYS 322 139.080 67.050 53.350 1.00 0.00
ATOM 5088 CA CYS 322 139.740 65.110 53.140 1.00 0.00
ATOM 5089 HA CYS 322 140.630 64.640 52.750 1.00 0.00
ATOM 5090 CB CYS 322 139.510 64.570 54.540 1.00 0.00
ATOM 5091 HB1 CYS 322 138.800 65.130 55.180 1.00 0.00
ATOM 5092 HB2 CYS 322 139.290 63.490 54.480 1.00 0.00
ATOM 5093 SG CYS 322 141.140 64.810 55.360 1.00 0.00
ATOM 5094 HG1 CYS 322 141.000 66.040 55.840 1.00 0.00
ATOM 5095 C CYS 322 138.570 64.660 52.220 1.00 0.00
ATOM 5096 OT1 CYS 322 138.720 63.850 51.280 1.00 0.00
ATOM 5097 OT2 CYS 322 137.440 65.210 52.480 1.00 0.00
Does any see a problem with this??
Thanks, Steve
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- djurre
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10 years 5 months ago #2988
by djurre
Replied by djurre on topic lose c-term with protein.pdb to protein.dssp conv
Steve,
I've tried to reproduce your problem but not succeeded so far.
I've seen a similar problem before when running a multi chain protein through the Gromacs utility "do_dssp" (which calls the dssp library). However, in my current version (G4.6.3/dssp-2.0.4-linux-amd64) it doesn't occur anymore.
Some questions: Do you have a multi chain protein? Are you running the dssp library directly or via do_dssp? Or is this specific for the output of martinize.py? Which pdb file are you using (so I can try to reproduce the problem)?
If you are running do_dssp or the dssp library, this would be strictly speaking not a martinize bug. But since it would heavily influence martinize, I would be happy to help you pin down the problem.
I've tried to reproduce your problem but not succeeded so far.
I've seen a similar problem before when running a multi chain protein through the Gromacs utility "do_dssp" (which calls the dssp library). However, in my current version (G4.6.3/dssp-2.0.4-linux-amd64) it doesn't occur anymore.
Some questions: Do you have a multi chain protein? Are you running the dssp library directly or via do_dssp? Or is this specific for the output of martinize.py? Which pdb file are you using (so I can try to reproduce the problem)?
If you are running do_dssp or the dssp library, this would be strictly speaking not a martinize bug. But since it would heavily influence martinize, I would be happy to help you pin down the problem.
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- tsjerk
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10 years 5 months ago #2994
by tsjerk
Replied by tsjerk on topic lose c-term with protein.pdb to protein.dssp conv
Hi,
The problem, I think, is with the naming OT1/OT2, where dssp, I think, wants to have O and OXT. You can make the replacement with sed:
sed -i 's/OT1/O /;s/OT2/OXT/' file.pdb
The problem, I think, is with the naming OT1/OT2, where dssp, I think, wants to have O and OXT. You can make the replacement with sed:
sed -i 's/OT1/O /;s/OT2/OXT/' file.pdb
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- stevesei
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10 years 5 months ago #3023
by stevesei
Replied by stevesei on topic lose c-term with protein.pdb to protein.dssp conv
Thanks...It was a naming problem in my case.
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- xavier
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10 years 5 months ago #3024
by xavier
Replied by xavier on topic lose c-term with protein.pdb to protein.dssp conv
Could you be more specific. We want to fix this issue.
stevesei wrote: Thanks...It was a naming problem in my case.
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