- Chimera-users - RBVI Mailing Lists

Problem
by Reza Heidari 25 Jul '10

25 Jul '10

1 0

More on extracting data from the reply log
by Jean Didier Pie Marechal 21 Jul '10

21 Jul '10

Hi everyone, I want to write only a part of the reply log in a file. I was trying to use the script you gave to katrina months ago but I have a problem in parsing the reply log text output. If I understand correctly the reply log text is a raw text. I'd like to parse it in "lines" and then only write in the output file a intersting bit, like for example lines that contains "RMSD". I thought it would be enough to split text using the '\n' return character but that does not work. Could you give me a hand please? Best JD def save_reply_log(path): from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f= open(path, 'w') i=text.split("\n") f.close() save_reply_log("d:/tmplog.txt") Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Divendres, Juliol 16, 2010 7:33 pm Assumpte: Chimera-users Digest, Vol 87, Issue 13 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: alignment + missing residues (Gesa Volkers) > 2. Re: alignment + missing residues (Gesa Volkers) > 3. Re: alignment + missing residues (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 16 Jul 2010 11:58:48 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402D58.7090906(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Eric, > > thanks for your suggestions. Unfortunately removing the SEQRES > record > did not help. I also downloaded and installed the new chimera- > version > today. The false numbering in the alignment still occurs. Also when > I > remove the SEQRES record and try with the new chimera version the > false > numbering appears. Quite annoying... The pdb-file is not in the > protein > data bank yet. > > Any more suggestions? Could I add "dummy atoms" in the structure? > > Thanks, > Gesa > > > > Eric Pettersen schrieb: > > On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > > > >> Dear All, > >> > >> I observed an issue with the alignment function of Chimera. > >> I loaded a crystal structure where in between a loop is not > modelled > >> due to low electron density- so these residues are missing in > the > >> structure and the numbering also has this gap. When I align this > >> structure with others, the missing residues are not recognized > and > >> chimera just overrides the numbering so after this loop all the > >> numbers in the alignment do not fit anymore to the residues they > >> should belong to although the structure and numberings are shown > in > >> the right way in the graphics window. How can I overcome this > issue? > >> Should I change the pdb-file? In which way? > >> > >> Thanks for all responses! > > > > Hi Gesa, > > I had a similar problem reported with 1JFF 12 days ago and > haven't yet > > worked on fixing it. It seems to only happen for a small subset > of > > structures. 1JFF has a missing loop and also exactly one missing > > residue at the N terminus. Is your structure like that? Is it a > > standard PDB entry (if so, what's the ID code)? I'll add you to > the > > recipient list for the ticket we have open in our bug database > for > > this (#8585) so you will be notified when it gets fixed. It'll > > probably be fairly soon. > > Until then the only workaround that occurs to me is for you to > remove > > the SEQRES records from the PDB file before you open it. Then > the > > Sequence viewer will depict only the residues physically present > in > > the structure -- no gaps (incorrect or otherwise) will be depicted. > > > > --Eric > > > > Eric Pettersen > > > > UCSF Computer Graphics Lab > > > > http://www.cgl.ucsf.edu > > > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 2 > Date: Fri, 16 Jul 2010 12:06:56 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402F40.2010604(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Additionally I downloaded 1JFF and did an alignment with another > tubulin-structure. And still the numbering does not recognize this > gap > between 34 and 61. > > Gesa Volkers schrieb: > > Dear Eric, > > > > thanks for your suggestions. Unfortunately removing the SEQRES > record > > did not help. I also downloaded and installed the new chimera- > version > > today. The false numbering in the alignment still occurs. Also > when I > > remove the SEQRES record and try with the new chimera version the > > false numbering appears. Quite annoying... The pdb-file is not in > the > > protein data bank yet. > > > > Any more suggestions? Could I add "dummy atoms" in the structure? > > > > Thanks, > > Gesa > > > > > > > > Eric Pettersen schrieb: > >> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >> > >>> Dear All, > >>> > >>> I observed an issue with the alignment function of Chimera. > >>> I loaded a crystal structure where in between a loop is not > modelled > >>> due to low electron density- so these residues are missing in > the > >>> structure and the numbering also has this gap. When I align > this > >>> structure with others, the missing residues are not recognized > and > >>> chimera just overrides the numbering so after this loop all the > >>> numbers in the alignment do not fit anymore to the residues > they > >>> should belong to although the structure and numberings are > shown in > >>> the right way in the graphics window. How can I overcome this > issue? > >>> Should I change the pdb-file? In which way? > >>> > >>> Thanks for all responses! > >> > >> Hi Gesa, > >> I had a similar problem reported with 1JFF 12 days ago and > haven't > >> yet worked on fixing it. It seems to only happen for a small > subset > >> of structures. 1JFF has a missing loop and also exactly one > missing > >> residue at the N terminus. Is your structure like that? Is it > a > >> standard PDB entry (if so, what's the ID code)? I'll add you to > the > >> recipient list for the ticket we have open in our bug database > for > >> this (#8585) so you will be notified when it gets fixed. It'll > >> probably be fairly soon. > >> Until then the only workaround that occurs to me is for you to > remove > >> the SEQRES records from the PDB file before you open it. Then > the > >> Sequence viewer will depict only the residues physically present > in > >> the structure -- no gaps (incorrect or otherwise) will be depicted. > >> > >> --Eric > >> > >> Eric Pettersen > >> > >> UCSF Computer Graphics Lab > >> > >> http://www.cgl.ucsf.edu > >> > >> > >> > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 3 > Date: Fri, 16 Jul 2010 10:32:39 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] alignment + missing residues > To: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <CF134751-B951-403B-B9E3-E441DB44644D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gesa, > I suspect you are using a Mac, since the daily builds failed last > night for the Mac platforms. You need to get a daily build dated > July > 16 or later. I tried opening the sequence view for 1JFF in one of > the > successful daily builds and it was correct, e.g.: > > > > You can see that the interior gap is correctly recognized now. > Hopefully the daily builds on the Mac platforms will work tonight. > > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > > Ah, the "remove SEQRES records" hack will only work for the single- > sequence viewer, not an alignment. I tested that in the 1.4.1 > release > and it indeed worked as I expected: > > > > The whole sequence is smushed together with no gaps, but the > correspondences are correct. You could then align additional > sequences to the smushed sequence and the correspondences would > remain > correct. Nonetheless it's probably simply better to wait for a > daily > build to succeed than to use the hack now. So make sure you check > the > date in the download table. If you still have problems with a > release > later than July 16, let me know. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Jul 16, 2010, at 3:06 AM, Gesa Volkers wrote: > > > Additionally I downloaded 1JFF and did an alignment with another > > tubulin-structure. And still the numbering does not recognize > this > > gap between 34 and 61. > > > > Gesa Volkers schrieb: > >> Dear Eric, > >> > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > >> > >> Any more suggestions? Could I add "dummy atoms" in the structure? > >> > >> Thanks, > >> Gesa > >> > >> > >> > >> Eric Pettersen schrieb: > >>> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >>> > >>>> Dear All, > >>>> > >>>> I observed an issue with the alignment function of Chimera. > >>>> I loaded a crystal structure where in between a loop is not > >>>> modelled due to low electron density- so these residues are > >>>> missing in the structure and the numbering also has this gap. > >>>> When I align this structure with others, the missing residues > are > >>>> not recognized and chimera just overrides the numbering so > after > >>>> this loop all the numbers in the alignment do not fit anymore > to > >>>> the residues they should belong to although the structure and > >>>> numberings are shown in the right way in the graphics window. > How > >>>> can I overcome this issue? Should I change the pdb-file? In > which > >>>> way? > >>>> > >>>> Thanks for all responses! > >>> > >>> Hi Gesa, > >>> I had a similar problem reported with 1JFF 12 days ago and > haven't > >>> yet worked on fixing it. It seems to only happen for a small > >>> subset of structures. 1JFF has a missing loop and also exactly > > >>> one missing residue at the N terminus. Is your structure like > >>> that? Is it a standard PDB entry (if so, what's the ID code)? > >>> I'll add you to the recipient list for the ticket we have open > in > >>> our bug database for this (#8585) so you will be notified when > it > >>> gets fixed. It'll probably be fairly soon. > >>> Until then the only workaround that occurs to me is for you to > >>> remove the SEQRES records from the PDB file before you open it. > > >>> Then the Sequence viewer will depict only the residues > physically > >>> present in the structure -- no gaps (incorrect or otherwise) > will > >>> be depicted. > >>> > >>> --Eric > >>> > >>> Eric Pettersen > >>> > >>> UCSF Computer Graphics Lab > >>> > >>> http://www.cgl.ucsf.edu > >>> > >>> > >>> > >> > >> > > > > > > -- > > Gesa Volkers > > Institut f?r Biochemie, Molekulare Strukturbiologie > > Felix-Hausdorff-Stra?e 4 > > 17489 Greifswald > > Germany > > +49 (3834)-864392 > > > > > > > > >

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Re: [Chimera-users] save density map relative to...
by Tom Goddard 20 Jul '10

20 Jul '10

Hi Jie, You want to save a map that has been rotated relative to another map so that when you open both maps later they align. The difficulty is that the common map file formats like MRC and Spider don't have any place in the file header to specify a rotation. There are two ways to work around this limitation. One is that Chimera does some special trickery and puts the rotation information into a "label" in MRC map files so that when it later reads the file it can restore it in the right position. The trouble is that no other software will recognize that rotated position -- only Chimera. Another difficulty is that Chimera won't record the rotated position when you fit one map in another. The reason for that is because Chimera saves the rotation of the map grid relative to the maps local coordinate system. But fitting doesn't change the orientation of the grid -- instead it moves the local coordinate system (the map coordinate axes move instead of the data moving). Each map has its own set of coordinate axes. I think it would be pretty easy to add a "save relative to" option to the Same Map As... dialog that would take account of both types of rotation. But again, the orientation would only be restored by Chimera. The second method is to resample the rotated map on the grid of the map you fit into and save that resampled map. This will allow other software to open the maps and show the correct alignment. The drawback here is that the resampled map may have degraded quality since it interpolated the original map (trilinear interpolation). The Chimera command to do that looks like vop resample #3 onGrid #2 Here #3 is the id number (shown in Favorites / Model Panel or the volume dialog) of the rotated map that was fit into map #2. This will make a new map that you can save and it will align with map #2 when opened in another session or with other software since they share identical grids. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample Tom > Hi Tom, > > Hope this email finds you well. This is Jie from Joachim Frank's lab. > We met at the UCSF molecular animation workshop. > > I am writing about the "save map as" function in Chimera. Is there a > way to save map relative to another map (like the option available in > "save PDB")? The fitting algorithm ("fit in map" function) in Chimera > is very good, and I sometimes use it to align two density maps. > However, I couldn't save the density map after it was shifted. If > there's no such option, is it possible to add it? > > Best regards, > > > -Jie >

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Re: [Chimera-users] Chimera-users Digest, Vol 87, Issue 13
by Jean Didier Pie Marechal 20 Jul '10

20 Jul '10

Hi again, I'd like to do a mmaker for a region of space leading to something like this: mmaker #(ref-model and part of the selection) #(flex-model and part of the selection) So far I haven't found the correct syntax to do so but I am pretty sure we can do that. any help? Cheers JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Divendres, Juliol 16, 2010 7:33 pm Assumpte: Chimera-users Digest, Vol 87, Issue 13 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: alignment + missing residues (Gesa Volkers) > 2. Re: alignment + missing residues (Gesa Volkers) > 3. Re: alignment + missing residues (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 16 Jul 2010 11:58:48 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402D58.7090906(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Eric, > > thanks for your suggestions. Unfortunately removing the SEQRES > record > did not help. I also downloaded and installed the new chimera- > version > today. The false numbering in the alignment still occurs. Also when > I > remove the SEQRES record and try with the new chimera version the > false > numbering appears. Quite annoying... The pdb-file is not in the > protein > data bank yet. > > Any more suggestions? Could I add "dummy atoms" in the structure? > > Thanks, > Gesa > > > > Eric Pettersen schrieb: > > On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > > > >> Dear All, > >> > >> I observed an issue with the alignment function of Chimera. > >> I loaded a crystal structure where in between a loop is not > modelled > >> due to low electron density- so these residues are missing in > the > >> structure and the numbering also has this gap. When I align this > >> structure with others, the missing residues are not recognized > and > >> chimera just overrides the numbering so after this loop all the > >> numbers in the alignment do not fit anymore to the residues they > >> should belong to although the structure and numberings are shown > in > >> the right way in the graphics window. How can I overcome this > issue? > >> Should I change the pdb-file? In which way? > >> > >> Thanks for all responses! > > > > Hi Gesa, > > I had a similar problem reported with 1JFF 12 days ago and > haven't yet > > worked on fixing it. It seems to only happen for a small subset > of > > structures. 1JFF has a missing loop and also exactly one missing > > residue at the N terminus. Is your structure like that? Is it a > > standard PDB entry (if so, what's the ID code)? I'll add you to > the > > recipient list for the ticket we have open in our bug database > for > > this (#8585) so you will be notified when it gets fixed. It'll > > probably be fairly soon. > > Until then the only workaround that occurs to me is for you to > remove > > the SEQRES records from the PDB file before you open it. Then > the > > Sequence viewer will depict only the residues physically present > in > > the structure -- no gaps (incorrect or otherwise) will be depicted. > > > > --Eric > > > > Eric Pettersen > > > > UCSF Computer Graphics Lab > > > > http://www.cgl.ucsf.edu > > > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 2 > Date: Fri, 16 Jul 2010 12:06:56 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402F40.2010604(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Additionally I downloaded 1JFF and did an alignment with another > tubulin-structure. And still the numbering does not recognize this > gap > between 34 and 61. > > Gesa Volkers schrieb: > > Dear Eric, > > > > thanks for your suggestions. Unfortunately removing the SEQRES > record > > did not help. I also downloaded and installed the new chimera- > version > > today. The false numbering in the alignment still occurs. Also > when I > > remove the SEQRES record and try with the new chimera version the > > false numbering appears. Quite annoying... The pdb-file is not in > the > > protein data bank yet. > > > > Any more suggestions? Could I add "dummy atoms" in the structure? > > > > Thanks, > > Gesa > > > > > > > > Eric Pettersen schrieb: > >> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >> > >>> Dear All, > >>> > >>> I observed an issue with the alignment function of Chimera. > >>> I loaded a crystal structure where in between a loop is not > modelled > >>> due to low electron density- so these residues are missing in > the > >>> structure and the numbering also has this gap. When I align > this > >>> structure with others, the missing residues are not recognized > and > >>> chimera just overrides the numbering so after this loop all the > >>> numbers in the alignment do not fit anymore to the residues > they > >>> should belong to although the structure and numberings are > shown in > >>> the right way in the graphics window. How can I overcome this > issue? > >>> Should I change the pdb-file? In which way? > >>> > >>> Thanks for all responses! > >> > >> Hi Gesa, > >> I had a similar problem reported with 1JFF 12 days ago and > haven't > >> yet worked on fixing it. It seems to only happen for a small > subset > >> of structures. 1JFF has a missing loop and also exactly one > missing > >> residue at the N terminus. Is your structure like that? Is it > a > >> standard PDB entry (if so, what's the ID code)? I'll add you to > the > >> recipient list for the ticket we have open in our bug database > for > >> this (#8585) so you will be notified when it gets fixed. It'll > >> probably be fairly soon. > >> Until then the only workaround that occurs to me is for you to > remove > >> the SEQRES records from the PDB file before you open it. Then > the > >> Sequence viewer will depict only the residues physically present > in > >> the structure -- no gaps (incorrect or otherwise) will be depicted. > >> > >> --Eric > >> > >> Eric Pettersen > >> > >> UCSF Computer Graphics Lab > >> > >> http://www.cgl.ucsf.edu > >> > >> > >> > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 3 > Date: Fri, 16 Jul 2010 10:32:39 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] alignment + missing residues > To: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <CF134751-B951-403B-B9E3-E441DB44644D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gesa, > I suspect you are using a Mac, since the daily builds failed last > night for the Mac platforms. You need to get a daily build dated > July > 16 or later. I tried opening the sequence view for 1JFF in one of > the > successful daily builds and it was correct, e.g.: > > > > You can see that the interior gap is correctly recognized now. > Hopefully the daily builds on the Mac platforms will work tonight. > > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > > Ah, the "remove SEQRES records" hack will only work for the single- > sequence viewer, not an alignment. I tested that in the 1.4.1 > release > and it indeed worked as I expected: > > > > The whole sequence is smushed together with no gaps, but the > correspondences are correct. You could then align additional > sequences to the smushed sequence and the correspondences would > remain > correct. Nonetheless it's probably simply better to wait for a > daily > build to succeed than to use the hack now. So make sure you check > the > date in the download table. If you still have problems with a > release > later than July 16, let me know. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Jul 16, 2010, at 3:06 AM, Gesa Volkers wrote: > > > Additionally I downloaded 1JFF and did an alignment with another > > tubulin-structure. And still the numbering does not recognize > this > > gap between 34 and 61. > > > > Gesa Volkers schrieb: > >> Dear Eric, > >> > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > >> > >> Any more suggestions? Could I add "dummy atoms" in the structure? > >> > >> Thanks, > >> Gesa > >> > >> > >> > >> Eric Pettersen schrieb: > >>> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >>> > >>>> Dear All, > >>>> > >>>> I observed an issue with the alignment function of Chimera. > >>>> I loaded a crystal structure where in between a loop is not > >>>> modelled due to low electron density- so these residues are > >>>> missing in the structure and the numbering also has this gap. > >>>> When I align this structure with others, the missing residues > are > >>>> not recognized and chimera just overrides the numbering so > after > >>>> this loop all the numbers in the alignment do not fit anymore > to > >>>> the residues they should belong to although the structure and > >>>> numberings are shown in the right way in the graphics window. > How > >>>> can I overcome this issue? Should I change the pdb-file? In > which > >>>> way? > >>>> > >>>> Thanks for all responses! > >>> > >>> Hi Gesa, > >>> I had a similar problem reported with 1JFF 12 days ago and > haven't > >>> yet worked on fixing it. It seems to only happen for a small > >>> subset of structures. 1JFF has a missing loop and also exactly > > >>> one missing residue at the N terminus. Is your structure like > >>> that? Is it a standard PDB entry (if so, what's the ID code)? > >>> I'll add you to the recipient list for the ticket we have open > in > >>> our bug database for this (#8585) so you will be notified when > it > >>> gets fixed. It'll probably be fairly soon. > >>> Until then the only workaround that occurs to me is for you to > >>> remove the SEQRES records from the PDB file before you open it. > > >>> Then the Sequence viewer will depict only the residues > physically > >>> present in the structure -- no gaps (incorrect or otherwise) > will > >>> be depicted. > >>> > >>> --Eric > >>> > >>> Eric Pettersen > >>> > >>> UCSF Computer Graphics Lab > >>> > >>> http://www.cgl.ucsf.edu > >>> > >>> > >>> > >> > >> > > > > > > -- > > Gesa Volkers > > Institut f?r Biochemie, Molekulare Strukturbiologie > > Felix-Hausdorff-Stra?e 4 > > 17489 Greifswald > > Germany > > +49 (3834)-864392 > > > > > > > > >

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alignment + missing residues
by Gesa Volkers 20 Jul '10

20 Jul '10

Dear All, I observed an issue with the alignment function of Chimera. I loaded a crystal structure where in between a loop is not modelled due to low electron density- so these residues are missing in the structure and the numbering also has this gap. When I align this structure with others, the missing residues are not recognized and chimera just overrides the numbering so after this loop all the numbers in the alignment do not fit anymore to the residues they should belong to although the structure and numberings are shown in the right way in the graphics window. How can I overcome this issue? Should I change the pdb-file? In which way? Thanks for all responses! -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald Germany +49 (3834)-864392

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Positions Available in Electron Crystallography of Membrane Proteins
by Iban Ubarretxena 14 Jul '10

14 Jul '10

Positions Available: Electron Crystallography of Membrane Proteins A number of different positions are available with the Transcontinental Electron Microscopy Initiative for Membrane Protein Structure (TEMIMPS;http://temimps.nysbc.org) TEMIMPS is a new center funded by the NIH Protein Structure Initiative and is composed of five research groups with combined expertise in membrane protein production, 2D crystallization, electron microscopy, image processing, and structure determination. Our center will focus on the development and implementation of high-throughput and high-resolution approaches to structure determination of membrane proteins using cryo-electron microscopy and 2D crystals. We are seeking highly motivated individuals with good communication skills and ability to interact with an interdisciplinary group ranging from biochemists to mathematicians. Individual positions will be available in New York, Cleveland, Seattle and Houston, working in the laboratories of Drs. David Stokes, Iban Ubarretxena, Andreas Engel, Tamir Gonen and Pawel Penczek. These positions include a project manager, postdoctoral associates, software engineers and technical staff; up-to-date descriptions of the individual positions can be obtained at http://temimps.nysbc.org/jobs . Further questions or applications should be sent to temimps(a)nysbc.org. Applications should include a cover letter, a curriculum vitae and contact information for three referees. Applications will be reviewed as they are received and will continue until the positions are filled. Iban Ubarretxena-Belandia, PhD Assistant Professor Dept. Structural and Chemical Biology Mount Sinai School of Medicine Icahn Medical Institute Bldg., Room 16-70E 1425 Madison Avenue, Box 1677 New York, NY 10029 Office: 212-659-5593 Fax: 212-849-2456 Email: iban.ubarretxena(a)mssm.edu WWW: http://www.mssm.edu/physbio/ This e-mail is confidential and may well also be legally privileged. If you have received it in error, you are on notice of its status. Please notify us immediately by reply e-mail and then delete this message from your system. Please do not copy it or use it for any purposes, or disclose its contents to any other person: to do so could be a breach of confidence. Thank you for your co-operation

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volume and area measurements
by Chinthaka Silva 13 Jul '10

13 Jul '10

Hi, Could you please tell me what is the difference between the values we get from the following two options? Volume Viewer: Tools --> Measure Volume and Area Tools --> Volume Mean, SD, RMS Is SD means standard deviation? What is RMS? In the 2nd option, we get 'Surface V and A'. What does 'Surface' mean in here? Thanks, Chinthaka.

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SAXS Profile
by yann sterckx 13 Jul '10

13 Jul '10

Dear all, I'm trying to run the SAXS Profile Option in Chimera, but it doesn't seem to work properly. Every time I try to run the option, I get the following error message. Error processing trigger "check for changes": HTTPError: HTTP Error 504: Gateway Time-out File "/Applications/Chimera.app/Contents/Resources/lib/python2.6/urllib2.py", line 516, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) See reply log for Python traceback. I work in Snow Leopard. Can anybody help me out? Thanks, Yann

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Fwd: request for stick and ball size in Atoms/Bonds menu
by Bala subramanian 12 Jul '10

12 Jul '10

Friends, I apologize that i sent the following mail wrongly to chimera-bugs. So i am fwdg it to the users list once again. ---------- Forwarded message ---------- From: Bala subramanian <bala.biophysics(a)gmail.com> Date: Mon, Jul 12, 2010 at 7:18 AM Subject: request for stick and ball size in Atoms/Bonds menu To: chimera-bugs(a)cgl.ucsf.edu Dear developers, Greetings. I downloaded a recent daily builds (July 8th) and I am quite happy to see the new additions on the Atoms/Bonds menu. I thank you all for your effort. I would like to request you for the addition the Stick and Ball size settings in the Atoms/Bonds menu. Because when i change the stick/Ball size from preference-New molecules option. I am not able to see the change for the molecule presently loaded in Chimera. It would be of great help to have this option in Atoms/Bonds menu itself. Regards, Bala

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Structural alignment of a protein-ligand complex with other ligands only
by N.R. Jena 09 Jul '10

09 Jul '10

Hi, We are new to Chimera. Can you please let us know, if we have to superpose a protein-ligand complex with other ligands or a DNA-protein complex with few nucleotide-peptide complex, what is the better way to do in Chimera. I guess MatchMaker option is meant for superposition of one DNA or Protein on another DNA or Protein, right?

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Best density map contour level
by Thomas Goddard 08 Jul '10

08 Jul '10

Hi Maria, Unfortunately I don't think your procedure for setting the contour level will work very well. The problem is that the isosurface is not just the outside surface of the capsid. Usually the virus genome has lower density then the protein capsid so there contour surface may show the virus as hollow, or maybe layers of RNA/DNA will appear. So the expected volume is not going to be the volume of a solid ball. There are no well accepted standards for how to set the contour level when showing EM maps. On the other hand there probably is no "right" answer. A good level for looking at the protein capsid will be different from a good level for looking at the genome packing. If a capsid feature of an icosahedral virus does not appear at all 60-fold symmetric locations then symmetry averaged maps will show lower density and you will need a lower contour level to see such features. In practice I believe people analyzing map primarily choose the contour level by eye that best suits their analysis. Tom > Hi Tom, > > Thank you very much for your help. > I'll measure the radius of my 2 d images afterwards I'll use the radius to calculate the volume of my virus and finally > set the contour level so that this volume is enclosed. > > Thanks a lot, > Maria > > >> Hi Maria, >> >> Chimera shows the volume data as an "isosurface" meaning all points >> on the surface are at a specific map value. That map value is called >> "level" in the volume viewer dialog. The values in a map (volume data >> file) determined by electron microscopy are often not normalized in any >> way -- useful values could be 10000 or 0.1 depending on the map. For >> x-ray maps it is common to normalize so that standard deviation over the >> unit cell is 1.0. In EM there no unit cell so the standard deviation >> would depend on how big a box surrounded the virus density -- so this is >> not as useful a normalization. There is no standard accepted EM map >> normalization that I know of. If you knew the expected volume occupied >> by the structure you could set a contour level so that the surface >> encloses that volume. Here's an explanation of how to do that in Chimera >> >> >> http://www.cgl.ucsf.edu/chimera/tutorials/eman07/chimera-eman-2007.html#par… >> >> More often you just visually choose a level that you believe gives a >> surface matching the envelope of the proteins in the structure. The map >> mean, standard deviation and root mean square value can be calculated >> with menu entry >> >> Tools / Volume Data / Volume Mean, SD, RMS >> >> Tom >> >> >> >>> Dear Chimera users, >>> >>> I'm using Chimera to inspect my calculated density maps of viruses. In >>> order to compare different tree d reconstructions I would like to know >>> what the 'Level' value in Volume Viewer dialog means. At present I'm using >>> the level value 1 but I'm not sure if this is correct. >>> >>> Could you please give me some advice how to define the right contouring >>> threshold to present my data in order to inspect it? >>> >>> Thank you for your help, >>> >>> Maria L. >>> >>

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Alternative to the model panel
by Varela, Lawrence Rocco 07 Jul '10

07 Jul '10

Chimera seems to be consistently crashing or slows down drastically when I open the model panel when I have a lot of molecules loaded (200 or more). I'm often times looking at hundreds of small molecules and there relative conformations which requires me to load such big data sets. Is there an alternative to using the model panel? Like for example writing to file all the info that displays in the model panel including most importantly the model ids? Thanks in advanced, --Rocco

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structural alignment
by Bala subramanian 07 Jul '10

07 Jul '10

Friends, I have 10 conformations of the same RNA molecule obtained from 5 separate MD simulations. Now to compare the conformations, I want to make a structural alignment of these conformations and make an alignment map ( something like multiple seq. alignment for protein ) so as to show residues (or residue positions) that higher flexibility among these ten conformations. What is the best way to do it in Chimera. Thanks, Bala

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Parameters choice for match->align and quality assessment
by compchem compchems 06 Jul '10

06 Jul '10

Dear Chimera developers, great thanks to you for possibility to work with your very useful program. I am new in structural alignment studies and have some questions about parameters in match->align. My set cosists of few closely related proteins with same function and conservative spatial structure, but with some divergence in aminoacid sequences except of conservative functional residues. First, what "Residue aligned in column if within cutoff of" influences on and what preferable choice may be in my case. Second, "Superimpose full column" - how can i decide what to select for my set or what play can help me. Third, how can i evaluate quality or correctness of obtained alignment (may be, common procedure). I am sorry for long letter and thanks for your attention to my problem. D. Yegorov.

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(no subject)
by Maria Ingrid Liebl 06 Jul '10

06 Jul '10

Dear Chimera users, I'm using Chimera to inspect my calculated density maps of viruses. In order to compare different tree d reconstructions I would like to know what the 'Level' value in Volume Viewer dialog means. At present I'm using the level value 1 but I'm not sure if this is correct. Could you please give me some advice how to define the right contouring threshold to present my data in order to inspect it? Thank you for your help, Maria L.

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movie panel
by Susan Tsutakawa 02 Jul '10

02 Jul '10

Dear Users List, I apologize for these novice questions. I looked in the archives and could not find it. How do I get a MD molecular movement panel if I accidentally close it or I start a new session? I made a morph and I can see it on the model panel. Another very novice question is how do I delete a pdb in my model panel. Thank you in advance. Sincerely, Susan

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Chimera Installation - NOVELL SUSE Enterprise Linux Desktop 11 (64bit)
by Madhumita Pattanayak 01 Jul '10

01 Jul '10

Request you let me know, whether the following specification will support the installation of Chimera: Operating System Novell SUSE Enterprise Linux 11 (64 bit) Processor Intel® Core?2 Duo Processor E8400 Chipset Intel® Q43 Express Memory (RAM) 4 GB PC-3-10600 (1333 MHz) DDR3 SDRAM Memory Graphics ATI Radeon HD 3470 256MB Appreciate an early reply in this regard. Many thanks for your help. Regards, Madhumita Senior Research Fellow CCMB, Hyderabad India "The person addressed in the email is the sole authorized recipient. Should you receive it in error, immediately notify the sender of the error and delete the e-mail. Any unauthorized dissemination or copying of this e-mail (or any attachment to this e-mail) or the wrongful disclosure of the information herein contained is prohibited. Also note that this form of communication is not secure, it can be intercepted, and may not necessarily be free of errors and viruses in spite of reasonable efforts to secure this medium."

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renumber model IDs
by Dougherty, Matthew T 24 Jun '10

24 Jun '10

There are a number of times I would like to change the model ID numbers. Sometimes it is because a researcher gives me a session file that has sequences like monomer-b, monomer-d, monomer-a, monomer-c; or sometimes when I got an easy sequence to memorize (monomer-a, monomer-b, monomer-c, monomer-d), I do a colorzone split map that causes sequence names to comeback in a different order (monomer-b, monomer-d, monomer-a, monomer-c). Is there a way using commands to maintain better ID order?

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Re: [Chimera-users] structure based sequence alignment
by Eric Pettersen 24 Jun '10

24 Jun '10

Hi Sonya, On Jun 24, 2010, at 7:39 AM, Sona Vasudevan wrote: > Hello Eric, > > Thanks for all the great features you have added in the last couple > of years since I was last in touch with you. This is a fantastic tool! Thanks! Glad you like it. > I need some help with the alignment editor. > > I am trying to import an alignment in fasta format (fasta aligned) > (see attached). The alignment as you can see has three structures. I > use Load structures from the sequence > window and it brings in all the chains corresponding to teh > structures. It does, but there's a subtlety here that I should point out. The first two sequences in the alignment are for 1XVA, chain A and chain B. Chimera opens two copies of 1XVA and associates one copy with each sequence, but it associates chain A in both, since the sequences of the two chains are identical. It doesn't really look at the sequence name to try to figure out which chain to associate, just how well the sequences match and in this case they both match perfectly. By hovering the mouse over the sequence name you can see which structure/ chain it is associated with. To change the association of the second sequence to use chain B, you need to go to the alignment's Structure menu and choose "Associations...". Thus will bring up a panel showing the association of each structure to a sequence. Change the association of "1xva (#1)" from "chain A" to "chain B" and then click OK. > I then use Matchmaker to align them. I have a few questions: > > 1. Does the match maker use the info from the imported alignment > since the structures are already aligned? In other words is the > structural alignment I am seeing the saem as that was imported. No. MatchMaker is its own tool and doesn't use any open alignments. After all, you could have several alignments involving those structures open. If you want to superimpose the structures based on your alignment, use the alignment's own "Structure->Match" menu item. That brings up a dialog offering a variety of options as to how to carry out the match. I like using the "Iterate" option, but it's totally up to you. > 2. Is there a way to just output the superposed co-ordinates without > the chains that are not being used? There are probably several ways. One that comes to mind is to click on one of the alignment's "Consensus" letters to select all the residues in that column. Then click into the graphics window and hit the up-arrow key to expand the selection to the entire chain. Then either choose Select->Invert or hit right-arrow to invert the selection -- now the unused chains are selected. Actions->Atoms/Bonds- >delete will delete them. You can then write out what's left. Keep in mind that if you want to get model 2's coordinates as superimposed with model 0's original coordinates (for instance) then make sure to use the "relative 0" option in the "write" command or check the "Save relative to" option in the Write PDB dialog and choose model 0. Or you could just write out all models current coordinates. They will all differ from their originals, but they will be superimposed. > 3. Looks like I can add sequences to the alignement. Can I add a > fasta file with many sequences? No. It is on my to-do list but I haven't gotten to it yet. I'll open a feature-request ticket in our Trac database with you on the recipient list so you'll know when it gets implemented. Sorry! > Thanks so much! I have alignment files for 100 families which are > high-qualityas they were manually aligned with Cn3d and I would like > to import them into chimera for further analysis. > > Thanks so much for your time! You're welcome! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Paint a pseudobond....
by Yasser Almeida Hernández 24 Jun '10

24 Jun '10

Hi... I want to connect two atoms that belongs to different models with a pseudobond. It's that possible with Chimera? If it does, how would be the Python API code? Thanks ;) -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

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Question about attribute assignment file
by Peng Ni 24 Jun '10

24 Jun '10

Hi, I am trying to use the define attribute function. However, the attribute assignment sheet I generated cannot be read. It reports: "Line 1 of file is either not 'name: value' or is missing initial tab". I cannot spot anything wrong in my txt file, which is also attached in the e-mail. I'd greatly appreciate it if you could help me fix this problem. Regards Peng

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Lost hydrogens when saving mol2 file
by Varela, Lawrence Rocco 23 Jun '10

23 Jun '10

I'm encountering a problem where I'm loosing hydrogens from my small molecules after saving them in Chimera. Here is the situation: the original mol2 file I open has a number of small molecules listed under separate MOLECULE tag identifiers. Using the GUI menu I select "save Mol2", select all the models to save, and select the Save multiple models in "a single file [combined @MOLECULE section] option. When I open the newly saved Mol2 file with the combined MOLECULE section it's obvious that the hydrogens have been removed. How do a save multiple models in a combined MOLECULE section without loosing any hydrogen atoms? Thanks :-) Rocco

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PDB
by Dougherty, Matthew T 23 Jun '10

23 Jun '10

Hi, When PDF files are read by Chimera and the session is written, the PDB data becomes part and parcel with the session files. That is, Chimera does not go back to the PDB files when it reloads the session, it uses the PDB data within the session file instead; as contrasted to density volume files, which are referenced by the session file, and the density volume files reloaded when the session file is read by Chimera. Is there a way to force the session file not to save the PDB internally to the session file, and instead reference and interact with it similar to the way volume files are managed? Matthew

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Grouping Molecules
by Varela, Lawrence Rocco 23 Jun '10

23 Jun '10

Is there a way of grouping molecules in Chimera? Here is my situation. I have 4 molecules A, B, C, and D and I want to group A with B and C with D so that A and B has one center of rotation and C and D has another center of rotation. Rocco

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Fwd: Chimera 3-D viewing
by Eric Pettersen 21 Jun '10

21 Jun '10

Forwarding Ed Pate's question (below) to this list, in the hope that someone who actually knows the answer can chime in! --Eric Begin forwarded message: > From: Edward Pate <edpate(a)hotmail.com> > Date: June 19, 2010 2:39:09 PM PDT > To: <pett(a)cgl.ucsf.edu> > Subject: Chimera 3-D viewing > > Hi Eric: > > I am looking into getting a new workstation for Chimera. In the > past, we have gotten CRT displays in order to do 3-D visualization. > Could you recommend other display options that are available now and > that users have been happy with? Is a CRT still the best option? > > Thanks for the help. > > Ed

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